Article

Misidentification Rate in the Israeli Dairy Cattle Population and Its Implications for Genetic Improvement

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Abstract

The DNA microsatellites can be efficiently used to determine incorrect paternity attribution of cattle without genotyping of dams. Allelic frequencies of the population were determined for 12 microsatellites using the maternal alleles of 102 AI sires. The frequency of the most common microsatellite allele ranged from 0.27 to 0.58. Most loci had at least one allele that was present in only a single individual. Paternity of 9 of 173 cows (5.2%) and 3 of 102 bulls (2.9%) was excluded because putative paternal alleles were not present in progeny for at least one locus. For 4 of the 9 cows and all 3 bulls, exclusion was based on at least two loci. Mean probability of exclusion was 0.85 for cows and 0.99 for bulls. With an assumed cost of US $5 per genotype, a misidentification rate of 5%, and a discount rate of 0.05, additional profit for the Israeli-Holstein breeding program from genotyping 100 test daughters of each young sire becomes positive within 10 yr and reaches nearly US $2.4 million after 20 yr.

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... For instance, a 36% misidentification rate (Baron et al. 2002) was observed when assessing the paternity of probable offspring in progeny tests of Gir dairy sires. Other studies in cattle by Geldermann et al. (1986), Ron et al. (1996), and Rosa (1997) found misidentification rates varying between 4% and 23%. So far, there has been no documented study on paternity and kinship of African cattle, and the Ankole breed in particular. ...
... The paternity misidentification rate of 14.3% among Ankole cattle for this study was much lower than the 36% reported in Gir cattle (Baron et al. 2002) and was within range of 4% and 23% reported on dairy cattle by Geldermann et al. (1986), Ron et al. (1996) and Rosa (1997). ...
... However, due to errors reported in recorded system (e.g. Ron et al. 1996;Rosa, 1997) and memory-based systems (this study), more accurate procedures in identification of the animals are necessary. ...
Thesis
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This study aimed to investigate the production system, selection criteria, morphometric characteristics, genetic diversity and kinships of Ankole cattle. A total of 248 farms in Kiboga, Mbarara, Mpigi and Sembabule districts of Uganda were involved in a breed characterisation survey. Blood DNA from 304 individuals from eight farms of Mbarara district was analysed using 19 microsatellite markers to determine the genetic diversity, population differentiation, relatedness and assess accuracy levels of dyad relationship assignment based on cattle owners‟ memory information. Ankole cattle contribute to the livelihood of the majority of households, and for many, they are the only source of income. Pastoralists keep different types of livestock, serving diverse roles, and the stock is selected basing on various criteria. Results show that Ankole cattle owners have specific phenotypic traits they select for, to meet their cultural, social and economic needs. Due to changing socio-economic needs, breeding objectives targeting more milk and meat appear to be edging out cultural values and the need for survival traits of the cattle. Specific criteria based mainly on body coat colour are used to name animals at birth and assign parentage and kinship among dyads. The morphological markers for production are a large and tall body frame, long tail with large base, large testes and a deep scrotum, while a large dewlap is necessary for survival in the harsh climate of pastoral areas. These indicator/marker traits should be incorporated in selection indices and should be used to develop models for improvement of Ankole cattle for herds where conventional recording is missing. Ankole cattle DNA fragment analysis found 200 alleles across all loci. The Mean Number of Alleles (MNA) per locus ranged from 5.89 to 6.79 per herd. Polymorphism Information Content (PIC) ranged from 0.403 (ILSTS013) to 0.817 (ILSTS036), with a mean of 0.688. The average observed heterozygosity (Ho) ranged between 0.727 (Kaibanda) and 0.648 (Kituuha), and for all herds, did not significantly differ from expected heterozygosity. All 152 loci–herd combination tests were in Hardy-Weinberg equilibrium. FST estimates for all loci and herds were significant (P < 0.001), suggesting minimal gene flow between herds, also showed by the mean number of migrants per generation (n = 3.82). Phylogenetic analysis showed herds from the same geographical counties aggregating, demonstrating fairly wide genetic variation present in this breed and therefore, potential for genetic improvement. Confidence from likelihood tests performed on 285 dyads showed that first degree relationships were easier to assign by farmers than second degree relationships. A total exclusion probability of 99.99% was observed for both sire–offspring and dam-offspring relationships using the 19 marker panel. Accuracy of assigning dyad relationship by farmers based on memorised pedigrees was 91.9%, 85.7%, 75.6% and 60% for dam–offspring, sire–offspring, half sib and grand dam – grand offspring dyads. This study showed that capability to correctly assign kinship in a herd is well established among Ankole cattle keepers and that any cattle keeper could accurately use that capacity in large herd they had not been exposed to earlier. Oral history/memory of herdsmen can therefore be reliably used to trace relationships and for pedigree reconstruction within herds. However due to changing lifestyle, keeping of written records should be emphasized among pastoralists, as these will increasingly become very vital if the Ankole cattle breed, a vital resource in the Great Lakes region, is to be sustainably conserved. A vibrant breeding program should be put in place to improve the genetic merit of Ankole through open nucleus breeding scheme, with farmers organised into a breeders association. Some cows from this scheme should then be used for planned crossbreeding with Boran (for beef) and Ayrshire (for milk) so as to sustain the superior Ankole genes. Ex-situ banking of Ankole cattle genes needs to be promoted for new areas where these cattle did not exist but could favourably compete (ex-situ in vivo) e.g. in Eastern and Northern Uganda. Ex-situ in vitro through cryo-conservation of Ankole semen and embryos should also be undertaken to arrest the loss of diversity in aesthetic and productive genes of these cattle.
... For instance, a 36% misidentification rate (Baron et al. 2002) was observed when assessing the paternity of probable offspring in progeny tests of Gir dairy sires. Other studies in cattle by Geldermann et al. (1986), Ron et al. (1996), and Rosa (1997) found misidentification rates varying between 4% and 23%. So far, there has been no documented study on paternity and kinship of African cattle, and the Ankole breed in particular. ...
... The paternity misidentification rate of 14.3% among Ankole cattle for this study was much lower than the 36% reported in Gir cattle (Baron et al. 2002) and was within range of 4% and 23% reported on dairy cattle by Geldermann et al. (1986), Ron et al. (1996) and Rosa (1997). ...
... However, due to errors reported in recorded system (e.g. Ron et al. 1996;Rosa, 1997) and memory-based systems (this study), more accurate procedures in identification of the animals are necessary. ...
Preprint
A THESIS SUBMITTED TO THE GRADUATE SCHOOL FOR THE AWARD OF THE DEGREE OF DOCTOR OF PHILOSOPHY, AGRICULTURE OF MAKERERE UNIVERSITY, FACULTY OF AGRICULTURE, DEPARTMENT OF ANIMAL SCIENCE
... Significant levels of incorrect paternity (2.90-15%) were reported in analyses made with marker systems [5,[9][10][11] . Moreover, misidentification rates were reported to be higher in females [9,11] . ...
... Significant levels of incorrect paternity (2.90-15%) were reported in analyses made with marker systems [5,[9][10][11] . Moreover, misidentification rates were reported to be higher in females [9,11] . Paternity misidentification was determined to cause serious deviations (5-50%) in the estimation of genetic parameters and reduction of genetic gain in selection programs [12] . ...
... It was reported that more than 20% of paternity misidentification cases were caused by artificial insemination of more than one bull [3,11] and it can be reduced to 8% by using a quality control system which results in an increase of 1% in genetic progress [11] . It is well known that herd improvement can be performed to have extra profits by accurate estimation of parent identification [9] . In addition, even though the possibility of paternity identification for the estimation of breeding value is desired, there is still need for more cost-effective tests in commercial mean [7] . ...
Article
Full-text available
Objective of this study was to evaluate microsatellite markers in paternity testing of native cattle breeds in Turkey. Blood samples were collected from Anatolian Black (n=51), Anatolian Grey (n=54), South Anatolian Red (n=51), Native Southern Anatolian Yellow (n=51), East Anatolian Red (n=45) and Zavot (n = 19) cattle. From the blood samples DNA was isolated by using a standard phenol/chloroform method. A total of 20 microsatellite loci were selected from a FAO/ISAG-suggested list. Polymerase chain reaction products were separated by capillary electrophoresis and marker genotypes were determined by fragment analysis. In statistical analyses, allel numbers, observed (Ho) and expected (He) heterozygosities, deviation from Hardy-Weinberg Equilibrium and probability of exclusion (PE) at each microsatellite locus were calculated. A total of 269 different alleles were observed and the mean allele was identified as 13.45. Mean Ho and He values were observed as 0.619-0.852 and 0.669-0.877, respectively. The results indicated that the microsatellite test panel including the most informative 7 loci had total PE value of >0.9999 in each populations and can thereby be used for parentage testing studies of native cattle breeds in Turkey.
... Significant levels of incorrect paternity (2.90-15%) were reported in analyses made with marker systems [5,[9][10][11] . Moreover, misidentification rates were reported to be higher in females [9,11] . ...
... Significant levels of incorrect paternity (2.90-15%) were reported in analyses made with marker systems [5,[9][10][11] . Moreover, misidentification rates were reported to be higher in females [9,11] . Paternity misidentification was determined to cause serious deviations (5-50%) in the estimation of genetic parameters and reduction of genetic gain in selection programs [12] . ...
... It was reported that more than 20% of paternity misidentification cases were caused by artificial insemination of more than one bull [3,11] and it can be reduced to 8% by using a quality control system which results in an increase of 1% in genetic progress [11] . It is well known that herd improvement can be performed to have extra profits by accurate estimation of parent identification [9] . In addition, even though the possibility of paternity identification for the estimation of breeding value is desired, there is still need for more cost-effective tests in commercial mean [7] . ...
Article
Full-text available
Objective of this study was to evaluate microsatellite markers in paternity testing of native cattle breeds in Turkey. Blood samples were collected from Anatolian Black (n=51), Anatolian Grey (n=54), South Anatolian Red (n=51), Native Southern Anatolian Yellow (n=51), East Anatolian Red (n=45) and Zavot (n = 19) cattle. From the blood samples DNA was isolated by using a standard phenol/chloroform method. A total of 20 microsatellite loci were selected from a FAO/ISAG-suggested list. Polymerase chain reaction products were separated by capillary electrophoresis and marker genotypes were determined by fragment analysis. In statistical analyses, allel numbers, observed (Ho) and expected (He) heterozygosities, deviation from Hardy-Weinberg Equilibrium and probability of exclusion (PE) at each microsatellite locus were calculated. A total of 269 different alleles were observed and the mean allele was identified as 13.45. Mean Ho and He values were observed as 0.619-0.852 and 0.669-0.877, respectively. The results indicated that the microsatellite test panel including the most informative 7 loci had total PE value of >0.9999 in each populations and can thereby be used for parentage testing studies of native cattle breeds in Turkey.
... Por su parte, el locus BM6444 fue el menos informativo de los 9 seleccionados, por lo tanto si se excluye a dicho locus del panel se obtendría una probabilidad de exclusión combinada empleando estos 8 loci de 0.9986, valor aceptable para la asignación/verificación de relaciones de parentesco [7,15,27,29,31]. ...
... Al analizar un hato de ganado Charolais bajo condiciones similares a las presentes, se ha sugerido [34] que la dominancia reproductiva puede ser un factor determinante en hatos bajo empadre múltiple. En Israel se han reportado tasas de identificación errónea del 5% en ganado lechero teniendo como base reproductiva la inseminación artificial [27], lo cual indica que este problema no es exclusivo de los sistemas de producción extensivos. Por otro lado, en este estudio se encontró que solamente el 9% (3 de 33) de las madres "putativas" estaban asignadas correctamente, obteniéndose por lo tanto un error de asignación de maternidad de 91%. ...
... The classical method for estimating the inbreeding level of a population is by calculating the inbreeding coefficient through pedigree-based information (Wright, 1922), but pedigree errors are not rare in livestock populations (Ron et al., 1996). Therefore, several more efficient alternative methods based on genomewide sequencing data have been applied to calculate inbreeding coefficients, including ROH-based inbreeding coefficients (F ROH ) (McQuillan et al., 2008), which has recently become a popular method and has been successfully used in studying genomic inbreeding for various kinds of livestock populations (Ferencakovic et al., 2011;Szmatoła et al., 2019;Zhan et al., 2020). ...
Article
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Laiwu pigs, distinguished by their high intramuscular fat of 7–9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1–5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.
... Many flocks rely on a few males, and it is not possible to know with certainty which ram is the sire of an animal. In dairy cattle, it has been reported that paternity errors can reach up to 20% of registered animals (Ron et al., 1996) and this percentage is probably even higher in sheep, drastically reducing the genetic gain and the success of breeding programmes. To overcome this problem, it is possible for farmers to manage natural mating by grouping ewes with a single ram (i.e., mating group) during the mating period. ...
... showed genotypes without any allele of the putative sires. The obtained false parentage rate is within the range of paternity misidentification previously reported in dairy cattle (Ron et al. 1996;Lipkin et al.1998;Banos et al. 2001;Mosig et al. 2001;Visscher et al. 2002). ...
... It is routine to calculate inbreeding coefficients from pedigree records. In this approach, probability that a pair of alleles is IBD is estimated from statistical expectations, and the accuracy of the coefficients obtained is dependent on pedigree depth and completeness (Ron et al. 1996;Carothers et al. 2006). When calculations are performed using incomplete pedigrees with low number of generations, inbreeding coefficients may be underestimated because some of the genealogical relationships between ancestors may not be included. ...
Article
Controlling inbreeding in livestock populations is of great importance because excess relatedness among animals leads to a rapid loss of genetic variation and to adverse phenotypical effects associated with an inbreeding depression. Recent advances in genotyping technology have made it possible to study inbreeding at a molecular level by the analysis of genome-wide single nucleotide polymorphism panels. In this study, we used BovineSNP50 assay (Illumina) to estimate genomic inbreeding coefficient in 298 Holstein cattle by the analysis of the genome portion in runs of homozygosity (FROH) or using genomic relationship matrix (FGRM), and compared this data with conventional pedigree-based inbreeding coefficients (FPED). Weak or moderate Spearman’s rank correlations were observed between FROH and FPED which depended on the ROH length categories used for calculations and inclusion of animals with different number of complete generations registered in pedigrees. The highest correlations were observed when using ROH with lengths over 8 Mb (0.334). The correlations tended to increase as pedigree depth increased, and were the highest for animals with seven complete generations of pedigree data. FGRM correlated poorly with pedigree-based estimates, which suggests that ROH-based inbreeding coefficients better reflect recent relatedness among animals.
... Despite of the lack of efficient pedigree information on Egyptian buffalo, selecting animals based on genomic information can open a window of opportunity to genetically improve any recorded trait. Even for a population with a good recording system, the pedigree information can contain errors up to 25% (Ron et al. 1996). Alternatively, relationships can be measured by considering the fraction of DNA in common between individuals, based on shared alleles at a given locus. ...
... Previous studies of Holstein cattle populations reported higher pedigree errors, of 4%-23% (e.g. Bovenhuis & van Arendonk, 1991;Christensen et al., 1982;García-Ruiz et al., 2019;Geldermann et al., 1986;Ron et al., 1996;Visscher et al., 2002). Our result reflects the high accuracy of Japanese Black pedigree data. ...
Article
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Genome-wide single nucleotide polymorphism (SNP) markers in Japanese Black cattle enable genomic prediction and verifying parent–offspring relationships. We assessed the performance of opposing homozygotes (OH) for paternity testing in Japanese Black cattle, using SNP genotype information of 50 sires and 3,420 fattened animals, 1,945 of which were fathered by the 50 genotyped sires. The number of OH was counted for each sire–progeny pair in 28,764 SNPs with minor allele frequencies of ≥0.05 in this population. Across all pairs of animals, the number of OH tended to increase as the pedigree-based coefficient of relationship decreased. With a threshold of 288 (1% of SNPs) for paternity testing, most sire–progeny pairs were detected as true relationships. The frequency of Mendelian inconsistencies was 2.4%, reflecting the high accuracy of pedigree information in Japanese Black cattle population. The results indicate the utility of OH for paternity testing in Japanese Black cattle.
... O estudo da estrutura populacional baseado em informações de pedigree, embora apresente algumas desvantagens, como a baixa integridade ou imprecisão dos dados para animais de produção (Ron et al., 1996), tem sido realizado em diferentes populações ovinas de diversas partes do mundo (Maiwashe & Blackburn, 2004;Goyache et al., 2010;Paiva et al., 2011;Ghafouri-Kesbi, 2012). ...
Article
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The objective of this work was to evaluate the population structure of the sheep breed Santa Inês raised in Brazil. Pedigree data from 13,216 animals, belonging to 53 herds from eight Brazilian states, born between 1976 and 2010, were used. The program Endog was used for pedigree analysis and estimation of population parameters. From the total number of animals studied, 80.86% had a pedigree in the first ascendancy, 73.78% in the second, and 67.75% in the third. The maximum number of known generations was 19, and the average of equivalent generations was 4.67. The average generation interval was 3.22±1.77 years. The mean effective population size was of 172.5 animals. The number of founder animals was 829, but the effective number of founders was only 50. The 17 main ancestors accounted for 50% of the total genetic variability. The average relatedness coefficient was of 3.87% and the average inbreeding coefficient, of 6.92%. Despite the satisfactory average inbreeding coefficient in recent generations, this coefficient requires monitoring because of its proximity to the recommended limit. Gene flow among herds is the main factor for the increase of effective size and the maintenance of genetic variability in the breed Santa Inês.
... These conditions do not completely hold in practice, particularly in livestock breeds raised in extensive or semi-extensive production systems where it is difficult to control all mating events and where a low professional management increases the error rate of the recording. A high misidentification rate that creates pedigree errors has been even reported in cosmopolitan cattle populations in intensive production systems, where recording is expected to be more precise than in other breeds or conditions (Ron et al., 1996;Visscher et al., 2002;Weller et al., 2004;Russo et al., 2012). The negative effects of the incompleteness of pedigree information or the detrimental effect of registration errors on the genetic progress and on the effectiveness of the conservation strategies of livestock populations have been clearly demonstrated (Banos et al., 2001;Visscher et al., 2002;Sanders et al., 2006;Oliehoek and Bijma, 2009;Reverter et al., 2016). ...
Article
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Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (FPED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.
... Predictions of breeding values with the animal model assume correct pedigree and performance data are utilized. However, paternity errors have been reported in several studies, ranging from de 5.2% in cows and 2.9% in bulls in Israel (Ron et al. (1996)), 13.2% in Germany (Geldermann et al. (1986)), and 20% in Ireland (Beechinor and Kelly, (1987)), to 27.5% in Brazil (Curi and Lopes (2002)). In a study of Charolais cattle in Mexico, Sifuentes et al. (2006) reported 24% pedigree errors. ...
Conference Paper
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Abstract Text: The objective was to study the effectiveness of an 11 molecular panel for paternity testing in Mexican Jersey cattle. Seventy blood samples were collected from four sires, 32 dams, and 34 progeny. Commercial kit Maxwell 16 LEV blood AS1010 was used to extract DNA. Microsatellites were amplified using StockMarks for Cattle® Bovine Genotyping Kit. Results were read and analyzed using GeneMapper 4.0 and Cervus 3.0 software. The 11 microsatellites had: high polymorphic information content (0.66), combined probability of exclusion (CPE) of 0.9957, CPE for one candidate parent of 0.9917, CPE for one candidate parent given the genotype of a known parent of the opposite sex of 0.9997, average number of alleles per locus of 8.73, and frequency of the most common allele varied from 0.29 to 0.86. The 11 microsatellite panel evaluated yields enough information to test paternity in Jersey dairy cattle. Keywords: Jersey cattle Parentage verification DNA
... It has to be kept in mind, however, that the implementation of a breeding programme requires an accurate pedigree. It has been Stear et al. (2009) indeed shown that even in dairy cattle, which have well established breeding programme, over 20% of registered animals have paternity errors (Ron et al., 1996) and this percentage is probably even higher in small ruminants. In smallholder properties in tropical and subtropical environments usually there is no pedigree recording and no data recording at any time. ...
Article
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The control of gastrointestinal nematodes (GIN) is mainly based on the use of drugs, grazing management, use of copper oxide wire particles and bioactive forages. Resistance to anthelmintic drugs in small ruminants is documented worldwide. Host genetic resistance to parasites, has been increasingly used as a complementary control strategy, along with the conventional intervention methods mentioned above. Genetic diversity in resistance to GIN has been well studied in experimental and commercial flocks in temperate climates and more developed economies. However, there are very few report outputs from the more extensive low-input/output smallholder systems in developing and emerging countries. Furthermore, results on quantitative trait loci (QTL) associated with nematode resistance from various studies have not always been consistent, mainly due to the different nematodes studied, different host breeds, ages, climates, natural infections versus artificial challenges, infection level at sampling periods, among others. The increasing use of genetic markers (Single Nucleotide Polymorphisms, SNPs) in GWAS or the use of whole genome sequence data and a plethora of analytic methods offer the potential to identify loci or regions associated nematode resistance. Genomic selection as a genome-wide level method overcomes the need to identify candidate genes. Benefits in genomic selection are now being realised in dairy cattle and sheep under commercial settings in the more advanced countries. However, despite the commercial benefits of using these tools, there are practical problems associated with incorporating the use of marker-assisted selection or genomic selection in low-input/output smallholder farming systems breeding schemes. Unlike anthelmintic resistance, there is no empirical evidence suggesting that nematodes will evolve rapidly in response to resistant hosts. The strategy of nematode control has evolved to a more practical manipulation of host-parasite equilibrium in grazing systems by implementation of various strategies, in which improvement of genetic resistance of small ruminant should be included. Therefore, selection for resistant hosts can be considered as one of the sustainable control strategy, although it will be most effective when used to complement other control strategies such as grazing management and improving efficiency of anthelmintics currently.
... Combined Exclusion Probability (CEP) were calculated based on the data detected (Ron et al., 1996). ...
Article
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Polymorphism of microsatellite DNA in Thai domestic elephants (Elephas maximus) was studied using five genetic markers including LaT05, LaT07, LaT16, LaT17 and LaT26, in order to determine the efficiency of such markers in parentage identification. Eleven elephants from 5 families and 10 unrelated ones located in the northern, northeastern and central parts of Thailand were tested. It was found that LaT05, LaT16, LaT17 and LaT26 possessed marker sizes of 250-500 bp with numbers of alleles ranging from 4-13, heterozygosity 0.62-0.88 and PIC 0.56-0.87 whereas LaT07 could not be detected in all specimens used. LaT05 and LaT26 appeared to be the most desirable markers with PIC=0.87. Parentage identification using the 4 genetic markers showed the results corresponding to the family history and pedigree record of all specimens with up to 99.74% of efficiency and accuracy. It was concluded that LaT05, LaT16, LaT17 and LaT26 all together could be used in parentage identification.
... A técnica de DNA microssatélite vem sendo aplicada com sucesso em vários animais e tem sido usada para teste de paternidade em programas de melhoramento (ARRANZ et al., 1996;REGITANO, 1996;RON et al., 1996;e ROSA, 1997) e para identificação de paternidade de rotina (FREDHOLM & WINTERO, 1996;PIHKANEN et al., 1996 ;BINNS et al., 1995;BOWLING et al., 1997). ...
... DNA markers-based technologies enable the detection of different polymorphic types. Among those, microsatellites or short tandem repeats (STR) or simple sequences repeats (SSR) have been identified in all the eukaryotic species that have been investigated thus far (Ron et al., 1996). The use of microsatellites in population genetics has so far been mainly reported in buffalo population (Zhang et al., 2007;Kumar et al., 2006 andVan Hooft et al., 2002). ...
Article
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To evaluate the genetic polymorphism for DNA microsatellite markers of Egyptian buffalo, 471 unrelated Egyptian buffalo were genotyped with 11 microsatellite markers. The data were analyzed with GenALEx6 software. Nine (82%) of the microsatellite markers were polymorphic and two (18%) were monomorphic. A total 198 alleles were detected, with the number of alleles per marker ranging from 17 (RM28 and BM415) to 29 (BMC4203), giving a mean number of 22±1.302 alleles per marker. The effective number of alleles was lower than the observed values with a mean value of 16.502±1.137 per marker. The most frequent alleles were ranged from 0.086(BMC4203) to 0.127 (BM415). The mean observed and expected homozygosity was 0.113 and 0.063, respectively, while the observed and the expected heterozygosity was 0.887 and 0.937, respectively, over all loci. Polymorphism information content values were ranged from 0.909 (BM415) to 0.949 (ILSTS093 andILSTS097). At the nine microsatellite loci, the mean of fixation index was 0.052. Successful genotyping of Egyptian buffalo using these DNA microsatellite markers suggests that the latter can be a valuable resource for genome analysis in Egyptian buffalo.
... Mesmo utilizando marcadores recomendados pelo ISAG, tidos como os ideais para a determinação de parentesco em suínos ( Nechtelberger et al., 2001;Putnova et al., 2003), estes apresentaram baixo grau de polimorfismo, possivelmente em virtude dos animais utilizados serem da mesma genética (granja comercial), ou ainda pelo fato desta genética não ser a ideal para a utilização destes marcadores ( Ron et al., 1995). Somente 7 dos 9 marcadores microssatélites utilizados no experimento, contribuíram na determinação da paternidade (SW951, SW857, SO386, SO101, SW240, SO155, SO355). ...
Article
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1. INTRODUÇÃO Novos métodos de inseminação artificial (IA) tem sido utilizados de forma crescente na espécie suína. Na IA convencional (intracervical), o sêmen é depositado no interior da cérvix (Corrêa et al., 2001). Na IA intra-uterina, o sêmen é depositado no corpo do útero através de um cateter específico (Watson & Behan 2002). Estudos comparando as técnicas intracervical (IAIC) e intra-uterina (IAIU) demonstraram semelhantes taxas de parição e número total de leitões nascidos (Watson & Behan, 2002; Mezalira et al., 2003, Serret et al., 2005). Assim, a IAIU possibilitaria uma redução no volume e na concentração da dose inseminante, o que maximiza o potencial de machos doadores de sêmen com alto mérito genético, pois estes serão usados na IA de um maior número de matrizes. No entanto, mesmo que diferentes reprodutores tenham sido avaliados de forma semelhante através de métodos de determinação de qualidade de sêmen, diferenças individuais entre os machos podem ser responsáveis por diferenças em seu desempenho reprodutivo (Vesseur et al., 1996; Popwell & Flowers, 2004). Segundo Dziuk (1996), o uso de IA heterospérmica, com doses contendo sêmen de mais um de macho, poderiam minimizar essas diferenças. Portanto, com a IAIU potencializando o uso de poucos reprodutores para um grande número de fêmeas, métodos cada vez mais eficazes se tornam necessários para diferenciar o desempenho reprodutivo individual. Este trabalho comparou as técnicas de IAIC e IAIU, ambas com uso de doses heterospérmicas, em condições de rotina de granja, com posterior determinação genética da paternidade atribuída a cada macho na formação das leitegadas. 2. MATERIAL E MÉTODOS Foram utilizadas 25 fêmeas da linhagem Naïma, genética Penarlan ® , de ordem de parto (OP) 2-5, pertencentes a um plantel comercial. Estas fêmeas foram inseminadas com doses heterospérmicas, foram 6 pools contendo ejaculados de dois machos (34 – 48; 44 – 92; 34 – 41; 38 – 41; 38 – 92; 46 – 92). Dentre estas fêmeas, 10 receberam inseminação artificial intracervical (IAIC) e 15 receberam inseminação artificial intra-uterina (IAIU). Informações referentes ao total de leitões nascidos por parto foram registradas.
... The (TG)n probe has been used for identity testing among four breeds of horses (Ellegren et al., 1992). Microsatellite loci have been extensively exploited for parentage testing in cattle (Ron et al., 1996;Heyen et al., 1997;Schnabel et al., 2000). ...
Article
The advent of DNA technology over the recent years has led to the development of molecular markers that are highly precise, convenient and cost effective for detection of polymorphism among individuals and also for individual identification. These molecular marker techniques viz., Restriction fragment length polymorphism, Random amplified polymorphic DNA, Amplified fragment length polymorphism, DNA fingerprinting, microsatellites and the most recent, microarrays are advantageous over other conventional techniques like protein polymorphism and immunogenetic techniques. As these techniques directly assess the sample at the DNA level the probability of their accuracy is much greater. Among these marker systems the ideal marker should have many scorable and highly polymorphic loci with codominant alleles and should be densely distributed throughout the genome. Microsatellite markers meet these requirements and have therefore become the markers of choice for a variety of analyses related to linkage mapping, forensic investigations, paternity and kinship determination and population genetic studies. In the late sixties, the term satellite was associated with DNA when, on isopycnic centrifugation of DNA, it settled into a main band with some secondary bands (Waring and Britten, 1966, Britten and Kohne, 1968). These secondary bands were termed satellite bands as they appeared on the outskirts of the denser DNA bands. On analysis, it was revealed that the satellite bands comprised of DNA with long repetitive sequences, existing in millions of copies, which appeared to be associated to the heterochromatin. Based on reassociation kinetic studies, it was revealed that this repetitive pattern of DNA differed within and between species (Brutlag, 1980). Repetitive DNA can be classified into two types based on their arrangement in the genome, whether interspersed or arranged in a direct tandem fashion. Repetitive elements arranged in tandem form the most abundant class of repeats found in the genome. Satellite DNA is a broad term to describe such type of DNA, which includes the telomeres, minisatellites and the microsatellites. Shorter repetitive DNA sequence having repeats of 15 or more bases were termed as minisatellites (Jeffereys et al., 1985). In the late 1980s, even shorter repeats of satellites of two to six bases were isolated and named microsatellites (Litt and Luty, 1989). Since their discovery, microsatellites have been used in mapping programmes and by population biologists for studies of population genetic structure and kinship investigations.
... Genetic evaluation, which plays a key role in a genetic improvement program, requires accurate pedigree information. In practice, however, the proportion of pedigree error has been estimated at 3 to as high as 23% in the Holstein population in some countries (Ron et al., 1996;Visscher et al., 2002;Weller et al., 2004;Sanders et al., 2006). Incorrect paternity will consequently lead to biased estimates of heritability and reduced genetic gain (Visscher et al., 2002;Weller et al., 2004;Sanders et al., 2006). ...
Article
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To develop an efficient DNA typing system for Chinese Holstein cattle, 17 microsatellites, which were amplified in four fluorescent multiplex reactions and genotyped by two capillary electrophoresis injections, were evaluated for parentage verification and identity test. These markers were highly polymorphic with a mean of 8.35 alleles per locus and an average expected heterozygosity of 0.711 in 371 individuals. Parentage exclusion probability with only one sampled parent was approximately 0.999. Parentage exclusion probability when another parent’ genotype was known was over 0.99999. Overall probability of identity, i.e. the probability that two animals share a common genotype by chance, was . In a test case of parentage assignment, the 17 loci assigned 31 out of 33 cows to the pedigree sires with 95% confidence, while 2 cows were excluded from the paternity relationship with candidate sires. The results demonstrated the high efficacy of the 17 markers in parentage analysis and individual identification for Chinese Holstein cattle.
... The rate of misidentification of parents in different bovine populations worldwide is very variable from almost 25% to 4% (Banos et al., 2001). Lower values may be due to utilization of traditional markers with low polymorphism, such as blood groups and milk proteins, which underestimate the identification rates of incorrect parentage (Ron et al., 1996). The development of genotyping technologies and the use of markers such as microsatellites and SNPs enabled to increase the probability of detecting (and correcting) paternity errors. ...
Article
The purpose of this study was to identify genomic regions explaining a major proportion of the genetic variance in milk production and milk fat and protein content on a commercial herd of Holstein and Holstein x Jersey crossbred cattle bred in an extensive grazing system. We analyzed 305-day cumulative milk production records from 18876 cows at first lactation, of which 16907 and 16735 had milk fat and protein content records during the same period. After data quality control, genotypes from 998 animals on 40417 SNPs included in the Illumina Bovine SNP50 v2 BeadChip were available. Weighted single-step genome-wide association studies were conducted for milk yield (MY), fat content (FC) and protein content (PC). Windows of 10 adjacent single nucleotide polymorphisms explaining more than 0.31% of the genetic variance were considered relevant. Protein-coding genes located within those windows were retrieved, their functional relevance was assessed, the main functional categories and biological processes represented by them were identified, and an overrepresentation test was performed. Relevant windows for MY, FC and PC were 52, 57 and 56, and harbored 304, 293 and 269 protein-coding genes, respectively. The proteins encoded by those genes were mainly involved in cellular, metabolic and biological regulation processes. Cellular response to cytokine stimulus, GTPase activity and GTP binding, and heterotrimeric G-protein were the main overrepresented biological process, molecular functions, and protein class, respectively. Among the candidate genes found, some previously reported genes associated with milk traits, such as CDH2, DGAT1, GRINA, LIPA, PGR, RPGRIP1L, VPS28, MAF1, and FTO were identified. However, novel candidate genes related to transcriptional regulation and transporter activity were also found. These results contribute to a better understanding of the loci influencing milk traits in the main dairy cattle breeds in Argentina.
... The homozygous segments of the genome, with reduced variability within a population, may also arise as a result of strong artificial selection which leads to the fixation of favourable alleles in the population in a sort of "hitchhiking" process (Ron et al., 1996;McQuillan et al., 2008;Hildebrandt et al., 2009). The Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/livsci ...
Article
Runs of homozygosity (ROH) are defined as contiguous homozygous regions of the genome where the two haplotypes inherited from the parents are identical. It has been shown that the length and frequency of ROH may describe the history of the population in which an individual occurs; they may also reveal the level of inbreeding within populations, recent population bottlenecks or signatures of positive selection. In this study, BovineSNP50 whole-genome genotyping assay was used to analyse the lengths and distributions of the ROH found in the genomes of four cattle breeds maintained in Poland (Holstein, Polish Red, Limousin and Simmental) to assess both the level of autozygosity of each breed and to identify the genomic regions most commonly associated with ROH that may reflect directional selection pressure. Visible differences in the length and distribution of homozygous regions across the genome between selected breeds were observed. The breeds also varied in the level of autozygosity (inbreeding) estimated by FROH, which was lower for unselected cattle. Moreover, within the regions of the genome most commonly associated with ROH that may reveal signatures of recent selection a number of genes potentially connected with different production features characteristic for individual breeds were detected.
... All cows included in the analysis had genetic evaluations for the five milk production traits, but a few cows were lacking values for the secondary traits; SCS, herd-life, fertility, and PD01. Genotypes were considered "informative" if the sire was heterozygous, and the genotype of the daughter was different from the genotype of the sire [16]. Families with significant effects were genotyped for an additional 35 markers linked to the markers with significant effects, for a total of 108 markers. ...
Article
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Abstract Estimates of quantitative trait loci (QTL) effects derived from complete genome scans are biased, if no assumptions are made about the distribution of QTL effects. Bias should be reduced if estimates are derived by maximum likelihood, with the QTL effects sampled from a known distribution. The parameters of the distributions of QTL effects for nine economic traits in dairy cattle were estimated from a daughter design analysis of the Israeli Holstein population including 490 marker-by-sire contrasts. A separate gamma distribution was derived for each trait. Estimates for both the α and β parameters and their SE decreased as a function of heritability. The maximum likelihood estimates derived for the individual QTL effects using the gamma distributions for each trait were regressed relative to the least squares estimates, but the regression factor decreased as a function of the least squares estimate. On simulated data, the mean of least squares estimates for effects with nominal 1% significance was more than twice the simulated values, while the mean of the maximum likelihood estimates was slightly lower than the mean of the simulated values. The coefficient of determination for the maximum likelihood estimates was five-fold the corresponding value for the least squares estimates.
... Before genomic selection, the paternity misidentification rate in advanced breeding populations was estimated to be in the range of 5 to 12% (Ron et al., 1996). Highly accurate paternity validation or identification based on comparison of progeny and parent genotypes is a virtually no-cost byproduct of genotyping that is required for genomic evaluation (Weller et al., 2010), which should also increase rates of genetic improvement. ...
Article
Genomic evaluation has been successfully implemented in the United States, Canada, Great Britain, Ireland, New Zealand, Australia, France, the Netherlands, Germany, and the Scandinavian countries. Adoption of this technology in the major dairy producing countries has led to significant changes in the worldwide dairy industry. Gradual elimination of the progeny test system has led to a reduction in the number of sires with daughter records and fewer genetic ties between years. As genotyping costs decrease, the number of cows genotyped will continue to increase, and these records will become the basic data used to compute genomic evaluations, most likely via application of "single-step" methodologies. Although genomic selection has been successful in increasing rates of genetic gain, we still know very little about the genetic architecture of quantitative variation. Apparently, a very large number of genes affect nearly all economic traits, in accordance with the infinitesimal model for quantitative traits. Less emphasis in selection goals will be placed on milk production traits, and more on health, reproduction, and efficiency traits and on environmentally friendly production with reduced waste and gas emission. Genetic variance for economic traits is maintained by the increase in frequency of rare alleles, new mutations, and changes in selection goals and management. Thus, it is unlikely that a selection plateau will be reached in the near future.
... In this case, more errors in the pedigree also reduced the evaluation accuracy in those traits noticeably and that could be a great disadvantage to selection responses in the breeding program. Our results are also in accordance with Israel [10], Ron et al [13], and Bovenhuis and Van Arendonk [28] that similarly reported lower accuracy in EBV with the presence of errors in the pedigree. All traits in this study showed similar trends with respect to PE, even though there were differences in magnitudes of influences on each trait evaluation. ...
Article
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Objectives: This study evaluated the effect of pedigree errors (PEs) on the accuracy of estimated breeding value (EBV) and genetic gain for carcass traits in Korean Hanwoo cattle. Methods: The raw data set was based on the pedigree records of Korean Hanwoo cattle. The animals' information was obtained using Hanwoo registration records from Korean animal improvement association database. The record comprised of 46,704 animals, where the number of the sires used was 1298 and the dams were 38,366 animals. The traits considered were carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS). Errors were introduced in the pedigree dataset through randomly assigning sires to all progenies. The error rates substituted were 5, 10, 20, 30, 40, 50, 60, 70 and 80%, respectively. A simulation was performed to produce a population of 1650 animals from the pedigree data. A REML based animal model was applied to estimate the EBV, accuracy of the EBV, expected genetic gain, variance components, and heritability (h2) estimates for carcass traits. Correlation of the simulated data under PEs was also estimated using Pearson's method. Results: The results showed that the carcass traits per slaughter year were not consistent. The average CWT, EMA, BFT, and MS were 342.60 kg, 78.76 cm2, 8.63 mm, and 3.31, respectively. When errors were introduced in the pedigree, the accuracy of EBV, genetic gain and h2 of carcass traits was reduced in this study. In addition, the correlation of the simulation was slightly affected under PEs. Conclusion: This study reveals the effect of PEs on the accuracy of EBV and genetic parameters for carcass traits, which provides valuable information for further study in Korean Hanwoo cattle.
... Christensen et al (1982) reported misidentification rates between 5 and 15% in Danish dairy cattle, Geldermann et al., (1986) estimated misidentification rates of 13% using blood group factors and biochemical polymorphisms in cattle. Ron et al (1996) found a 5% misidentification rate using microsatellite analysis in Israeli dairy cattle. Rosa (1997) reported a misidentification rate of 15% in Brazilian livestock, based on restriction fragment length polymorphism (RFLP) and microsatellite analysis. ...
Article
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The study was undertaken with an objective to develop and validate a panel containing maximum number of microsatellite markers that can be amplified in a single PCR reaction for precise parentage verification in Indian HF cattle population. The study was based on a total of 210 HF cattle (100 calf, 100 dam and 10 sires). Genomic DNA was extracted from blood and semen samples. A panel of 12 microsatellite markers (BM1824, BM2113, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH10, ETH225, BM1818, ETH3, TGLA53) was amplified in a single multiplex reaction and analyzed by capillary electrophoresis on an automated DNA sequencer. The observed heterozygosity (Ho) of 12 markers ranged from 0.607 (TGLA53) to 0.904 (BM2113) while the expected heterozygosity (He) ranged from 0.581 (ETH225) to 0.873 (INRA23). Eleven out of 12 microsatellite loci revealed relatively high polymorphic information content (>0.6). The results suggest that multiplex microsatellite panel can be effectively used to verify the parentage as well as to assign the putative sire to daughters under progeny testing.
... Christensen et al. (1982) reported the misidentification in the range of 5 to 15% in Danish cattle. The value was reported to be 13% in German dairy cattle (Geldermann et al. 1986) while the values were 5% for Israeli Holstein cows based on 173 cows and their 4 putative sires (Ron et al. 1996). There has been only one report in Mehsana buffaloes of Gujarat where the parentage was tested under field conditions based on 100 dam-daughter pairs and 12 sires (using semen samples of 5 sires for extraction of DNA). ...
Article
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The accuracy of selection for sire's merit depends upon the number of daughters born to the sire and also the correctness of performance records. The accuracy of records depends on confirmed paternity of the daughters. In this paper, we report paternity confirmation of a large progeny testing program in buffaloes. The work was undertaken in collaboration with BAIF, Pune under National Agricultural Innovation Project. Murrah bulls (12) were selected and around 120, 000 buffaloes were inseminated at farmers' doorsteps. The area of operation was 52 districts of Uttar Pradesh. We targeted 1, 000 female calves to be born to each of the 12 sires. The experiment was an effort to develop a reference population for identification of quantitative trait loci for various economic traits in buffaloes using halfsib design. Owing to financial constraints, we targeted 10, 000 daughters born to these 12 sires. The DNA was isolated from these daughters. The DNA of sires was also isolated. Since there was no parentage verification kit commercially available for buffaloes, we developed a multiplex PCR reaction consisting of 11 microsatellite markers to confirm the paternity. The correctness of the paternity was established using microsatellite DNA markers and comparison of daughters' genotype with genotype of sires. The paper reports paternity testing of large reference family. We also developed a software 'Confirm Paternity' for comparing the genotypes of daughters with the respective sire. We report paternity correctness of 90.48% in buffaloes under field conditions. © 2018 Indian Council of Agricultural Research. All Rights Reserved.
... The increased levels of homozygosis may reflect what has occurred in the past or in a recent process with the intensification of the selection pressure among animals [13]. While the coefficient of traditional inbreeding (FST) reflects the inbreeding in later generations, the coefficients based on ROH are able to detect both the recent and more distant inbreeding [14,15]. The F ROH is based on the segments of homozygosis of each animal, being a more specific evaluation and accurate than the estimates performed with pedigree data, which sometimes can be incomplete and contain identification errors [16,17]. ...
Article
The Indubrasil breed was developed in the Brazilian region called Triângulo Mineiro as a result of a cross between zebu cattle. Initially, it was used as a terminal cross and currently it represents approximately 4.45% of all the Brazilian zebu cattle. Studies were conducted to estimate genetic parameters in the Indubrasil using pedigree information, however, until now, no study has been developed using large-scale genomic markers in this breed. Pedigree information are widely used to investigate population parameters; however, they can neglect some estimates when compared to the use of genomic markers. Therefore, the objective of this study was to investigate the population structure and the genetic diversity of Indubrasil cattle using a high-density Single Nucleotide Polymorphism (SNP) panel (Illumina BovineHD BeadChip 700k). Levels of genomic homozygosity were evaluated using three different approaches: Runs of homozygosity (F ROH), % of homozygosis (F SNP), and inbreeding coefficient (F x). Further, Runs of Homozygosity (ROH) segments conserved among the animals were investigated to identify possible regions associated with the breed characteristics. Our results indicate that even the Indubrasil breed having a small effective population size, the levels of homozygosity (F ROH = 0.046) are still small. This was possibly caused by the cross conducted among different breeds for its development. It suggests no immediate risks associated with loss of genetic variation. This information might be used in breeding programs, for the breed conservation and for the expansion of the Indubrasil breed.
... It aims to maximize genetic gain while controlling the rate of inbreeding by optimizing the genetic contribution of each selection candidate to the next generation (Meuwissen 1997;Grundy et al. 1998;). High-density marker panels of single-nucleotide polymorphisms (SNPs) allow us to obtain more accurate estimates of kinship than pedigrees, as it is common for pedigrees to contain errors ( Ron et al. 1996). In addition, genotype-based kinship reflects the actual relatedness between two individuals, whereas pedigree-based estimates are only expectations (Visscher et al. 2006). ...
Thesis
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For the management of local breeds with historical introgression, both genetic gain and the long-term evolution of genetic variability have to be taken into consideration. Traditional optimum contribution selection (traditional OCS) aims at maximizing genetic gain while controlling the rate of inbreeding by optimizing the genetic contribution of each selection candidate to the next generation. It is also a promising approach to maintain genetic diversity since the average kinship of selection candidates is restricted. However, for the breeds with historical introgression, this diversity may be caused by introducing genetic material from other breeds, which can be a risk of the conservation of small local populations. Therefore, the breeding objectives should not only focus on increasing genetic gain but also on maintaining the diversity of native alleles. The main aim of this project was to resolve the existing conflicts in the current breeding program of local breeds with historical introgression. Chapter 1 gave a brief introduction and background of the topic and formulated the objective of the thesis. In chapter 2, the current inbreeding status of German Angler cattle was evaluated based on both pedigree (F_PED) and genomic information. The genomic inbreeding coefficients of 182 Angler cattle were estimated via analyzing the genome proportion of run of homozygosity (F_ROH) and using the genomic relationship matrix (F_GRM). On average, the inbreeding level of Angler is relatively low compared to the other breeds ((F_PED ) ̅:0.013;(F_GRM ) ̅:-0.015; (F_(ROH>1Mb) ) ̅:0.031). Moderate to strong correlations (0.607–0.702) were found between F_PED and F_ROH based on different length categories of ROH segments. Moreover, it proved that F_ROH is a robust estimating method owing to its ability to capture both ancient and recent inbreeding. Although traditional OCS may achieve higher genetic gain with the restriction of the defined rate of inbreeding, in this case, inbreeding is not the main problem in the current breeding program and the advantage of OCS may be limited since the level of inbreeding may be lower than the threshold. In chapter 3, we developed the advanced optimum contribution selection strategy by considering migrant contribution and conditional kinship at native alleles in the OCS procedure. Different scenarios were compared for both functions of production and conservation based on pedigree information. It has been proved that the advanced OCS approach can effectively maintain the diversity of native alleles and genetic originality while ensuring genetic improvement with appropriate settings of constraint values. The availability of high-density single-nucleotide polymorphism (SNP) markers provides a solution for achieving accurate estimates of both coancestry and breed composition. In chapter 4 and chapter 5, we evaluated the long-term performance of advanced OCS strategies in both production and conservation function via simulating several subsequent generations based on genomic information. In chapter 4, we found that traditional OCS procedure has slight advantages in increasing genetic gain whilst controlling relatedness compared to truncation selection. However, the introgression of foreign genetic material by traditional OCS is not desirable in the local breed conservation. In the long run, constraining migrant contribution and kinship at native alleles in the OCS procedure is a promising approach to increase genetic gain whilst maintaining genetic uniqueness and diversity. Chapter 5 mimics a conservation program which aims at increasing the value of a breed for conservation by removing exogenous genetic material, maintaining within-breed genetic diversity, and increasing the genetic diversity among breeds. Simply minimizing the exogenous genetic contribution leads to the loss of both within and between population diversity. Moreover, the recovery process ended at a plateau after several generations. The best scenario was able to increase the native contribution from 0.317 to 0.706 before a segment-based kinship level of 0.10 was reached. This scenario maximized the native contribution, constrained the increase in kinship, and the increase in kinship at native alleles. Moreover, it constrained the mean kinship in a multi-breed core set to the current level, which is desirable for the conservation program. This thesis ends with a general discussion.
... Later due to intensive inbreeding and a lot of mistakes in pedigree information and incorrect relationships between the animal blood groups and proteins become uninformative (Adamov et al., 2011). The errors in cattle pedigrees were different in European countries: 5 -15% in Denmark (Christensen et al., 1982), 4 -23% in Germany ( Geldermann et al., 1986), 8 -20% in Ireland (Beechinor andKelly, 1987), 12% in Netherlands (Bovenhuis and Van Arendonk, 1991), 2,9 -5,2% (Ron et al., 1996) or 11,7% ) in Israel, 10% in dairy cattle in the United Kingdom (Visscher et al., 2002) and 10,7% in the Czeck Republic (Řehout et al., 2006). The use of these markers was limited because they are products of the gene expression (Drinkwater and Hetzel, 1991). ...
Article
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Molecular markers are essential tool for determining the specific genetic makeup of an individual and are valuable approach for genetic improvement of farm animals. In cattle breeding their application is useful for improvement of breeding programs for desired traits, better productivity and high quality products. These markers provide more accurate genetic information and better knowledge of the animal genetic resources. In this review we attempt to make a brief summary on the application of one of more advanced DNA-based molecular markers in cattle breeding, namely short tandem repeat (STR, microsatellites).
... High-density marker panels of single-nucleotide polymorphisms (SNPs) allow us to obtain more accurate estimates of kinship than pedigrees, as it is common for pedigrees to contain errors (Ron et al. 1996). In addition, genotype-based kinship reflects the actual relatedness between two individuals, whereas pedigree-based estimates are only expectations (Visscher et al. 2006). ...
Article
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The long-term performance of different selection strategies was evaluated via simulation at the example of a local cattle breed, the German Angler cattle. Different optimum contribution selection approaches to maximize genetic gain were compared to a reference scenario without selection and truncation selection. The kinships and migrant contribution were estimated from genomic data. Truncation selection achieved the highest genetic gain but decreased diversity considerably at native alleles. It also caused the highest increase in migrant contributions. Traditional optimum contribution selection, which only constrains on kinship, achieved almost the same genetic gain but also caused a small increase of migrant contribution and remarkably reduced the diversity at native alleles. When migrant contribution was required not to increase and the increase of kinship at native alleles was restricted, the migrant contribution levels and the diversity at native alleles were well managed, and the genetic gain was only slightly reduced. However, genetic progress was substantially lower in the scenario that aimed at recovering the original genetic background. Truncation selection and traditional optimum contribution selection both reduce the genetic originality of breeds with historical introgression. The inclusion of migrant contribution and kinship at native alleles as additional constraints in optimum contribution selection showed great potential for conservation. Recovering the original genetic background is possible but requires many generations of selection and reduces the genetic progress in performance traits. Hence, constraining the migrant contribution at their current values can be recommended to avoid further reduction of genetic originality.
... However, in practice, the rate of incorrect paternity ranges from 4% to 23%. Ron et al. obtained paternity rejection rates of 5.2% and 6.25% in the Israeli Holstein population based on 173 cows and 244 elite cows, respectively (Ron et al., 1996;Ron et al., 2003). Weller et al. reported a paternity misidentification rate of 11.7% in the same Israeli Holstein population, which was based on genotyping 6040 cows using 87 microsatellite markers (Weller et al., 2004). ...
Article
Incorrect paternity assignment in cattle can significantly influence the accuracy of genetic evaluation. Recent advances in high-throughput technology have facilitated the identification of single nucleotide polymorphism (SNP) markers and their applications for filiation and individual identification. We genotyped 1074 bulls from a reference population of Chinese Simmental cattle for genomic selection using a BovineSNP770K BeadChip. Among them, a total of 136 bulls were randomly selected to design a suitable low-density SNP panel for paternity testing in Simmental cattle. Our results showed that 50 SNPs were determined to be the most informative markers in parental testing, with an accuracy of 99.89% for CPE (cumulative probability of exclusion) in the unknown female parent case. The 50 highly informative SNP markers were distributed across 25 chromosomes, and the mean intermarker distance per chromosome was 26.72 Mb. The average minor allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) values were 0.3748, 0.4998, and 0.4818, respectively. Finally, the 50 identified SNPs were used to estimate paternity for the remaining 938 of 1074 bulls from 23 farms. Our results revealed that 76.75% of the 938 bulls were assigned parentage to the pedigree sires with 95% confidence, and the rate of pedigree record mistakes ranged from 9.52%-39.29% in different herds. Our study is the first attempt to provide valuable insights into the extraction of informative markers through the application of high-density SNP chips for paternity testing in Chinese Simmental cattle.
... There were no full siblings among the genotyped animals. As a DNA microsatellite-assisted survey of incorrect paternity attribution within the Israeli dairy cattle population revealed that such incorrect attributions are not rare (36), we opted to base our estimation of genetic relatedness between the cows solely on their genomic information. ...
Article
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Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host’s ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants’ genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome. We accomplished this by studying a population of 78 Holstein-Friesian dairy cows, using a combination of rumen microbiota data and other phenotypes from each animal with genotypic data from a subset of 47 animals. We identified 22 operational taxonomic units (OTUs) whose abundances were associated with rumen metabolic traits and host physiological traits and which showed measurable heritability. The abundance patterns of these microbes can explain high proportions of variance in rumen metabolism and many of the host physiological attributes such as its energy-harvesting efficiency. Interestingly, these OTUs shared higher phylogenetic similarity between themselves than expected by chance, suggesting occupation of a specific ecological niche within the rumen ecosystem. The findings presented here suggest that ruminant genetics and physiology are correlated with microbiome structure and that host genetics may shape the microbiome landscape by enriching for phylogenetically related taxa that may occupy a unique niche.
... The inbreeding coefficient has traditionally been estimated mainly from the information derived from pedigree data since Wright's (1922) ; molecular data are more effective for estimating autozygosity and for detecting the effects of inbreeding than are pedigree data ). It is not uncommon for pedigree data to contain errors (Ron et al. 1996). Further, pedigree relatedness is estimated from statistical expectations of the probable proportion of genomic identity by descent, whereas genotype-based estimates show the actual relatedness among individuals (Visscher et al. 2006). ...
Article
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This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.
... Errors in pedigrees are known to occur due to mis-mothering, misidentification and incorrect recording procedures. Several studies [5,7,14] show that the misidentification rate in cattle pedigrees varies between about 3 and over 20%. Even in Lipizzan horse pedigrees where a great importance is attached to correct pedigree recording, a small number of pedigree errors has been revealed by mtDNA analysis [10]. ...
Article
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Abstract There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.
... If there is no extra return from the commercial population (i.e., considering the payback period at only the nucleus level), the payback period of 15 reproduction cycles is still relatively high even with a gain:cost ratio of 10. A similar economic study, conducted by Ron et al. (1996) in the Israeli dairy cattle population, reported that profit became positive by year 10. ...
Article
In sheep and goat breeding programs, the proportion of females for which the sire is known (known paternity rate [KPR]) can be very low. In this context, paternity assignment using SNP is an attractive tool. The annual genetic gain (AGG) is impacted by the accuracy of the EBV. In populations with a low KPR, the number of known relatives for a given individual is low, and the EBV that are based on this information are imprecise. However, the impact of partially known paternal filiations, in terms of potential genetic and economic losses, has never been quantitatively evaluated in situations where natural mating is the main reproductive mode. A deterministic model was developed to assess, for a panel of real breeding programs, the influence of the female KPR on the AGG and economic benefit. First, males were divided into categories according to their status (natural mating or AI sire) and breeding cycle and females according to parity, sire status (including unknown sire), and breeding cycle of the sire. Second, a demographic model described, for each category, the accumulation of known records for individuals and their close relatives. The output from this model was used to compute the average accuracy of the EBV per category. Then, a genetic model based on the gene flow between categories over time was described. Using the average accuracy of EBV per category, it provided the asymptotic AGG of the nucleus given its KPR. In the economic studies, changes to the mean genetic values in the nucleus and the commercial population after an increase in KPR and various gain:cost ratios (monetary gain due to an extra genetic SD of the selected trait divided by the cost of 1 assignment) were considered. Relative profit and payback periods were computed. We showed that SNP-based parentage assignment aimed at increasing the female KPR was not always profitable and that the type of breeding program and the size of the commercial population should be taken into consideration. Notably, achieving a profit was largely dependent on obtaining a favorable gain:cost ratio. The maximum supplementary AGG (16.9%) was obtained for breeding programs using only natural mating. In such programs without AI, a gain:cost ratio of 5 was needed to make assignment profitable at the nucleus level whereas a gain:cost ratio of 2 was sufficient if the nucleus represented a third of the total population.
... Moreover, these studies do not take into account the stochastic nature of recombination, sometimes resulting in research results that are difficult to interpret. When evaluating the genetic diversity of animals, selected based on pedigree data, there are two aspects that should be pointed out: (1) pedigree errors due to misidentification, misinterpretation and wrong registry are common (Ron et al., 1996;Carneiro et al., 1999), thereby reducing selection speed; (2) F PED based studies assume that the entire genome is under neutral selection and do not take into account the effects of artificial selection which may cause some biases of evaluation. ...
Article
Genetic diversity is the one of the most important issues in conservation studies of livestock breeds or endangered species. In the present study, we tested the feasibility of describing the recent evolution in genetic diversity through genome-wide SNP genotyping and estimates of linkage disequilibrium decay patterns, effective population size, inbreeding coefficient based on runs of homozygosity and population structure. We choose the bovine indicine breed Guzerá because it has suffered recent bottlenecks which have been registered historically. A sample of 1,036 females was genotyped using Illumina BovineSNP50. A resampling strategy was applied to correct for sampling biases caused by the population structure in herds, and by the extensive use of some sires for artificial reproduction. A subsample of 210 animals and 32,806 markers with MAF>0.01 was used. Very low linkage disequilibrium was detected for distances greater than 120Kb between two markers. Furthermore, three points of decrease in effective population size between generations were detected, which coincide with the historically registered bottlenecks. The inbreeding coefficient, based on runs of homozygosity, confirmed a strong contribution of the last 20–30 generations to current inbreeding. In the population structure analysis, the most probable number of sub-populations is 2, reflecting selection purpose (beef or dual-purpose). Taken together, these results allow a retelling of the recent evolution of this breed. The strategy described here will be useful for other breeds or even species for which a careful historical registry is not available for conservation proposals.
... These breeds gradually adapted to the local environmental conditions and expanded southward but the Qinling Mountains and the temperature and weather conditions constituted natural barriers to their expansion. Meanwhile, the humped zebu inhabited the areas of the Yangtze and Zhujiang valleys and might have originated from the Bibos genus, such as the zebu, Bos bateng, and even Bos gaurus, which were also the progenitors of the zebu in Southeastern Asia [6,7,17]. The cattle breeds localized in the central parts of China and detouring the Qinling Mountains are situated at a cross-point and thus the analysis of their origin, domestication, and migration is much more complicated. ...
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Abstract Genetic variability and genetic relationships were investigated among eight Chinese cattle breeds using 12 microsatellite markers. Three hundred and fifty-two alleles were detected and the average number of alleles per locus ranged from 8.33 ± 1.67 in the Jiaxian breed to 21.33 ± 5.60 in the Qinchuan breed with a mean value of 13.91. The total number of alleles per microsatellite ranged from 21 (INRA005, HEL1) to 40 (HEL13), with a mean of 29.33 per locus. The fixation indices at the 12 loci in the eight breeds were very low with a mean of 0.006. A principal components analysis and the construction of a neighborjoining tree showed that these eight Chinese cattle breeds cluster into three groups i.e. the Yanbian andChineseHolstein, theNanyang and Jiaxian, and the four remaining breeds.This clustering agrees with the origin and geographical distributions of these Chinese breeds.
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The objectives of this study were to estimate genetic diversity and test possibility of conducting paternity testing at the DNA level as part of a breeding project of Kangal White Karaman sheep. As a pilot study, blood samples were collected from 13 rams that were used for breeding purposes in two different flocks in which level of inbreeding is proposed to be high. A total of 20 microsatellite markers were used to amplify genomic DNA by polymerase chain reaction (PCR). The resulting PCR products were separated by capillary electrophoresis and allele genotypes were determined. A total of 99 different alleles were determined ranging from 1 to 8 at each locus. The observed (Ho) and expected heterozygosities (He) values were ranged from 0.000 to 0.923 and from 0.000 to 0.871, respectively. Polymorphism information content (PIC) values were between 0.000 and 0.818. Total power of exclusion (PE) value was calculated as 0.999975 for twenty loci. Our results suggested that a panel, including the most informative twelve loci provides a total PE value of 0.999828, can be useful for parentage testing in Kangal White Karaman sheep.
Thesis
O registro genealógico confiável é fundamental para possibilitar a implantação de um programa de avaliação genética. Os marcadores de microssatélites constituem uma ferramenta amplamente utilizada atualmente para confirmação de paternidade. No Brasil, a caprinocultura possui um grande potencial para a pecuária, principalmente na agricultura familiar do semi-árido. As principais raças de caprinos especializadas para produção de leite no Brasil são a Alpina e a Saanen, ambas de origem européia. Na Região Nordeste, detentora do maior rebanho caprino do País, existem raças naturalizadas adaptadas às condições adversas do semi-árido, que possuem diversidade genética desconhecida. Estas raças têm sido cruzadas de forma indiscriminada com diversas raças importadas, pondo em risco o seu potencial genético. Os objetivos do trabalho foram estudar a utilização de um sistema de microssatélites para: 1) a verificação de paternidade, utilizando o método de exclusão e o método de inferência estatística da razão de verossimilhança, nos casos em que a mãe é ou não genotipada; e 2) o estudo de diversidade genética entre e dentro as raças/rebanhos estudados. Foram utilizados, em sistema de genotipagem semi-automático (ABI 310, Perkin Elmer), onze microssatélites anteriormente descritos em bovinos, ovinos ou caprinos. Foram genotipados 292 animais, pertencentes a três rebanhos, sendo que as raças leiteiras Alpina e Saanen foram amostradas em dois rebanhos (UFV e particular) e a raça naturalizada Moxotó foi proveniente do rebanho de conservação da Embrapa Caprinos, Ceará. As análises de frequências alélicas foram realizadas utilizando-se os programas SAS (1998) e CERVUS (Marshall et al., 1998). O teste exato para equilíbrio de Hardy Weinberg, estatística-F e distância genética foram obtidos no programa TFPGA (Miller, 1997). Os loci estudados apresentaram herdabilidade e informatividade de moderada à alta. A heterozigosidade esperada média para todos os loci foi de 0,717. O conteúdo de informação polimórfica (PIC1 e PIC2) e a probabilidade de exclusão combinada (PE1 e PE2) foram de 0,676 e 0,5420; e 0,999591 e 0,988375, respectivamente, quando se conhecia ou não o genótipo materno. Considerando erros de registros aqueles com mais de três incompatibilidades de genótipo, foram encontrados 27 registros errôneos. Pelo teste de inferência estatística, foram solucionados corretamente 210 dos 276 casos de paternidade (76%). Se fosse adotado apenas o método de exclusão, apenas 160 paternidades seriam assinaladas com certeza (sem incompatibilidades pai alegado-progênie). Desta forma, o método de inferência pode ajudar as verificações de paternidade em larga escala, diminuindo o custo para solucionar os erros de laboratório e as perdas parciais de genotipagem. Quando há conhecimento do genótipo materno, a probabilidade de exclusão foi superior e o programa CERVUS resolveu 95% dos casos. No estudo de diversidade, a heterozigosidade (HE) foi alta nos rebanhos leiteiros, sendo 0,6952 e 0,7043 para a raça Alpina e Saanen, respectivamente. No Moxotó a HE obtida foi moderada de 0,4984, provavelmente em decorrência do pequeno número amostrado. O número de alelos variou de cinco (INRA005) a onze (BM3205), com média de 7,0 alelos/locus nas raças importadas e 3,5 na Moxotó. A média FST (diferenciação entre populações) foi maior entre rebanhos (FST s = 0,0768) do que entre raças (FST p = 0,0263), indicando haver uma similaridade entre raças, dentro do rebanho. Tal similaridade pode ser devido ao fato de haver algum cruzamento entre raças, dentro do rebanho. A distância genética de Nei (DA) foi maior entre o rebanho Moxotó e os demais (DA > 0,50). Os resultados obtidos estão em coerência com o histórico das raças, demonstrando que este sistema poderá ser adotado em estudos futuros de diversidade em caprinos no Brasil.
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Además de todos los progresos que ha representado el mejoramiento genético animal clásico, este presenta algunas limitaciones como en algunos casos donde el fenotipo no se expresa en el individuo. Con el advenimiento de las enzimas de restricción, del secuenciamiento y de la amplificación del ADN, fue posible el uso de marcadores moleculares asociados con loci de características cuantitativas (QTL), como herramienta que auxilia y perfecciona el mejoramiento genético animal por medio de la selección asistida por marcadores (MAS), lo que aumenta el mérito genético para características de difícil medida, baja heredabilidad y limitadas por el sexo. La raza bovina gyr se caracteriza por su rusticidad y adaptación al trópico, y presenta una buena producción de leche para los países tropicales, por lo que es fundamental en la conformación de la raza gyrholando (5/8holstein y 3/8 gyr). El propósito del presente estudio fue complementar el análisis cuantitativo con la genética molecular, en el mejoramiento genético de la característica porcentaje de sólidos totales en la razagyr en Brasil. Catorce familias (toros) gyr con 657 hijas fueron analizadas, siendo el promedio 0,095 % y la desviación estándar 0,1923 del valor genético estimadopara porcentaje de sólidos totales. Al utilizar 27 marcadores microsatélites en el análisis a travésde las 14 familias para porcentaje de sólidos totales en el cromosoma 6, un QTL fue identificado con P< 0,05 y F = 2,34 en la posición 58 cm, próximo al marcador MNB-208 (60,21 cm). Al emplear las familias3 y 4, las más significativas, el mismo QTL fue identificado con P < 0,01 y F = 7,61, pero en la posición 58 cm, próximo al marcador MNB-208.
Thesis
Les programmes de sélection visent à produire des reproducteurs de bonnes valeurs génétiques pour la filière. La connaissance de marqueurs moléculaires du génome des individus et de mutations d’intérêt ouvrent des perspectives en termes d’organisation de la sélection. A l’aide de simulations déterministes et stochastiques, l’intérêt technique et économique de l’utilisation d’un panel de marqueurs moléculaires très basse densité a été évalué dans les populations ovines et caprines en sélection et permis d’obtenir les résultats suivants : i) utiliser un tel panel pour accroître, quand elle est limitée, la quantité de filiations paternelles n’est pas toujours rentable, ii) la stratégie de gestion des gènes d’ovulation qui maximise la rentabilité économique du plan de sélection a été déterminée par optimisation et des stratégies simples à implémenter, qui donnent des rentabilités proches de la rentabilité maximale, ont été proposées, iii) un programme de sélection génomique basé sur un panel très basse densité, permet à coût constant une efficacité supérieure aux programmes basés actuellement sur le testage sur descendance des mâles.
Chapter
Our understanding of genetic defects in cattle has greatly increased in the past decades due to improvements in disease investigations, molecular genetic tools as well as data analysis approaches. Information about single-gene disorders, chromosomal abnormalities and multifactorial disorders in cattle is summarized with a focus on occurrence and control of known genetic defects. A list of single-gene disorders with known disease-causing mutations is included and approaches to investigate emerging conditions are briefly discussed.
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The objective of this research was to study the population genetic structure of four herds of Mediterranean buffaloes in Brazil. It was used pedigree data from 6,588 buffaloes of Mediterranean breed born from 1980 to 2002. Of the total number of animals studied, 60.5, 15.3 and 2.1% had a pedigree in the first, second and third ascendancy, respectively. The effective number of herds that provided breeding males was 1.60 for parents, 1.16 for grandparents and 1.00 for great-grandparents. There were 923 founder animals and only 71 effective founders. The effective number of ancestors explaining the genetic variability of the population was 71 and only 30 ancestors accounted for 50% of the genetic variability of the population. The average relatedness coefficient (AR) between individuals and inbreeding (F) of the population were estimated at 0.37 and 0.34% respectively. The average estimate of generation interval was 8.71±2.85 years. The variability of the current population is the result of a few ancestors, who are mostly also founders showing that the population was developed from a narrow genetic base which characterizes the occurrence of founder effect.
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There is considerable interest in bovine DNA-level polymorphic marker loci as a means of mapping quantitative trait loci (QTL) of economic importance in cattle. Progeny of a sire heterozygous for both a marker locus and a linked QTL, which inherit different alleles for the marker, will have different trait means. Based on this, power to detect QTL, as a function of QTL effect, heritability of the trait, and number of animals tested was determined for 1) daughter design, marker genotype and quantitative trait values assessed on daughters of sires heterozygous for the markers; and 2) granddaughter design, a newly devised alternative design in which marker genotype is determined on sons of heterozygous sires and quantitative trait value measured on daughters of the sons. For equal numbers of assays, power increased with the number of daughters per sire (design 1) and sons per grandsire (design 2). For equal power and heritability less than or equal to .2, design 2 required half as many marker assays as design 1, e.g., with heritability of .2, QTL effect of .2 SD units, and type 1 error of .01, power was .70 if 400 daughters of each of 10 sires were assayed for the markers and .95 if markers were assayed on 100 sons of each of 20 sires with 50 granddaughters per son.
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We have exploited "progeny testing" to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of > 150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score > or = 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding.
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A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.
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A cattle genetic linkage map was constructed which marks about 90% of the expected length of the cattle genome. Over 200 DNA polymorphisms were genotyped in cattle families which comprise 295 individuals in full sibling pedigrees. One hundred and seventy-one loci were found linked to one other locus. Twenty nine of the 30 chromosome pairs are represented by at least one of the 36 linkage groups. Less than a 50 cM difference was found in the male and female genetic maps. The conserved loci on this map show as many differences in gene order compared to humans as is found between humans and mice. The conservation is consistent with the patterns of karyotypic evolution found in the rodents, primates and artiodactyls. This map will be important for localizing quantitative trait loci and provides a basis for further mapping.
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New sources of genetic polymorphisms promise significant additions to the number of useful genetic markers in agricultural plants and animals, and prompt this review of potential applications of polymorphic genetic markers in plant and animal breeding. Two major areas of application can be distinguished. The first is based on the utilization of genetic markers to determine genetic relationships. These applications include varietal identification, protection of breeder's rights, and parentage determination. The second area of application is based on the use of genetic markers to identify and map loci affecting quantitative traits, and to monitor these loci during introgression or selection programs. A variety of breeding applications based on these possibilities can be envisaged for Selfers, particularly for those species having a relatively small genome size. These applications include: (i) screening genetic resources for useful quantitative trait alleles, and introgression of chromosome segments containing these alleles from resource strain to commercial variety; (ii) development of improved pure lines out of a cross between two existing commercial varieties; and (iii) development of crosses showing increased hybrid vigor. Breeding applications in segregating populations are more limited, particularly in species with a relatively large genome size. Potential applications, however, include: (i) preliminary selection of young males in dairy cattle on the basis of evaluated chromosomes of their proven sire; (ii) genetic analysis of resource strains characterized by high values for a particular quantitative trait, and introgression of chromosome segments carrying alleles contributing to the high values from resource strain to recipient strain.
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Procedures were developed for animal model evaluation of dairy cattle for milk, fat, and protein yields as well as evaluation for fat and protein percentages as a function of yield evaluations. Data available for January and July 1987 Modified Contemporary Comparison evaluations were used to compute animal model evaluations. For each cow, records from her first five lactations are included. Cows without a first lactation record are evaluated separately. Relationships with all known male and female relatives influence evaluations. Solutions are computed by iteration on data for fixed management and random herd-sire, permanent environment, and breeding value effects. Iteration is by second-order Jacobi for breeding value and by Gauss-Seidel for other effects. Accuracy (expressed as repeatability) is computed as in Modified Contemporary Comparison procedures except that sire repeatability includes contributions from parents and dam repeatability is adjusted for number of daughters. A genetic base is imposed by subtracting average evaluation of cows born in 1984 from all evaluations. Results include predicted transmitting ability (one-half breeding value), predicted producing ability (sum of herd-sire, permanent environmental, and breeding value effects), parent average (average transmitting ability of parents), and average effect of management groups containing a cow's records.
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Twenty pairs of cattle twins were genotyped for 3 to 12 microsatellites each using semen, blood, milk and hair roots. Chimaerism was recognized in 19 pairs by discrepancies in microsatellite analysis from milk and blood as opposed to semen and hair, or by detection of more than 2 alleles per genotype from milk and blood. Chimaerism of 2, 3 or 4 alleles was demonstrated in genotypes of twins from blood as compared to 1 or 2 alleles only from hair. The appearance of predominant bands in genotypes from blood or milk representing alleles of only one of the co‐twins was not consistent among the different microsatellites for the same twins. No evidence for germ cell chimaerism was found in semen of dizygotic male twins although our PCR system could detect cell mixes as small as a 1:100 ratio. Genotyping from either hair or semen for 4 microsatellites are sufficient to confirm zygotic origin of twins at .98 accuracy. Researchers should be aware of the possibility of erroneous genotyping when analyzing DNA from twins derived from blood or milk and the potential of chimaerism as an experimental model to study different immunological characteristics of cattle co‐twins.
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The discounted cash flow procedure of management accounting is used to evaluate national breeding programmes. Alternative methods of improvement of meat production from cattle born in the dairy herd are taken as examples. These schemes utilize selection for beef characters either in the dairy breed itself or within a beef breed, maintained in a small herd and used as a source of bulls for crossing by AI. In each case young bulls are selected for growth rate in a performance test, which precedes the progeny test for milk production in the dairy breed. Greater rates of genetic progress and monetary returns are predicted from improvement of the beef breed, but both schemes are expected to yield a return on investment of over 15%. The net returns from the programme in the beef breed are influenced less by changes in assumptions. Approximate, but simple, methods of computing the discounted returns are described.
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Highly polymorphic microsatellite loci offer great promise for gene mapping studies, but fulfillment of this potential will require substantial improvements in methods for accurate and efficient genotyping. Here, we report a genotyping method based on fluorescently labeled PCR primers and size characterization of PCR products using an automated DNA fragment analyzer. We capitalize on the availability of three distinct fluorescent dyes to label uniquely loci that overlap in size, and this innovation increases by threefold the number of loci that can be analyzed simultaneously. We label size standards with a fourth dye and combine these with the microsatellite PCR products in each gel lane. Computer programs provide very rapid and accurate sizing of microsatellite alleles and efficient data management. In addition, fluorescence signals are linear over a much greater range of intensity than conventional autoradiography. This facilitates multiplexing of loci (since signal intensities often vary greatly) and helps distinguish major peaks from artifacts, thereby improving genotyping accuracy.
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A maximum likelihood method is presented to estimate the fraction of animals misclassified and breed effects for milk protein gene frequencies based on crossbred data. A simulation study indicates that the method provides estimates of gene frequencies that agree closely with the true values. Gene frequencies in the Dutch Black and White and the Dutch Red and White crossbred populations, based on data on 10,151 and 580 animals respectively, were estimated. Dutch Friesian and Holstein-Friesian breeds differ in gene frequencies for beta-casein and beta-lactoglobulin. Estimates for fractions misclassified are zero for alpha s1-casein, .09 for beta-casein and beta-lactoglobulin, and .12 for kappa-casein. Differences between Dutch Red and Whites and Red Holstein-Friesian breeds are small, and estimates for fractions misclassified are high but have high approximate standard errors. Compared with the Black and White breeds, the Red and Whites have a high kappa-casein B gene frequency.
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A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.
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For daughter groups of 15 test bulls, controls of paternity were performed by using blood group factors and biochemical polymorphisms. Data of incorrectly assigned daughters influenced the estimation of breeding values, heritabilities and correlations for milk performance traits. Formulae are given that show the effects of variable misidentification rates on estimation of breeding values, selection intensities, heritabilities, and genetic gains. For example, for milk fat yield, the genetic gains drop at a misidentification rate of 15% between 8.7% (for h2 = .5) and 16.9% (for h2 = .2) below values attained without misidentifications. Consequently, decreasing misidentification rates in progeny of test bulls can be used to diminish the progeny size per test bull for constant genetic gain, to achieve more precise ranking of all or distinct test bulls according to their "true" breeding values and(or) to increase the number of test bulls by using the same amount of test inseminations and the same precision of ranking. Actions to reduce misidentification rates in cattle populations are discussed.
Article
Individual loci affecting economically important traits can be located using genetic linkage between quantitative trait loci and genetic markers. In the 'granddaughter' experimental design, heterozygous grandsires and their sons are genotyped for the genetic marker, while the quantitative trait records of the granddaughters are used for statistical analysis. Ten DNA microsatellite markers were used to look for associations with quantitative trait loci affecting milk production traits in seven Israeli Holstein grandsire families. At least 60% more grandsires were heterozygous, and 40% fewer individuals were discarded because of unknown paternal allele origin, as compared with diallelic markers. The effects of paternal alleles for locus D21S4 on kg milk and protein were significant (P < 0.025). The allele substitution effects for sire 783 were 283 kg milk and 5.7 kg protein. For both traits, progeny of sire 783 that inherited allele '18' had higher evaluations than progeny that inherited allele '21'. These results were verified by genotyping 151 of his daughters. Thus, the rate of genetic gain for protein production can be increased by selecting progeny of sire 783 carrying allele '18' at this locus.
Article
Short tandem repeat (STR) loci are highly informative polymorphic loci that are gaining popularity for identity testing. We have conducted parentage testing by using nine STR loci on 50 paternity trios that had been previously tested using VNTR loci. These nine unlinked STR loci are amplified in three multiplex reactions and, when examined for genetic informativeness, provide a combined average power of exclusion of 99.73% (Caucasian data). The informative value of the selected loci is based on extensive STR typing of four racial/ethnic populations. In 37 of the 50 cases, paternity could not be excluded by any of the loci. In the remaining 13 cases, paternity was excluded by at least two of the STR markers. The probability of paternity calculated for the alleged father of each matching trio was > 99% in 36 of the 37 inclusion cases. All data agreed with the results reported using VNTR loci and conventional Southern technology. Our studies validate the use of DNA typing with STR loci for parentage testing, thus providing an accurate, highly sensitive, and rapid assay.
Article
Human identification through DNA analysis has faced tremendous changes in the past seven years. The advent of the polymerase chain reaction (PCR) technology coupled with the discovery of amplifiable minisatellites and microsatellites known as amplified fragment length polymorphisms and short tandem repeats (STRs), respectively, allow allelic profiles to be obtained with minute amounts of target DNA even in a degraded state. Very recently, a new dimension in DNA typing analysis was opened with the development of instruments for automated real-time analysis of fluorescent amplification products. In order to derive an automated approach to DNA typing, STR systems were evaluated for sensitivity and accuracy using the Gene Scanner and compared to other DNA typing methods currently in use. Eight different STR systems (encompassing tri-, tetra- and pentanucleotide repeats) were investigated, and conditions for their amplification with fluorescence-tagged primers, resolution on polyacrylamide gels and analysis on a fluorescent DNA fragment analyzer were optimized. Using these conditions, discrete allelic profiles were obtained following amplification of DNA extracted from various cell lines, liquid blood, dry bloodstains and hair samples. Amplification from serial dilutions of template DNA indicated that the minimal amount of target DNA required to detect a fluorescent signal on the Gene Scanner for any of the eight STR systems examined is approximately 100 picograms. The level of precision obtained for real-time allele size determination was observed to be +/- 0.2 to 0.5 base pair (intragel) and +/- 0.5 to 1.5 base pairs (intergel). Consequently, PCR-based DNA typing with fluorescent STR primers and automated analysis provides the enhanced level of precision, accuracy and sensitivity required for forensic casework analysis. Moreover, this approach offers significant advantages for the routine processing of large numbers of DNA samples, greatly facilitates and expedites the generation of allelic profile databases and enables investigators to perform the simultaneous survey of several different loci from single individuals and/or forensic samples.
Article
The effect of a segregating economic trait locus (ETL) can be detected with the aid of a linked genetic marker, if specific alleles of each locus are in association among the individuals genotyped for the genetic marker. For dairy cattle this can be achieved by application of the 'granddaughter design'. If only the sires and their sons are genotyped for the genetic markers, then the allele origin of sons having the same genotypes as their sires cannot be determined. Seven sires and 101 sons were genotyped for five microsatellites. The mean frequency of heterozygous sires was 77%. The mean number of alleles per locus was 8.2. Frequency of informative sons per locus ranged from 60% to 80% with a mean of 72%. With highly polymorphic microsatellites, at least 60% more grandsire families can be included in the analysis, and the number of sons assayed can be reduced by 40%, as compared to diallelic markers.
Article
A total of 20,000 parent-offspring transfers of alleles were examined through the genotyping within 40 CEPH reference families of 28 short tandem repeat polymorphisms (STRPs) located on chromosome 19. Forty-seven initial mutation events were detected in the STRPs using DNA from transformed lymphoblastoid cell lines, but less than half (39%) could be verified using DNA from untransformed cells. None of the cases where three alleles were observed In a single Individual could be verified using DNA from untransformed cells. The average mutation rate for the chromosome 19 STRPs after correction for events which would not be detectable as Mendelian errors was 1.2 × 10−3 per locus per gamete per generation. This rate may have been Inflated by somatic as opposed to germline events. Observed mutation rates for individual STRPs ranged from 0 to 8 × 10−3. The average mutation rate for tetranucleotide STRPs was nearly four times higher than the average rate for dinucleotide STRPs. For determination of the mode of mutation, events Involving STRPs on other chromosomes were also examined. Of the events which were verified using DNA from untransformed lymphocytes or which were likely among those for which DNA from untransformed cells was not available: none were located at the sites of melotic recombination, 91% Involved the gain or loss of a single repeat unit, and 15 occurred In the male germline compared to 4 in the female germline (p = 0.01).
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Animal model, a memory efficient computational strategy applied to the genetic evaluation of the Israeli dairy cattle population
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