[Show abstract][Hide abstract] ABSTRACT: This study aimed to confirm and improve the identified chromosomal regions associated with genetic variation in fleece traits in a backcross Angora x Creole goats design. Five caprine chromosomes (CHI1, CHI2, CHI5, CHI13 and CHI19) were studied by genotyping 297 offspring from 5 F1 (Angora x Creole) families using 2918, 2544, 2038, 1514 and 1107 SNPs on each chromosome and nineteen fleece fiber traits recorded. QTL detection was based on linkage analysis and on the joint linkage (LA) and linkage disequilibrium analysis (LDLA) using the QTLmap software. Six putative QTL detected in previous microsatellite based study were confirmed here and at least 12 additional new QTLs were identified from both LA and LDLA method. Nevertheless to refine deeply these regions should be necessary to use more elaborate analysis approaches.
[Show abstract][Hide abstract] ABSTRACT: Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.
Full-text · Article · Oct 2012 · Journal of Animal Breeding and Genetics
[Show abstract][Hide abstract] ABSTRACT: Summary Recently, a Haley-Knott-type regression method using combined linkage disequilibrium and linkage analyses (LDLA) was proposed to map quantitative trait loci (QTLs). Chromosome of 5 and 25 cM with 0·25 and 0·05 cM, respectively, between markers were simulated. The differences between the LDLA approaches with regard to QTL position accuracy were very limited, with a significantly better mean square error (MSE) with the LDLA regression (LDLA_reg) in sparse map cases; the contrary was observed, but not significantly, in dense map situations. The computing time required for the LDLA variance components (LDLA_vc) model was much higher than the LDLA_reg model. The precision of QTL position estimation was compared for four numbers of half-sib families, four different family sizes and two experimental designs (half-sibs, and full- and half-sibs). Regarding the number of families, MSE values were lowest for 15 or 50 half-sib families, differences not being significant. We observed that the greater the number of progenies per sire, the more accurate the QTL position. However, for a fixed population size, reducing the number of families (e.g. using a small number of large full-sib families) could lead to less accuracy of estimated QTL position.
Full-text · Article · Aug 2012 · Genetics Research
[Show abstract][Hide abstract] ABSTRACT: A quantitative trait loci (QTL) analysis of wool traits from experimental half-sib data of Merino sheep is presented. A total of 617 animals distributed in 10 families were genotyped for 36 microsatellite markers on four ovine chromosomes OAR1, OAR3, OAR4 and OAR11. The markers covering OAR3 and OAR11 were densely spaced, at an average distance of 2.8 and 1.2 cM, respectively. Body weight and wool traits were measured at first and second shearing. Analyses were conducted under three hypotheses: (i) a single QTL controlling a single trait (for multimarker regression models); (ii) two linked QTLs controlling a single trait (using maximum likelihood techniques) and (iii) a single QTL controlling more than one trait (also using maximum likelihood techniques). One QTL was identified for several wool traits on OAR1 (average curvature of fibre at first and second shearing, and clean wool yield measured at second shearing) and on OAR11 (weight and staple strength at first shearing, and coefficient of variation of fibre diameter at second shearing). In addition, one QTL was detected on OAR4 affecting weight measured at second shearing. The results of the single trait method and the two-QTL hypotheses showed an additional QTL segregating on OAR11 (for greasy fleece weight at first shearing and clean wool yield trait at second shearing). Pleiotropic QTLs (controlling more than one trait) were found on OAR1 (clean wool yield, average curvature of fibre, clean and greasy fleece weightand staple length, all measured at second shearing).
[Show abstract][Hide abstract] ABSTRACT: Eight paternal half-sib families were used to identify chromosomal regions associated with variation in the lactation curves of dairy goats. DNA samples from 162 animals were amplified by PCR for 37 microsatellite markers, from Capra hircus autosomes CHI3, CHI6, CHI14 and CHI20. Milk samples were collected during 6 years, and there were 897 records for milk yield (MY) and 814 for fat (FP) and protein percentage (PP). The analysis was conducted in two stages. First, a random regression model with several fixed effects was fitted to describe the lactation function, using a scale (alpha) plus four shape parameters: beta and gamma, both associated with a decrease in the slope of the curve, and delta and phi that are related to the increase in slope. Predictions of alpha, beta, gamma, delta and phi were regressed using an interval mapping model, and F-tests were used to test for quantitative trait loci (QTL) effects. Significant (p < 0.05) QTLs were found for: (i) MY: CHI6 at 70-80 cM for all parameters; CHI14 at 14 cM for delta and phi; (ii) FP: CHI14, at 63 cM was associated with beta; CHI20, at 72 cM, showed association with alpha; (iii) PP: chromosomal regions associated with beta were found at 59 cM in CHI3 and at 55 cM in CHI20 with alpha and gamma. Analyses using more families and more animals will be useful to confirm or to reject these findings.
Full-text · Article · Jun 2008 · Journal of Animal Breeding and Genetics
[Show abstract][Hide abstract] ABSTRACT: With the aim of identifying QTL affecting wool production and wool quality in Merino sheep, specific regions of chromosomes 3, 4, 11 and 25 were analyzed in eight half-sib families, with an average of 63 offspring per sire. Greasy fleece weight and body weight were recorded at hogget and adult shearing. Individual mid-side fleece samples were collected to measure seven wool traits. The regression interval mapping analysis evidenced QTL related to fiber diameter on chromosome 3, on the region of type II keratin genes (KRT2) and fleece weight on chromosome 4, both in two families. We detected a QTL segregating for yield on chromosome 25, being the first description of QTL related to this trait. A second QTL was found for coefficient of variation of fiber diameter, in concordance with previous references. These results contribute to the understanding of the variability of wool traits. The reduction of the confidence intervals for QTL positions, would allow including them on marker-assisted selection schemes accelerating genetic progress of wool sheep.
No preview · Article · Jan 2008 · Small Ruminant Research
[Show abstract][Hide abstract] ABSTRACT: With the aim to detect chromosome segment (quantitative traits loci, QTL) affecting fleece traits in Angora goats, a genome scan using 76 microsatellite markers spanning 1261 cM on 21 chromosomes was conducted. Eight paternal half-sib families were used, which included a total of 288 kids from a dispersed nucleus herd. Mid-side mohair samples were taken from kids at 4 months of age and eight phenotypic fleece traits were measured. We found putatives QTL for coefficient of variation of average fiber diameter (CVAFD) in chromosome 1 and 13, for kemp fiber (KEMP) in chromosome 5 and for discontinuous medullated fibers (DISC) and staple length (SL) in chromosome 2. These results demonstrate the segregation of quantitative traits involved in mohair production. Further studies will concentrate on these regions to characterize the variation of these QTL.
Full-text · Article · Aug 2007 · Small Ruminant Research
[Show abstract][Hide abstract] ABSTRACT: A genomic screen for quantitative trait loci (QTL) affecting conformation traits was performed by genotyping 288 Angora goats offspring from 8 half-sub families with 76 microsatellite markers. The following traits were recorded: weaning weight (WW, Kg); stature (S, cm); chest depth (CD, cm); shoulder width (SW, cm); rump length (RL, cm); rump width (RW, cm); head length (HL, cm); head width (HW, cm); shin circumference (SC, cm); chest circumference (CC, cm) and body length (BL, cm). Data were analyzed using the QTL Express program. A total of 5 QTL were detected in five chromosomes with chromosome wide significance level. For the 11 analysed traits the results were: evidence of two possible QTL for HL were found in chromosomes 1 and 4, a putative QTL for trait CD was found in chromosome 2, evidence for BL was found in chromosome 8 and a possible QTL was found for trait CC in chromosome 9. The results reported here show the existence of chromosomal regions in Angora goats involved in conformation traits and represent the first in depth search in some specific-genome sections in order to identify and characterize the genetic variability involved in these traits.
Full-text · Article · Aug 2007 · Small Ruminant Research
[Show abstract][Hide abstract] ABSTRACT: Several previous studies have indicated the presence of gene or gene families involved in
fleece traits in different species. The aim of this study was to confirm the location of a QTL on chromosome (CHI) 1 and the location of a new QTL on CHI5 using new microsatellites and enlarged families in Angora goats. The population analyzed had a total of 418 kids from 10 Angora bucks. The number of half-sib offspring per buck ranged between 26 to 73 kids. Eight phenotypic fleece traits were recorded. An interval analysis was performed under a half-sib model using the QTL Express program. Our results confirm a QTL for CVAFD on CHI1 in Angora goats and we found a new QTL for KEMP on CHI5. Nevertheless, new families, increased number of kid in extant families and a fine mapping on the candidate regions should be the next steps to carry out.