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Predicting the relationship between molecular marker heterozygosity and hybrid performance using RAPD markers in rice (Oryza sativa L.)
Abstract
Successful prediction of heterosis and performance of F 1 -hybrids from genetic similarity of their parents based on molecular markers has been reported in various crops. Estimation of genetic diversity and distance among various rice (Oryza sativa L.) genotypes and the correlation between genetic distance (GD) and hybrid performance would determine breeding strategies, define heterotic groups and predict future hybrid performance. In the present study, we surveyed genetic divergence among 26 rice genotypes using DNA markers and assessed the relationship between genetic distance and hybrid performance of 64 hybrids in a Line x Tester (4 lines x 16 testers) mating design. The 64 F 1 hybrids together with the 20 parents were evaluated for nine traits of agronomic importance, including yield, in a replicated field trial. The 20 parents along with the other six rice varieties were examined for DNA polymorphism using 53 random decamer oligonucleotide primers of which 36 primers generated clear banding profiles. A total of 245 polymorphic variants were generated and based on the polymorphism data, genetic distances (GDs) ranged from 0.23 to 0.53. Heterosis was observed in hybrids for most of the traits and yield exhibited the highest heterosis among the nine traits examined. The correlation values of GDs with F 1 performance were mostly non-significant, except for days to 50% flowering and test weight. The correlations of GDs with mid parent, better-parent heterosis and standard heterosis were not significant enough to be of predictive value. However, when specific combining ability (SCA) value was correlated with GD values of a group of hybrid (BPT 5204), there was high significance pertaining to a particular hybrid with relatively higher yield. These results indicated that GDs based on the random amplified polymorphic DNA (RAPD) markers may be useful for predicting heterotic combinations in rice and support the idea that the level of correlation between hybrid performance and genetic divergence is dependent on the germplasm used.
... Four cross combinations viz., IR 68897A×IR 79906-B-5-3-3, IR 68897A×IR 80461-B-7-1, IR 68897A×IR 83376-B-B-91-3 and IR 79156A×IR 77298-5-6-18 showed significant positive average heterosis, heterobeltiosis and standard heterois over both the hybrid checks. The heterosis in both positive and negative direction were also reported byAmudha and Thiyagarajan (2008),Malarvizhi et al. (2009), Selvaraj et al. (2010 andMuthuramu et al. (2010). ...
The three-line hybrid system involving cytoplasmic male sterile A- line, maintainer B-line and restorer R-line is a common approach for hybrid development in rice. The hybrids developed through this technique has been successful in increasing the rice production under favourable irrigated condition but hybrids under water-limited rainfed condition has not been much evaluated. Hybrids developed for non-irrigated rainfed lowland environment can help in sustaining the rice production under decreasing water and land resources. The emphasis therefore should be given for developing improved hybrids specifically suited for unfovourable water limited rainfed conditions. Keeping this in view, F1 crosses were generated using line x tester mating design to evaluate rice hybrids under rainfed stress. Assessment of heterosis in 64 F1 cross combination under water-limited rainfed condition revealed scope of exploiting hybrid vigour and developing heterotic hybrids for non-irrigated rainfed lowland environment. Significant standard heterosis over commercial hybrid checks (KRH 2 and PA 6444) observed in many cross combinations for various traits viz., filled grain per panicle, spikelet fertility percent, grain yield per plant, biomass per plant and harvest index highlight the importance of these traits in selecting parents based on above traits and developing hybrids with drought tolerance and high yield for water limited rainfed lowland ecology
... In general, when the genetic difference between parents is high, the heterosis observed in the progeny is also high (Falconer and Mackay, 1996). The procedure most frequently used has been the selection of parental using DNA-marker-based genetic distance between inbred lines, and the estimation of its relationship with heterosis (Lee et al., 2007) due to its simple application (Dreisigacker et al., 2005;Shanthi et al., 2006;Biswas et al., 2008;Gvozdenović et al., 2009;Selvaraj et al., 2010). However, the researchers have different views on molecular marker based prediction. ...
Efficient parent's selection and heterosis prediction in pea have been of great interest for breeders in order to determine with anticipation, those crosses capable of producing a high frequency of transgresive recombinant lines. The combining ability is the most frequently used criteria to select parents, though its estimation is costly and time-consuming. In this study we examine heterotic crosses for yield determined by morphological and molecular genetic distances between parents, and compare these with the heterotic crosses established by specific combing ability in a line × tester design. To select parental lines that would generate heterotic hybrids, different criteria were applied: genetic distances between lines obtained through morphological traits and molecular markers and cluster analysis. Inspite genetic distances were more efficient than cluster analysis, the correlations values between them and heterosis were weak, and so, we propose to change the way to measure the importance of the genetic distances using the percentage of heterotic crosses that can be successfully predicted as parameter to evaluate. The percentage of heterotic crosses comparing best parent heterosis was higher than the one obtained comparing midparent heterosis. SRAP methodology based on Dice distance between the parental lines and the Euclidean distances based in morphological data collection are the best alternative to SCA grouping association, since 69% and 65% of heterotic crosses can be predicted.
More than 2.0 million-hectare area was affected by flash floods of various grades and reduced the average yield in Bangladesh by 5%. It involves introgression of Sub1 QTL into the genetic background of HYV rice through marker-assisted breeding and to evaluate submergence tolerance of high yielding rice varieties. SSR profiling was performed to tag the submergence tolerant QTL by using sub1 flanking markers and F 1 confirmation of Binadhan-7 x BRRI dhan52 (F 1) by using the primer RM1115. The gene diversity value was 0.7610 and the polymorphism information content (PIC) values were 0.7432 & allele frequencies (%) were 0.3328. Binadhan-7 x BRRI dhan52 (F 2) crosses were possessed the highest grain yield plant-1 (38.00 g) which was significantly higher than its both parents and also early maturing as 124 days from all crosses. The genetic similarity analysis using UPGMA (Unweighted Pair-Group Method using the Arithmetic Average) clustering system generated 5 major genetic clusters. Maximum intra-cluster degree of diversity was observed in cluster4 (79.93) and minimum in cluster3 (31.44). Highly significant and positive correlations were found among the grain yield (GY) and Total tillers/plant, effective tillers/plant, panicle length and filled grains/panicle. The first three principal components with Eigen values explained 73.7 % of the total variation among 16 rice genotypes for the 9 quantitative traits studied. However, it is hoped that promising Sub1 cross combination Binadhan-7x BRRI dhan52 will be able to develop three to four weeks tolerance with high yielding submergence tolerant varieties to increase rice production in submerged prone areas of Bangladesh where single flash floods occur under different cropping patterns.
The present study of this investigation was aimed to use RAPD markers and phenotypic distances based on yield traits to assess the genetic diversity among six inbred lines (three Egyptian and three American inbred lines) widely used in maize breeding programs and to evaluate the association of the genetic diversity with their F 1 performance. Five primers succeeded to evaluate six inbred lines of maize using RAPD technique. This technique was efficient in detecting polymorphism with an average of 91.3% and determining genetic diversity among the six studied inbred lines. But they were not effective enough to distinguish some inbred lines by unique markers. The molecular distances and phenotypic distances were found to range from 0.355 to 0.600 and from 27.37 to 164.46, respectively. According to cluster analysis and principal coordinate analysis, the parental inbred lines divided into three and two groups based on molecular and phenotypic distances, respectively. Also, using principal coordinate analysis based on two types of distances observed that the separation between the American inbred lines was higher than separation between the Egyptian inbred lines. On the other hand, poor correlation (r = 0.297) among molecular and phenotypic distances were found. This poor correlation also found for two types of distance with specific combining ability and mid parents heterosis and better parent heterosis. Coefficient of determination for F 1 performance against molecular distance and phenotypic distances were extremely low and ranged from 0.0002 to 0.189 and from 0.0001 to 0.351, respectively. This result demonstrated the reliability impairment of regression models in predicting for F 1 performance.
Показано особливості використання різних маркерних систем у селекції високогетерозисних гібридів кукурудзи. Встановлено недостатньо високі значення асоціацій між генетичною дивергенцією, розрахованою за дескрипторами UPOV, та індексами гетерозису. Показано, що більш тісні асоціації між константами СКЗ та індексами гетерозису спостерігаються при аналізі гібридів, отриманих за діалельною схемою схрещувань. Доведено доцільність використання SSR маркерної системи для підбору батьківських компонентів при отриманні високогетерозисних гібридів кукурудзи.
A special class of rice germplasm, referred as wide-compatible can produce hybrids with enhanced spikelet fertility when crossed with japonica × indicia rice lines having neutral allele. Present study was conducted to identify the presence of neutral allele and relationship in the hybrid performance. The wide-compatible genotype screening resulted positive selection having neutral allele and responsible for increased spikelet fertility with possible utilization as donor parent in hybrid development programme for achieving higher yield. Combining ability and heterosis for grain yield and its component traits derived from japonica × indica experimental hybrids revealed higher general combining ability variance than their respective specific combining ability variances indicating the predominance of additive gene action, opened the way for fixing the yield contributing gene by breeding through transgressive selection. Most of the experimental hybrids showed significant and positive SCA effects for grain yield as well as several other yield related component traits. Wide compatibility gene investigation clearly demonstrated the utility of InDel primer in the identification of wide compatible genotypes possessing neutral allele at S5 locus. The genotypes having natural allele (281-bp) can give rise to fully fertile panicle and significant contribution towards yield and heterosis. Association index between genetic diversity and three SH of GY hybrids on the basis of microsatellite data set surprisingly exhibited significant and positive correlation indicated the possible utility of microsatellite markers for successful utilization and establishing the strong heterotic relationship.
Hybrid breeding technology is one of the most feasible options to meet the future food
challenges and sustainable agriculture. Large number of cross combinations are attempted
and evaluated in hybrid breeding programs, but a few are selected. This is labour intensive,
time consuming and costly; despite of it selection efficiency is too low. Therefore, it is
important to explore alternate approaches to enhance the selection efficiency to predict
hybrid performance. Pedigree data of the parental lines and molecular marker have been
effectively employed to predict field performance of hybrids. Marker technologies, wider
gene compatibility and QTL approaches on the basis of parental genomic variation are
predominantly used for predicting hybrid performance. Informative markers having high
PIC would be considered as key markers for heterotic performance prediction. Prediction
ability depends on association between QTL and selected molecular markers with major
effect on the desired trait, size of population and the recombination frequencies.
Transcriptomic and metabolomics data are becoming useful and may provide means for
heterosis prediction. Joint analysis of the genomic, transcriptomic and metabolomics data
for molecular-based prediction of heterosis needs to be studied for its potential to improve
the efficiency of applied hybrid breeding programs. Inter-sub-specific cross combinations
depends on genetic remedy to the persisting hybrid semi-sterility problem and entire
diversity, and present of neutral wide compatible genes.
Combining ability and heterosis were studied in a 7×7 diallel set of bread wheat. Analysis of variance revealed that mean squares due to genotypes, parents and F 1 crosses, were highly significant for all studied characters. The mean squares due to both general (GCA) and specific (SCA) combining abilities were highly significant for all studied characters. Significant and highly significant desirable heterosis relative to the better parent was recorded in all studied characters. The maximum useful heterosis (78.05%) was observed in grain yield/plant for the cross (P 4×P 7). Many hybrids showed desirable significant or highly significant specific combining ability effects for all studied traits, except days to 50% heading and plant height. The genetic relationships among the seven parental genotypes were investigated using 10 RAPD primers. The highest similarity index was found between P 5 and P 6, while the lowest similarity index was found between P 2 and P 6. Among the studied parents, five out of seven, were characterized by 13 negative and 2 positive unique markers. Non significant correlations were observed between genetic distance with both of the amount of heterosis and SCA as well as between heterosis with SCA for grain yield/plant.
Efficiency of breeding programs depends on choice of optimal parental combinations. The ability to identify parental combinations that will result in greater genetic variance of progeny would help to maximize genetic gain from selection in plant breeding programs. Substantial efforts have been invested to study the possible correlations between various predictors based on parental information with population mean and genetic variance of segregating population. With the development of DNA-based markers, it became possible to determine genetic distances among parental lines. However, prediction based on DNA marker data remains a challenging issue. In view of the weakness of traditional marker-assisted selection in prediction potential the use of genomic selection (GS) is considered as promising approach. Rather than seeking to identify individual markers significantly associated with a quantitative trait, GS could use all marker data as predictors of parental line performance and contributes to accurate predictions of the usefulness of parental combinations. The ability to predict hybrid performance (HP) of breeding lines based on molecular-based genetic data would greatly enhance the efficiency of hybrid breeding programs. Therefore, the relationship between genetic distance and HP was intensively studied by many authors, predominantly by allogamous crop breeders. Prediction of HP without having to produce and assess hundreds of single-cross hybrids would reduce the time and effort required to identify promising combinations. Earlier studies indicated that the success of predicting HP based on of parental information was not encouraging and at best inconsistent. However, recent marker-based prediction approaches based on expression profiling and those based on multiple linear regressions gave results often superior or at least similar to phenotypic and pedigree data approaches. © 2013 Springer Science+Business Media Dordrecht. All rights reserved.
Texts in agricultural and biological sciences are full of numbers, but far too often these numbers are not presented well. The way that numbers are reported does matter, as it can either help or hinder the reader in understanding the message. In particular, how many digits are chosen for each number is important. This choice should be governed by the so-called effective digits, that is, those digits that vary in the given set of data. We give various examples to demonstrate this facet, and offer some guidelines for the selection of number of digits to be used. Our hope is that authors of research articles will use these guidelines in order to make their reports more readable and understandable.
Isozymes and restriction fragment length polymorphisms (RFLPs) have been proposed for use in varietal identification and selection for agronomic traits. Although the use of isozymes for these purposes has been well documented, evaluation of the efficacy of RFLP technology as applied to crop improvement is far from complete. This investigation was conducted to study the relationship between RFLP-derived genotypes and heterotic patterns of a group of maize (Zea mays L.) inbred lines. A total of 22 inbreds was crossed to four testers (B73, B76, Mo17, and Va26) in combinations that minimized crossing within heterotic groups. Forty-seven single-cross progeny were subsequently evaluated for several agronomic traits (including grain yield and moisture, ear height, and root lodging) over 2-4 consecutive years at two to four Iowa locations in a randomized complete-block design. The inbred lines were subjected to RFLP analysis, which involved 47 genomic clones and the restriction enzymes EcoRI and HindIII. Hybrid RFLP patterns were predicted from their inbred parents. Modified Roger's distances were computed to estimate genetic distance among the inbred lines. Principal component analysis facilitated ascertainment of relative dispersion of the inbreds based on the frequency of variants at specific RFLP loci. Evident associations of variants with genes affecting agronomic traits were identified by principal component regression analysis, in which adjusted hybrid means were regressed on the matrix of hybrid variants frequencies. The hybrid means were adjusted by removing environmental effects, using residuals as dependent variables in the regression analysis. Results from this study suggest that RFLP analysis may be of value in allocating maize inbreds to heterotic groups, but no relationship between RFLP-based genetic distance and hybrid performance was apparent. Principal component regression identified variants potentially linked to genes that control specific agronomic traits.
Genetic variation of nine upland and four lowland rice cultivars (Oryza sativa L.) was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). Forty-two random primers were used to amplify DNA segments and 260 PCR products were obtained. The results of agarosegel electrophoretic analysis of these PCR products indicated that 208 (80%) were polymorphic. All 42 primers used in this experiment were amplified and typically generated one-to-four major bands. Only two primers showed no polymorphisms. In general, a higher level of polymorphism was found between japonica and indica subspecies while fewer polymorphisms were found between upland and lowland cultivars within the indica subspecies. A dendrogram that shows the genetic distances of 13 rice cultivars was constructed based on their DNA polymorphisms. Classification of rice cultivars based on the results from the RAPD analysis was identical to the previous classification based on isozyme analysis. This study demonstrated that RAPD analysis is a useful tool in determining the genetic relationships among rice cultivars.
A set of accessions of Oryza sativa from the International Rice Research Institute (Philippines) that included known and suspected duplicates as well as closely related germplasm has been subjected to RAPD analysis. The number of primers, the number of polymorphic bands and the total number of bands were determined that will allow the accurate discrimination of these categories of accessions, including the identification of true and suspected duplicates. Two procedures have been described that could be employed on a more general basis for identifying duplicates in genetic resources collections, and further discussion on the values of such activities is presented.
Selection of donor lines to improve parents of single crosses and the relationship between inbred per se and hybrid performance are major concerns of corn (Zea mays L.) breeders. We attempted to use molecular marker technology to address these concerns. Our specific objectives were to evaluate methods of using molecular marker data to (i) identify parents useful for improving single cross hybrid and (ii) compare marker genotypic means measured at the inbred level to those measured at the hybrid level. Performance data from a diallel cross among 14 corn inbreds were used. Molecular marker data were obtained on the 14 inbreds for 14 allozyme and 52 restriction fragment length polymorphism loci. Number of unique marker alleles in a donor inbred was not a good measure of the value of the donor for improving a single cross. A donor value calculated using genotypic means for loci that showed significant associations with grain yield was highly correlated with ltG, a measure of the value of a donor. Means of homozygous marker genotypes measured at the inbred level were significantly correlated with means measured at the hybrid level. These correlations (0.71 for yield, 0.75 for plant height, 0.51 for ear height, and 0.82 for flowering date) were generally higher than those between midparent and Ft means, but not high enough to accurately predict hybrid performance if selection were based on inbred genotypic means.
The potential of ISSR-PCR for diversity analysis was evaluated in 86 accessions of Indian rice using 14 anchored primers based on (AG) and (GA) repeats. The accessions included 50 landraces, 20 improved varieties and 16 other accessions for comparison. In all, 220 band positions (loci) and 5514 bands were generated and all loci were polymorphic. The 14 primers revealed genetic relationships among the 86 accessions adequately. The wild accessions, japonica varieties, improved indica varieties, hybrids and landraces were clearly delineated. The frequency of clustered GA repeats was more in varieties than in landraces. The polymorphism information content (PIC) and resolving power (Rp) values of each primer were different in landraces and varieties. Both PIC and Rp were negatively correlated to mean genetic similarity among accessions. Primers with 3' dinucleotide anchor revealed a higher PIC than those with one nucleotide anchor. The most informative primer (GA)(8) YG alone could help distinguish 81 accessions. The average expected heterozygosity of landraces was higher than that of varieties. The four wild accessions of Oryza nivara and O. rufipogon were together more distant from the landraces than from the varieties. The landraces are quite distinct from the cultivated varieties and need to be conserved and used to widen the genetic base of rice varieties. (AG)(n) and (GA)(n) based primers are highly informative for cost-effective assessment of genetic diversity in rice germplasm.
The challenge to maize breeders is to identify inbred lines that produce highly heterotic hybrids. In the present study we
surveyed genetic divergence among 13 inbred lines of maize using DNA markers and assessed the relationship between genetic
distance and hybrid performance in a diallel set of crosses between them. The parental lines were assayed for DNA polymorphism
using 135 restriction fragment length polymorphisms (RFLPs) and 209 amplified-fragment polymorphisms (AFLPs). Considerable
variation among inbreds was detected with RFLP and AFLP markers. Moreover AFLPs detect polymorphisms more efficiently in comparison
to RFLPs, due to the larger number of loci assayed in a single PCR reaction. Genetic distances (GDs), calculated from RFLP
and AFLP data, were greater among lines belonging to different heterotic groups compared to those calculated from lines of
the same heterotic group. Cluster analysis based on GDs revealed associations among lines which agree with expectations based
on pedigree information. The GD values of the 78 F1 crosses were partioned into general (GGD) and specific (SGD) components. Correlations of GD with F1 performance for grain yield were positive but too small to be of predictive value. The correlations of SGDs, particularly
those based on AFLP data, with specific combining-ability effects for yield may have a practical utility in predicting hybrid
performance.
Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to evaluate
genetic relationships within the Theobroma cacao species and to assess the organization of its genetic diversity. Genetic variability was estimated with 18 primers and 43
RFLP probes on 155 cocoa trees belonging to different morphological groups and coming from various geographic origins. The
majority of the RFLP probes issued from low-copy DNA sequences. On the basis of on the genetic distance matrices, the two
molecular methods gave related estimates of the genetic relationship between genotypes. Although an influence of cocoa morphological
groups and geographical origins of trees was observed, a lack of gene differentiation characterized the T. cacao accessions studied. The continuous RFLP variability observed within the species may reflect the hybridization and introgressions
between trees of different origins. Nevertheless, the Nacional type was detected to be genetically specific and different
from well-known types such as Forastero, Criollo and Trinitario. Some of those genotypes were characterized by a low heterozygosity
rate and may constitute the original Nacional pool. These results also provide information for the constitution of a cocoa
tree core collection.
RFLPs, AFLPs, RAPDs and SSRs were used to determine the genetic relationships among 18 cultivated barley accessions and the
results compared to pedigree relationships where these were available. All of the approaches were able to uniquely fingerprint
each of the accessions. The four assays differed in the amount of polymorphism detected. For example, all 13 SSR primers were
polymorphic, with an average of 5.7 alleles per primer set, while nearly 54% of the fragments generated using AFLPs were monomorphic.
The highest diversity index was observed for AFLPs (0.937) and the lowest for RFLP (0.322). Principal co-ordinate analysis
(PCoA) clearly separated the spring types from the winter types using RFLP and AFLP data with the two-row winter types forming
an intermediate group. Only a small group of spring types clustered together using SSR data with the two-row and six-row winter
varieties more widely dispersed. Direct comparisons between genetic similarity (GS) estimates revealed by each of the assays
were measured by a number of approaches. Spearman rank correlation ranked over 70% of the pairwise comparisons between AFLPs
and RFLPs in the same order. SSRs had the lowest values when compared to the other three assays. These results are discussed
in terms of the choice of appropriate technology for different aspects of germplasm evaluation.
In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility
and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence
repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight
new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms
(SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported
here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified
in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were
isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along
rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution
of polymorphism detected by these markers varies between different regions of the genome.
In Cicer arietinum isozyme analysis has revealed only a limited amount of genetic variation. Molecular markers are reported to be able of better disclosing differences among genotypes. In order to estimate the potential of RAPD markers in chickpea genetic studies, six genotypes, including 'Calia', a recently constituted chickpea variety, were evaluated using 60 different 10-mer primers of arbitrary sequence. Most primers did not reveal any polymorphism, however, a moderate level of variation was detected among the six genotypes. Different amplification protocols were also compared in order to evaluate their reproducibility and to identify the ones best fitting the evaluation needs. The results indicate that RAPDs may constitute a relatively simple and efficient method for analyzing variation in C. arietinum collections.
A total of 57.8 Mb of publicly available rice ( Oryza sativa L.) DNA sequence was searched to determine the frequency and distribution of different simple sequence repeats (SSRs) in the genome. SSR loci were categorized into two groups based on the length of the repeat motif. Class I, or hypervariable markers, consisted of SSRs ≥20 bp, and Class II, or potentially variable markers, consisted of SSRs ≥12 bp <20 bp. The occurrence of Class I SSRs in end-sequences of Eco RI- and Hin dIII-digested BAC clones was one SSR per 40 Kb, whereas in continuous genomic sequence (represented by 27 fully sequenced BAC and PAC clones), the frequency was one SSR every 16 kb. Class II SSRs were estimated to occur every 3.7 kb in BAC ends and every 1.9 kb in fully sequenced BAC and PAC clones. GC-rich trinucleotide repeats (TNRs) were most abundant in protein-coding portions of ESTs and in fully sequenced BACs and PACs, whereas AT-rich TNRs showed no such preference, and di- and tetranucleotide repeats were most frequently found in noncoding, intergenic regions of the rice genome. Microsatellites with poly(AT)n repeats represented the most abundant and polymorphic class of SSRs but were frequently associated with the Micropon family of miniature inverted-repeat transposable elements (MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was developed and integrated into the existing microsatellite map of rice, providing immediate links between the genetic, physical, and sequence-based maps. This contribution brings the number of microsatellite markers that have been rigorously evaluated for amplification, map position, and allelic diversity in Oryza spp. to a total of 500.
[Clone sequences for 199 markers (RM1–RM88, RM200–RM345) developed in this lab are available as GenBank accessions AF343840 – AF343869 and AF344003 – AF344169 .]
To study genetic diversity and relationships of wild relatives of rice, 58 accessions of Oryza rufipogon, Oryza nivara, Oryza sativa f. spontanea and the cultivated Oryza sativa, representing a wide range of their distribution, were analyzed using the restriction fragment length polymorphism (RFLP) technique. All 30-used RFLP probes detected polymorphisms among the Oryza accessions, with an average of 3.8 polymorphic fragments per probe. Considerable genetic diversity was scored among the Oryza accessions with a similarity coefficient ranging from 0.28 to 0.93; but the cluster analysis of the accessions did not show an apparent grouping based on the species classification, instead they were scattered randomly in different groups. Noticeably, the Oryza accessions from the same geographic region, or near-by geographic regions, tended to be clustered in the same groups. The indica rice varieties showed relatively high genetic diversity and were scattered in different groups of their wild relatives, but the japonica varieties showed a relatively low variation and formed an independent group. It is concluded from the molecular analytical result that: (1) the four Oryza taxa have a remarkably close relationship and their independent species status need to be carefully reviewed; (2) geographic isolation has played a significant role in the differentiation of the Oryza accessions; therefore, a wide geographic range needs to be covered in collecting wild rice germplasm for ex situ conservation; and (3) the conventional conclusion of indica rice being directly domesticated from its ancestral wild species, and japonica rice being derived from indica, gains support from our data.
The underlying mechanisms for hybrid vigor or heterosis are elusive. Here we report a population of recombinant inbred lines (RILs), derived from the two ecotypes, Col and Ler, which can serve as a permanent resource for studying the molecular basis of hybrid vigor in Arabidopsis. Using a North Carolina mating design III (NCIII), we determined the additive and dominant nature of gene action in this population. We detected heterosis among crosses of RILs with one of the two parents (Col and Ler) and analyzed genotypes and heterozygosities for RILs and test cross families (RILs crossed to Col and Ler) using a total of 446 published molecular markers. The performance of RILs and additive and dominant components in the test cross families were used to analyze QTLs for 16 traits, using QTL cartographer and composite interval mapping with 1,000 permutations for each trait. Our data suggest that locus-specific and/or genome-wide differential heterozygosity, including epistasis, plays an important role in the generation of the observed heterosis. Furthermore, the hybrid vigor occurred between two closely related ecotypes, and provides a general mechanism for novel variation generated between genetically similar materials.
Uniola paniculata, commonly known as sea oats, is a C4 perennial grass capable of stabilizing sand dunes. It is most abundant along the Gulf of Mexico and southeastern Atlantic coastal regions of the United States. The species exhibits low seed set and low rates of germination and seedling emergence, and so extensive clonal reproduction is achieved through production of rhizomes, which may contribute to a decline in genetic diversity. To date, there has been no systematic assessment of genetic variability and population structure in naturally occurring stands in the USA. This study was conducted to assess the genetic relationship and diversity among nineteen U. paniculata accessions representing eight states: Texas, Louisiana, Mississippi, Alabama, Florida, South Carolina, North Carolina, and Virginia, using amplified fragment length polymorphism (AFLP). Twelve AFLP EcoRI + MseI primer combinations generated a wide range of polymorphisms (42-81%) with a mean of 59%. Overall, the sea oats plants exhibited a low range of genetic similarity. Florida accessions, FL-33 and FL-39, were most genetically diverse and the accessions from both Carolinas and Virginia (NC-1, NC-11, SC-15, and VA-53) harbored less genetic variability. Cluster analysis using the UPGMA approach separated U. paniculata plants into four major clusters which were also confirmed by principal coordinate analysis (PCO). Further examination of the different components of genetic variation by analysis of molecular variance (AMOVA) indicated the largest proportion of variability at the state level (47.8%) followed by the variation due to the differences among the genotypes within an accession (34.4%), and the differences among the accessions within a state (17.8%). The relationship between genetic diversity and geographic source of sea oats populations of the United States as revealed through this comprehensive study will be helpful to resource managers and commercial nurseries in identifying suitable plant materials for restoration of new areas without compromising the adaptation and genetic diversity.
Random amplified polymorphic DNA (RAPD) banding patterns are useful in identifying genotypes of various crops. In particular, this technology has important applications in plant breeding, seed production and seed testing programmes. However, before this potential is realized, studies must demonstrate that environmental factors do not influence RAPD results and that the test protocol can be standardized. This study showed that artificial and natural seed deterioration, contamination by fungi, and differing seed production environments did not generally affect the stability of RAPD markers in soybean (Glycine max [L.] Merr.) seed. RAPD markers obtained from maize (Zea mays L.) seed were dominant and hybrid seed generally possessed the same markers as both inbred parents. RAPD markers obtained from the maize seed coat and endosperm were not representative of their genetic heritage while those from the embryo were. The use of RAPD banding patterns appears applicable to a number of crops and can be successfully used to enhance and determine the genetic purity of individual seeds.
Fourteen different primers were used to amplify DNA from selfed progenies of 117 diploid plants regenerated from haploid cell suspension protoplasts of rice (cv. Miara). This survey, which permitted to generate 69 different major fragments in control Miara plants as well as in protoclone DNA, did not reveal genetic change among protoclones compared to the donor variety except independent amplification of an additional fragment in nearly half of the lines by two 10-mers. This polymorphism in the protoclonal population was attributed to natural intravarietal variation among the donor plants which have been collected to establish the microscope-callus suspension culture. However, polymorphism could not be detected in calluses grown from cell clumps collected in the 21-month old cell suspension. This apparent lack of tissue culture-induced polymorphism at the molecular level contrasts with the results of a previous field evaluation of the progenies which exhibited both wide range and high frequency morphological changes. These observations highlight the absence of apparent relationship between morphological variation and molecular changes. The interest of RAPDs as a convenient method to test genetic integrity of the regenerants, that would preclude the need for further field evaluation, is discussed. (Résumé d'auteur)
Genetic distances were calculated among 37 inbred lines representing a wide range of related and unrelated elite Corn Belt germ plasm of maize (Zea Mays L.), using 257 probe restriction enzyme combinations. Genetic distances based on RFLP data were highly correlated with coefficients of parentage among pairs of lines. The RFLP-based distance had a higher correlation with single-cross grain yield performance and grain yield heterosis than any of the other measures of similarity we calculated using these same lines. The coefficients of determination (r
2) from regressing the coefficient of parentage, grain yield, and grain yield heterosis on Nei's measure of genetic similarity based on RFLP data were 0.81, 0.87 and 0.77, respectively. A cluster diagram based upon the RFLP data grouped the lines into families consistent with the breeding history and heterotic response of these lines. We believe that measures of similarity calculated from RFLP data, coupled with pedigree knowledge and using molecular markers to locate quantitative trait loci (QTL), could allow maize breeders to predict combinations of lines that result in high-yielding, single-cross hybrids.
Changes that may have occurred over the past 50 years of hybrid breeding in maize (Zea maize L.) with respect to heterosis for yield and heterozygosity at the molecular level are of interest to both maize breeders and quantitative geneticists. The objectives of this study were twofold: The first, to compare two diallels produced from six older maize inbreds released in the 1950's and earlier and six newer inbreds released during the 1970's with respect to (a) genetic variation for restriction fragment length polymorphisms (RFLPs) and (b) the size of heterosis and epistatic effects, and the second, to evaluate the usefulness of RFLP-based genetic distance measures in predicting heterosis and performance of single-cross hybrids. Five generations (parents, F1; F2, and backcrosses) from the 15 crosses in each diallel were evaluated for grain yield and yield components in four Iowa environments. Genetic effects were estimated from generation means by ordinary diallel analyses and by the Eberhart-Gardner model. Newer lines showed significantly greater yield for inbred generations than did older lines but smaller heterosis estimates. In most cases, estimates of additive x additive epistatic effects for yield and yield components were significantly positive for both groups of lines. RFLP analyses of inbred lines included two restriction enzymes and 82 genomic DNA clones distributed over the maize genome. Eighty-one clones revealed polymorphisms with at least one enzyme. In each set, about three different RFLP variants were typically found per RFLP locus. Genetic distances between inbred lines were estimated from RFLP data as Rogers' distance (RD), which was subdivided into general (GRD) and specific (SRD) Rogers' distances within each diallel. The mean and range of RDs were similar for the older and newer lines, suggesting that the level of heterozygosity at the molecular level had not changed. GRD explained about 50% of the variation among RD values in both sets. Cluster analyses, based on modified Rogers' distances, revealed associations among lines that were generally consistent with expectations based on known pedigree and on previous research. Correlations of RD and SRD with f1 performance, specific combining ability, and heterosis for yield and yield components, were generally positive, but too small to be of predictive value. In agreement with previous studies, our results suggest that RFLPs can be used to investigate relationships among maize inbreds, but that they are of limited usefulness for predicting the heterotic performance of single crosses between unrelated lines.
Twenty-one maize (Zea mays L.) inbred lines were analysed using isozyme electrophoresis, restriction fragment length polymorphism (RFLP), and two-dimensional electrophoresis of denatured proteins (2-D PAGE). Our goal was (1) to assess the genetic variability among these lines which are potential progenitors for the development of forage maize hybrids in Europe, and (2) to compare the relationship pattern revealed by the polymorphism at marker loci with the one derived from the amount of protein variability assessed by computer-assisted analysis of the 2-D electrophoregrams. Fourteen markers were obtained from isozyme polymorphism, 84 from the restriction fragment length polymorphism, and 70 from protein shifts revealed by 2-D PAGE. The Rogers' distance computed on the set of molecular markers was the most efficient to describe the pedigree relationships between lines. Quantitative protein data gave a picture of relationships between lines clearly different from the monogenic markers. When unrelated pairs of lines were considered, the Rogers' distance was weakly correlated to distances based on quantitative variations in the amount of protein which may be consistent with their polygenic control and the occurrence of gene interactions.
Hybrid rice has contributed significantly to the dramatic increase of rice production in the world. Despite this, little attention has been given to studying the genetic basis of heterosis in rice. In this paper, we report a diallel analysis of heterosis using two classes of molecular markers: restriction fragment length polymorphisms, (RFLPs) and microsatellites. Eight lines, which represent a significant portion of hybrid rice germ plasm, were crossed in all possible pairs, and the F1s were evaluated for yield and yield component traits in a replicated field trial. The parental lines were surveyed for polymorphisms with 117 RFLP probes and ten microsatellites, resulting in a total of 76 polymorphic markers well-spaced in the rice RFLP map. The results indicated that high level heterosis is common among these crosses: more than 100% midparent and 40% better-parent heterosis were observed in many F1s, including some crosses between maintainer lines. Heterosis was found to be much higher for yield than for yield component traits, which fits a multiplicative model almost perfectly. Between 16 and 30 marker loci (positive markers) detected highly significant effects on yield or its component traits. Heterozygosity was significantly correlated with several attributes of performance and heterosis. Correlations based on positive markers (specific heterozygosity) were large for midparent heterosis of yield and seeds/panicle and also for F1 kernel weight. These large correlations may have practical utility for predicting heterosis.
Molecular characterization of 32 Indian rice varieties of different agro-climatic zones resulted in mean heterozygosity value of 0.622, 0.819 and 0.890 over polymorphic loci and marker index value of 1.00, 6.75 and 4.16, respectively for RAPD, ISSR and STMS primers. The three marker systems resulted in 201 polymorphic bands (94.36%) out of a total of 213 bands. The probability of a chance identical match between two varieties was very low (2.08x1010) in combined molecular marker analysis as compared to individual marker system (RAPD, 7.5 x 10-4; ISSR, 1.5 x 10-3 and STMS, 3.9 x 10-6). The combined average genetic similarity for molecular markers and coefficient of parentage (COP) across all 496 pairwise combinations revealed a non-significant relationship (r = 0.215).
A set of 18 accessions from an Indian scented rice (Oryza sativa L.) collection was subjected to random amplified polymorphic DNA (RAPD) analysis. Polymerase chain reaction (PCR) with 10 arbitrary 10-mer oligonucleotide primers, applied to the 18 accessions, produced a total of 144 different marker bands of which 95.1 per cent were polymorphic. The size range of the amplified DNAs was mostly between 0.5 kbp and 4 kbp. Thus, with the selected primers sufficient polymorphism could be detected to allow identification of individual accessions. Visual examination of electrophoresis gels and analysis of banding patterns confirmed that many of the scented rice varieties under cultivation with similar names are genetically quite different. A dendrogram displaying the relative genetic similarities between the accessions showed a range of 25 to 77.5 per cent similarity. The RAPD analysis offered a rapid and reliable method for the estimation of variability between different accessions which could be utilized by the breeders for further improvement of the scented rice genotypes.
Improving grain and milling yields of long-grain rice (Oryza sativa L.) continues to be a major objective of southern U.S. breeding programs. The objective of this study was to determine the relationship between molecular marker polymorphism of the parents and performance of the F1 hybrids. A diallel cross was made by intermating eight lines commonly used in U.S. southern long-grain rice breeding programs. The 28 F1 hybrids and the parents were evaluated for rough rice yield, head rice percentage, and head rice yield in replicated field trials. Very little heterosis was detected among hybrids for head rice percentage, whereas heterosis was high for rough rice yield and head rice yield. A survey for DNA polymorphisms with 82 RFLPs and 26 microsatellites revealed high levels of variation among the eight parents. A cluster analysis resolved these eight lines into indica (one line) and tropical japonica (seven lines) rice subgroups. A majority of the markers detected statistically significant effects on one or more traits by an analysis of variance. Marker F1 heterozygosity was highly correlated with rough rice yield (0.79**) and head rice yield (0.82**), and was also significantly correlated with heterosis of these two traits (0.47*, 0.50**, respectively). However, the correlations were largely attributed to the concurrence between high levels of heterozygosity and high performance in crosses between the indica variety Jasmine 85 and the remaining seven lines. Compared with the data published in previous studies, it was concluded that the level of correlations between marker distance and hybrid performance is dependent on the germplasm used.
Restriction fragment length polymorphisms (RFLPs) have been suggested as molecular markers to facilitate improvement of agronomic traits in maize. To evaluate the utility of RFLP data in elucidating heterotic patterns among maize lines, 8 maize inbred lines and their 28 singlecross hybrids were evaluated for grain yield at 2 Iowa locations in each of 2 years in a randomized-complete block design. The diallel mating design permitted estimation of general and specific combining ability effects. RFLP analysis of inbred lines included 5 restriction enzymes and 5 cDNA and 28 genomic clones distributed over the maize genome. RFLP patterns of crosses were predicted from analysis of the inbred parents. Genetic distances between inbred lines were estimated as modified Rogers' distance (MRD). Grain yield and specific combining ability were significantly correlated with MRD for 6 of the 10 chromosomes. Dispersion of inbred lines and hybrids for RFLP allele frequencies was generally consistent with expectations based on known pedigrees. Results from this study suggest RFLP analysis as a potential alternative to field testing when attempting to assign maize inbred lines to heterotic groups
Restriction fragment length polymorphisms (RFLPs) have been proposed for predicting the yield potential of different types of cross. Their has been evaluated in 15 flint and 12 dent inbreds from the European maize (Zea mays L.) germplasm as well as in 68 F 1 crosses (21 flint × flint, 14 dent × dent, and 33 flint × dent) produced between them. The materials were evaluated for F 1 performance and midparent heterosis of grain yield, dry matter content (DMC) and plant height in two environments in Germany. Genetic distances (GDs) between parental lines, calculated from RFLP data of 194 clone-enzyme combinations, showed greater means for flint × dent (0.67) than dent × dent (0.62) and flint × flint (0.55) crosses
al., 1990; Godshalk et al., 1990; Boppenmeier et al., 1992; Melchinger, 1993). Genetic distance has been used Estimation of genetic diversity and distance among tropical maize to predict hybrid performance and the efficiency of pre- (Zea mays L.) lines and the correlation between genetic distance (GD) and hybrid performance would determine breeding strategies, diction was greater with crosses between inbred lines classify inbred lines, define heterotic groups, and predict future hybrid from the same heterotic group than in crosses between performance. The objectives of this study were to estimate (i) heterosis inbred lines from different heterotic groups (Melch- and specific combining ability (SCA) for grain yield under stress and inger, 1999). Linkage disequilibrium between DNA non-stress environments; (ii) genetic diversity for restriction fragment markers and genes involved in the expression of target length polymorphisms (RFLPs) within a set of tropical lines; (iii) GD traits is required for GD and hybrid performance to be and classify the lines according to their GD; and (iv) correlation correlated. The effect of the population structure on between the GD and hybrid performance, heterosis, and SCA. Seven- the relationship between genetic distance and heterosis teen lowland, white tropical inbred lines were represented in a diallel was described by Charcosset and Essioux (1994). study. Inbred lines and hybrids were evaluated in 12 stress and non- Tropical maize is grown on approximately 45 million stress environments. The expression of heterosis was greater under
The Indica-Japonica differentiation of three photoperiod-sensitive and/or thermosensitive genetic male-sterile rice (PGMS or TGMS, respectively) lines and 47 male parental lines from seven ecotypes were studied for their restriction fragment length polymorphism marker data to determine which ecotype crosses with the three PGMS and/or TGMS lines could lead to higher yield potential, and to estimate the relationship between the Indica-Japonica differentiation of parents and heterosis in grain yield and its components. The results indicated that hybrids derived from ‘N422s’ and the early-middle ripening Indica varieties from southern China, and hybrids between ‘Pei'ai64s’ and three Japonica ecotypes, including North-eastern Japonica varieties, restoring lines of Japonica hybrid rice and north China Japonica varieties, showed the highest grain yields. There was less variation of yield among the F1s between ‘108s’ and the seven ecotypes than among the other F1s. Highly significant positive correlations between heterosis of the F1 yield and genetic distance of the parents were detected, although the correlation between F1 yield performance and genetic distance did not reach a significant level. Considerable variation of correlation between heterosis and genetic distance was also detected in the Indica × Indica crosses and Indica × Japonica crosses. There was much higher correlation (r = 0.63) between the F1 yield performance and the genetic distance of parents in the Indica × Indica crosses than in the others. It is proposed that a genetic distance of 0.4-0.8 between the two parents of hybrid rice might be appropriate not only for F1 performance, but also for heterosis.
Improving grain yield and quality of ‘Tongil’-type rice (indica/japonica) continues to be a major breeding objective in Korea. In this study, genetic divergence among 13‘Tongil’-type rice cultivars was evaluated and the relationship between genetic distance and hybrid performance in all possible nonreciprocal crosses between them assessed. The 78 F1 hybrids together with the 13 parents were evaluated for eight traits of agronomic importance, including yield, in a replicated field trial. The 13 parents were examined for DNA polymorphism using 71 micro-satellite or simple sequence repeats and 46 random decamer oligonucleotide primers. A total of 319 polymorphic variants were generated and, based on the polymorphism data, genetic distances (GDs) ranged from 0.021 to 0.437. Cluster analysis based on GDs revealed associations among cultivars which was in agreement with the pedigree data. Heterosis was observed in hybrids for most of the traits, and yield exhibited the highest heterosis among the eight traits examined. The correlation values of GDs with F1 performance were mostly nonsignificant, except for yield, culm length and spikelets per panicle. The correlations of GDs with midparent and better-parent heterosis were not significant enough to be of predictive value. These results indicate that GDs based on the microsatellite and random amplified polymorphic DNA (RAPD) markers may not be useful for predicting heterotic combinations in ‘Tongil’-type rice and support the idea that the level of correlation between hybrid performance and genetic divergence is dependent on the germplasm used.
The genetic diversity of 50 wild and semi-wild accessions of the Coffea arabica L. germplasm collection, gathered by the FAO and ORSTOM missions to Ethiopia, and maintained in Colombia by CENICAFE, was evaluated with RAPD markers. The evaluation was carried out in two phases: In phase one, the polymorphism of 8 Ethiopian accessions of different geographic origin, plus the cultivated variety ''Caturra'' was assessed with the RAPD technique with forty-two 10-mer oligonucleotides. In phase two, 51 accessions were assessed with a set of 5 polymorphic primers that reproduced, with a correlation of 95%, the groups generated by the 24 polymorphic primers found in phase one. Principal Coordinate Analysis of molecular data revealed that a closely related group consisting of 86% of the Ethiopian C. arabica accessions evaluated are significantly different from the Caturra variety and could be used in a genetic breeding initiative to increase the variability of cultivated varieties. The results also indicate that a larger polymorphism is present in the Colombian replica of FAO Ethiopian coffee germplasm collection than previously reported.
The availability of an array of molecular marker systems allowed comparing the efficiency of two of these marker systems to
estimate the relationships among various taxa. The objective of this study was to assess the genetic diversity among 40 cultivated
varieties and five wild relatives of rice, Oryza sativa L. involving simple sequence repeat (SSR) randomly amplified polymorphic DNA (RAPD) markers. The accessions were evaluated
for polymorphisms after amplification with 36 decamer primers and 38 SSR primer pairs. A total of 499 RAPD markers were produced
among the 40 cultivated varieties and five wild relatives with a polymorphism percentage of 90.0. Out of 38 SSR primer pairs
used, only one locus viz., RM115 was monomorphic. The average Polymorphism Information Content (PIC) value was 0.578 and it
ranged from a low of zero (RM 115) to a high of 0.890 (RM 202). The Mantel matrix correspondence test was used to compare
the similarity matrices and the correlation coefficient was 0. 582. The test indicated that clusters produced based on RAPD
and SSR markers were not conserved since matrix correlation value was 0.582 as against the minimum required value of 0.800.
The two marker systems contrasted most notably in pair-by-pair comparisons of relationships. SSR analysis resulted in a more
definitive separation of clusters of genotypes indicating a higher level of efficiency of SSR markers for the accurate determination
of relationships between accessions that are too close to be accurately differentiated by RAPD markers.
The genetic relationships among 33 coconut germplasm accessions were analyzed using RAPD markers. The germplasm accessions were collected from various coconut growing regions viz. South Asia (SA), South East Asia (SEA), South Pacific (SP), Atantic and America, and Africa. Forty-five random primers produced a total of 399 polymorphic markers. The Polymorphism Information Content (PIC) ranged from 0.031 to 0.392 and the Marker Index (MI) ranged from 6.28 to 0.031 among the primers. Based on the MI a set of 5, 10 and 15 informative and reproducible primers were identified. The mantel matrix correlation was calculated to compare the similarity matrices of a set of reproducible informative primers and global primers. There was significant correlation among the similarity matrices (r ≥ 0.50). The similarity matrix based on 399 polymorphic markers was used to construct the dendrogram to show the genetic relationship among the accessions. Similarity values ranged between 0.573 and 0.846. There was less genetic similarity (based on Jaccard's coefficient) among South Pacific and South East Asian accessions. The clustering pattern obtained in the present study was in agreement with the earlier reports based on RFLP, SSRs and AFLPs.
This study was undertaken to determine the relationship between genetic distance of the parents based on molecular markers and F1 performance in a set of diallel crosses involving eight commonly used parental lines in hybrid rice production. The F1s and their parents were measured for five traits including heading date, plant height, straw weight, grain yield and biomass. The parental lines were assayed for DNA polymorphisms using two classes of markers: 140 probes for restriction fragment length polymorphisms (RFLPs) and 12 simple sequence repeats (SSRs), resulting in a total of 105 polymorphic markers well spaced along the 12 rice chromosomes. SSRs detected more polymorphism than RFLPs among the eight lines. A cluster analysis based on marker genotypes separated these eight lines into three groups which agree essentially with the available pedigree information. Correlations were mostly low between general heterozygosity based on all the markers and F1 performance and heterosis. In contrast, very high correlations were detected between midparent heterosis and specific heterozygosity based on the markers that detected significant effects for all the five traits; these correlations may have practical utility in predicting heterosis. The analyses also suggest the existence of two likely heterotic groups in the rice germplasm represented by these eight lines.
AFLP markers were successfully employed to detect diversity and genetic differentiation among Indian and Kenyan populations
of tea (Camellia sinensis (L.) O. Kuntze). Shannon's index of diversity was used to partition the total phenotypic variation into between and within
population components. On average, most of the diversity was detected within populations, with 79% of the variation being
within and 21% being between populations of Indian and Kenyan tea. A dendrogram constructed on the basis of band sharing distinctly
separated the three populations of tea into China type (sinensis), Assam type (assamica) and Cambod type (assamica ssp. lasiocalyx) in a manner consistent with the present taxonomy of tea, the known pedigree of some of the genotypes and their geographical
origin. Principal coordinate (PCO) analysis grouped Assam genotypes both from India and Kenya supporting the suggestion that
the Kenyan clones have been derived from collections made in this region. The China types were more dispersed on the PCO plot
which is a reflection of wider genetic variation. As would be expected, clones collected from the same region exhibited less
overall genetic variation. AFLP analysis discriminated all of the tested genotypes from India and Kenya, even those which
cannot be distinguished on the basis of morphological and phenotypic traits.
Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints. The
AFLP diversity of sunflower has not been described, and much of the public germ plasm of sunflower has not yet been fingerprinted.
Our objectives were to: (1) estimate genetic similarities, polymorphism rates, and polymorphic information contents (PICs)
for AFLP markers among elite public oilseed inbred lines, and (2) assess the genetic diversity of inbred lines using genetic
similarities estimated from AFLP fingerprints. We produced fingerprints for 24 public inbred lines of sunflower (Helianthus annuus L.) using six AFLP primer combinations. These primers produced a total of 359 AFLP markers or about 60 markers per primer
combination. Genetic similarities ranged from 0.70 to 0.91, polymorphism rates ranged from 7 to 24%, and PICs ranged from
0.0 to 0.5. Genetic similarities were lower overall for maintainer (B)×restorer (R) crosses than for B×B or R×R crosses. Principal-coordinate
and cluster analyses separated lines into two groups, one for B-lines and another for R-lines. These groupings illustrate
the breeding history and basic heterotic pattern (B×R) of sunflower and the widespread practice of using B×B and R×R crosses
to develop new lines. There were, nevertheless, distinct subgroups within these groups. These subgroups may represent unique
heterotic groups and create a basis for formally describing heterotic patterns in sunflower.
Genetic diversity in five cytoplasmic male-sterile and seven restorer lines of pearl millet was determined by DNA fingerprinting
using a (GATA)4 microsatellite and randomly amplified polymorphic DNAs (RAPDs). A total of 160 polymorphic loci were generated and, based
on the polymorphism data, similarity index values ranged from 0.81 to 0.50. Cluster analysis was performed and relationships
among these lines revealed that they were not in agreement with the available pedigree data. The per se performance of parents
and hybrids was analyzed for days-to-50% flowering, plant height, productive tillers, ear length, ear width, 1000-grain weight
and grain yield per plot. Path co-efficient analysis revealed that productive tillers, ear width and days-to-50% flowering
had a relatively large positive effect. The correlation values were mostly not significant with respect to genetic distance,
except for days-to-50% flowering, ear length and ear width. Our results have indicated that genetic-distance measures based
on the (GATA)4 microsatellite and RAPDs may be useful for the grouping of parents, but not for predicting heterotic combinations, in pearl
millet.
In studies involving isozymes or restriction fragment length polymorphisms (RFLPs), correlations of parental molecular marker diversity with grain yield of maize (Zea mays L.) single-crosses have been too low to be of any predictive value. The relationship of molecular marker heterozygosity (Dij) with hybrid performance (
ij) and combining ability was examined. For a simple genetic model involving uncorrelated parental allele frequencies and complete coverage of quantitative trait loci (QTL) by molecular markers, the correlations between
ij and Dij were 0.25.
ij and Dij were partitioned into general and specific effects. The expected correlation between specific combining ability and specific molecular marker heterozygosity is high. Expected correlations between general combining ability and general molecular marker heterozygosity are either positive or negative, depending on allele frequencies in the tester lines. Computer simulation was used to investigate a more complex but more realistic genetic model involving incomplete coverage of QTL by molecular markers. All of the following conditions are necessary for effective prediction of hybrid performance based on molecular marker heterozygosity: (1) dominance effects are strong; (2) allele frequencies at individual loci in the parental inbreds are negatively correlated; (3) trait heritability is high; (4) average parental allele frequencies vary only within a narrow range; (5) at least 30–50% of the QTL are linked to molecular markers; and (6) not more than 20–30% of the molecular markers are randomly dispersed or unlinked to QTL.
A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.
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