Marker assisted diversity analysis and creation of spring wheat genotypic panel for association mapping
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Genetic structure and allelic richness of the wheat core collection for association mapping of yield
Knowledge about genetic structure and allelic diversity of bread wheat (Triticum aestivum L.) collections is a key to developing modern wheat cultivars, able to cope with various abiotic and biotic stress factors, through purposeful selection of parents.Further, information about population structure of a material is the first prerequisite of association mapping, which prevents declaring of spurious marker-trait associations.The aim of this study was to assess genetic diversity and presence of population structure within the panel of wheat accessions chosen for association mapping of yield and yield related traits in wheat.The material consisting of 282 wheat accessions, highly variable for 10 agronomically important traits, was evaluated using microsatellite markers that were distributed all over three wheat genomes.The 397 alleles were detected at 31 SSR markers, with an average number of 12.4.The highest diversity was detected at microsatellite loci from B genome, while the lowest number of alleles was observed for D genome.Structure analysis indicated the existence of three subpopulations, where genotypes were grouped according to their origin as well as pedigree data.In each subpopulation, private alleles were detected, indicating informativeness of analysed microsatellite loci for the elucidation of population structure.Statistically significant differences among groups were observed for 8 out of 10 wheat agronomically important traits, while PCA did not show a clear separation of genotypes.The analysed wheat accessions demonstrated a sufficiently high level of genetic diversity, considering both molecular and phenotypic data, which makes them suitable for the association study of breeding traits in wheat.
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Plant Breeding
Molecular breeding
Genetic Analysis
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Genetic Resources
Molecular marker
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A major effort of a plant breeder is the constant improvement of the best available genotypes for further enhancement in their yield potential either directly or through improvement of various factors which contribute indirectly to high yield.Genetic diversity of wheat cultivars is very important in reducing genetic vulnerability during plant breeding efforts.In order to estimate the genetic diversity, molecular markers provide excellent tools.The aim of this study was to molecularly characterize the fifty wheat accessions to assess phylogenetic relationship and mutual genetic distances through the use of 10 ISSR markers and 50 accessions of wheat.The dendrogram separated genotypes into two clusters I and II comprising of 49 and 1 accessions, respectively.The allelic polymorphism information content (PIC) value ranged from 0.147 to 0.467 with an average of 0.287.The similarity co-efficient ranged from .41 to .89.Significant correlation of microsatellite genetic distance was tested by mantel test (r= 0.77557).Results shows that high level of polymorphism among the wheat accessions.Cluster analysis suggested that ISSR markers were efficient tools for estimating intra-specific genetic diversity in wheat and this molecular marker could differentiate the accessions obtained from different locations.ISSRs have been successfully used to estimate the extent of genetic diversity at inter-and intra-specific level in a wide range of crops.The genetic relationships estimated by the polymorphism of ISSR markers revealed greater level of genetic variability in wheat accessions of wide adaptability and applicability.
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Characterization of germplasm by agro-morphological, biochemical and DNA-markers provide powerful tools to precise germplasm identification, quantify the genetic diversity and to estimate the phylogenetic relationship among accessions in many crop species. The objective of the present study was to characterize a subset of 23 Moroccan relevant durum wheat (Triticum turgidum L. var. durum) accessions selected from the National Gene Bank of Morocco for their genetic diversity using agro-morphological and microsatellite markers, and to measure the genetic distance among these accessions using UPGMA cluster analysis. Durum wheat accessions were planted under field condition and their agro-morphological characters such as days to emergence, days to tillering, days to booting, days to head emergence, days to flowering, days to physiological maturity, plant height, and thousands kernel weight were recorded. The same set of accessions was also analyzed for polymorphism with 7 genomic microsatellite markers. The results indicated that the evaluated germplasm comprises of useful variation for future breeding activities. Furthermore, the cluster analysis based on microsatellite data showed the closest correlation with the groupings of particular genotypes based on agro-morphological characters. The authors results suggest that the characterization based on agro-morphological traits and genotypic markers will be a useful tool to the breeders to choose genotypes with appropriate diversity.
Key words: Durum wheat, Triticum germplasm, agro-morphological and microsatellite markers, genetic diversity.
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The genetic diversity among 10 Iranian bread wheat (Triticum aestivum) genotypes was analysed using 12 quality traits, 320 amplified fragment length polymorphisms (AFLP) polymorphic fragments, 491 simple sequence repeats (SSR) alleles and 294 proteome markers. The results revealed that the genotypes differed for quality traits, AFLP, SSR and proteome markers. The average genetic diversity based on quality traits (0.684 with a range of 0.266–0.997) was higher than AFLP (0.502 with a range of 0.328–0.717), SSR (0.503 with a range of 0.409–0.595) and proteome (0.464 with a range of 0.264–0.870) markers. Although there were apparent similarities between the groupings of particular genotypes, the overall correspondence between the distance matrices appeared to be rather low. In this study the cluster analysis based on AFLP data showed the closest agreement with the region of origin or pedigree information of each genotype. In addition to the genetic diversity assessment, specific proteins with known function were detected uniquely for the studied genotypes. Our results suggest that the classification based on quality traits and genotypic markers of these wheat genotypes will be useful for wheat breeders to plan crosses for positive traits.
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Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 ≥ 0.1 and r2 ≥ 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 ≥ 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 ≥ 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.
Germ plasm
Gossypium barbadense
Linkage Disequilibrium
Association mapping
Gossypium
Genome-wide Association Study
Genetic Association
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Germ plasm
SNP genotyping
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