Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers

Zhang, Liyi; Liu, Dongcheng; Guo, Xiaoli; Yang, Wenlong; Sun, Jiazhu; Wang, DaoWen; Sourdille, Pierre; Zhang, Aimin

doi:10.1186/1471-2156-12-42

Cited by 72 publications

(56 citation statements)

References 42 publications

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“…Previous results showed that LD differs between the chromosomes [10], [22], [25]. In line with the findings of Chen et al [40] and Hao et al [10], we found the highest levels of LD for markers located on the D genome (Table 5).…”

Section: Discussionsupporting

confidence: 92%

Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

et al. 2014

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Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.

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Section: Discussionsupporting

confidence: 92%

Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

et al. 2014

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“…Low genetic differentiation between landraces and modern cultivars suggests that selection during wheat breeding, when we consider the total population, has not dramatically altered allele frequency genome-wide, but may have been accomplished by selection on a relatively limited number of loci. At the same time strong geographic differentiation among wheat populations found in the current and previously published studies (25)(26)(27)(28) and the relatedness of landraces and cultivars suggest that the use of distinct founders as well as allele-frequency divergence from the ancestral population of landraces could have contributed to the development of regional breeding populations. Relatively few alleles were exclusive to to wheat cultivars.…”

Section: Discussionmentioning

confidence: 49%

“…Although multiple studies have reported the genetic basis of individual phenotypes associated with wheat improvement and adaptation (9,12,(20)(21)(22)(23)(24) or sought to characterize the structure of genetic variation in regional populations (25)(26)(27)(28), the genome-scale impact of selection for improvement on the patterns of genetic variation in wheat remains largely unknown. Here we performed single-nucleotide polymorphism (SNP) discovery in the wheat transcriptome and developed a high-throughput SNP genotyping array.…”

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confidence: 99%

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

Cavanagh

Chao

Wang

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

864

915

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Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genomewide association studies in wheat.SNP genotyping | polyploid wheat | selection scans | wheat improvement | breeding history

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“…Many studies have demonstrated the effectiveness of simple sequence repeat (SSR) markers for the characterisation of germplasm collections, because of their ease of use, high polymorphism, locus specificity, and codominance [9], [23], [30]. Diversity array technology (DArT) markers are also widely used for genome analysis; these offer deep genome coverage and high effectiveness, as many genotypes can be screened in a time-effective and cost-effective manner [9], [31]–[32]. More recently, the availability of the sequences of 2,000 wheat DArT clones (http://www.diversityarrays.com/sequences) has provided functional meaning to these markers, opening a number of applications, such as collinearity studies, fine mapping of loci of interest, and identification of candidate genes in association mapping [33].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

et al. 2013

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Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.

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Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers

Cited by 72 publications

References 42 publications

Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

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