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

Abstract

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.

Mining Centuries Old In situ Conserved Turkish Wheat Landraces for Grain Yield and Stripe Rust Resistance Genes

“…The whole genome LD decay rate in the current study (~10 cM; Figure 3) is faster than previously published values in CIMMYT's Elite Spring Wheat materials (~30 cM; Crossa et al, 2007; Dreisigacker et al, 2012) and/or Chinese or European elite germplasm (~20–23 cM; Zhang et al, 2013; Nielsen et al, 2014). However, compared to other wheat global landrace collections (~4–5 cM; Neumann et al, 2011; Adhikari et al, 2012), LD decay rate of the present collection was slower.…”

A unified framework for hybrid breeding and the establishment of heterotic groups in wheat

“…1, S1). This finding is substantiated by the rather low genotypic variance jointly explained by the first two principal coordinates which is in agreement with other studies (Miedaner et al 2011;Würschum et al 2013;Nielsen et al 2014;Albrecht et al 2015) and can be explained by the history of wheat line breeding in Europe resulting in a widespread exchange of germplasm between breeding companies within and across countries. 1, S1).…”

“…Varieties released in Eastern and South Eastern Europe, in China, and in the United States were moderately separated from lines released in Western and Central Europe which corroborates previous findings (Cavanagh et al 2013). Second, several studies agree (Roussel et al 2005;Balfourier et al 2007;Horvath et al 2009;Nielsen et al 2014;Wingen et al 2014) that the European wheat germplasm can be roughly separated into a Western and Eastern background which might be explained by: (i) general adaptation to different environmental conditions; (ii) oldest migration pathways of the initial wheat germplasm as mountain ranges acted as barriers for gene flow; Second, several studies agree (Roussel et al 2005;Balfourier et al 2007;Horvath et al 2009;Nielsen et al 2014;Wingen et al 2014) that the European wheat germplasm can be roughly separated into a Western and Eastern background which might be explained by: (i) general adaptation to different environmental conditions; (ii) oldest migration pathways of the initial wheat germplasm as mountain ranges acted as barriers for gene flow;…”

“…While there is a large body of published genetic diversity studies in hexaploid winter wheat (Roussel et al 2005;Balfourier et al 2007;Chao et al 2010;Hao et al 2010;Chen et al 2012;Cavanagh et al 2013;El-Basyoni et al 2013;Nielsen et al 2014;Bonman et al 2015), most of these studies discussed genetic diversity in the context of wheat line breeding improvement or tackled questions of wheat domestication but little attention has yet been paid to the analysis of genetic diversity in winter wheat in the context of hybrid breeding. The objective of this study was therefore to propose a unified framework for the establishment of hybrid breeding and heterotic groups in autogamous crops and to assess genetic diversity in a global winter wheat collection as well as two phenotypic traits of relevance for hybrid seed production to exemplarily demonstrate the utility of the approach for hybrid wheat breeding in Germany.…”

Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

“…Molecular markers previously used for characterization of genetic diversity in watermelon genotypes include random amplified polymorphic DNA (RAPD; Mujaju et al, 2010), amplified fragment length polymorphism (AFLP; Che et al, 2003), simple sequence repeat (SSR; Kwon et al, 2010) and expressed sequence tags-SSRs (EST-SSR; Mujaju et al, 2013). The method has been widely applied to various crop species, such as rice (Singh et al, 2013), maize (Van Inghelandt et al, 2010), wheat (Nielsen et al, 2014) and melon (Esteras et al, 2013), for genetic variability analysis. In contrast, single nucleotide polymorphism (SNP) markers offer substantial advantages over PCR-based methods such as large-scale genotyping, generation of highabundance sequence information and whole-genome coverage to allow genetic studies (Gupta et al, 2008;Singh et al, 2013).…”