Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.))

Abstract

Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.

SNP-based association analysis for seedling traits in durum wheat (<i>Triticum turgidum</i> L. <i>durum</i> (Desf.))

“…The experimental details and results were reported in Hu et al (2015). Means of plant height (PH, cm), grain weight per plant (GWP, g) and 1000-grain weight (KGW, g) over the four years were used for correlation analysis with the seedling traits.…”

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

“…The mean marker density of 95-96 markers per chromosome, ranging from 66 (3B) to 130 (7A) for all the 14 chromosomes, were used to calculate the extent of LD. At the chromosomal level, the LD decay distance ranged from 1.90 Mb (1A) to 96.05 Mb (2A) [33,36]. The associations were estimated under the mixed linear model (MLM) using software TASSEL 3.0 (http// www.Misogynistic.net/tassel), accounting for Q-Matrix of the population structure as a covariate and pair-wise kinship coefficients (K matrix) as random effects [33].…”

Genotyping, phenotyping and transcriptomic analysis of accessions of Vicia faba, Pisum sativum and Vigna unguiculata

“…Our findings are an agreement with the observation that multiple loci confer to one quantitative trait and that QTLs conferring multiple agronomic traits with pleiotropic effects may be organized in form of clusters around SNP marker regions (X. Hu et al, 2015). The identified associations may be valuable as molecular markers for future research programmes on the improvement of the aforementioned traits.…”