Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique

Abstract

A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0.09) and higher in 2010 (0.29). Cell wall polymers in culms were quantified by means of the monoclonal antibodies LM6, LM11, JIM13 and BS-400-3 and the carbohydrate-binding module CBM3a using the high-throughput CoMPP technique. Of these, LM6, which detects arabinan components, showed a relatively high GD in both years and a significantly negative correlation with grain yield (GYLD). Overall, heritability (H2) was calculated for GYLD, LM6 and JIM and resulted to be 0.42, 0.32 and 0.20, respectively. A total of 4,976 SNPs from the 9K iSelect array were used in the study for the analysis of population structure, linkage disequilibrium (LD) and genome-wide association study (GWAS). Marker-trait associations (MTA) were analyzed for grain yield and cell wall determination by LM6 and JIM13 as these were the traits showing significant correlations between the years. A single QTL for GYLD containing three MTAs was found on chromosome 3H located close to the Hv-eIF4E gene, which is known to regulate resistance to BaYMV. Subsequently the QTL was shown to be tightly linked to rym4, a locus for resistance to the virus. GWAs on arabinans quantified by LM6 resulted in the identification of major QTLs closely located on 3H and hypotheses regarding putative candidate genes were formulated through the study of gene expression levels based on bioinformatics tools.

Fig 1. Population structure analysis.

Scores plot of PC1 vs. PC2 from PCA on the markers analyzed. Blue and yellow colors correspond to 6-row and 2-row groups respectively as assigned based on results from STRUCTURE. Branches and closed circles in black color correspond to genotypes not uniquely assigned to a group.

Fig 2. Average intra-chromosomal LD decay.

r² values of LD are plotted as a function of the distance between pairs of markers considered. Black line: r² values of the 95^th percentile for unlinked (>50 cM) markers. Red line: second degree smoothed loess curve.

Fig 3. Manhattan plots from GWAS results.

GWA scan results for A) GYLD 2009; B) GYLD 2010; C) LM6 2009; D) LM6 2010. The blue horizontal line in each plot represents the arbitrary significant threshold at -log10 (p value) = 3.