Bi-parental mapping and genome-wide association studies for grain quality traits in winter wheat under contrasting soil moisture conditions

Abstract

Wheat grain quality is characterized by parameters such as grain protein concentration (Gpc), grain ash concentration (Gac), kernel weight (Kw), kernel diameter (Kd), and kernel hardness (Kh). Grain protein determines dough strength and loaf volume, while kernel hardness and size impact milling efficiency. Drought stress at flowering time can cause floral organ necrosis, thus, decreasing the number of grains per spike and filled grain percentage, while drought stress during grain filling reduces kernel weight and size, but increases grain protein concentration. A previous study reported three chromosomal regions (1B, 6B, and 7B) associated with many quantitative trait loci (QTL) co-located for grain quality traits in a doubled haploid (DH) population derived from the cross CO940610/Platte. To validate those QTL, three objectives of this study were (1) QTL mapping in a CO940610/Platte recombinant inbred line (RIL) population, (2) transferring alleles of interest from CO940610 to the recurrent parent Platte by marker-assisted backcross (MABC), and (3) genome-wide association studies for grain yield (Gy), Gpc, grain protein deviation (Gpd), Gac, and test weight (Tw) in an association mapping panel. A population of 186 CO940610/Platte RIL was grown in the Akron rainfed and Greeley fully irrigated environments in 2009/10. The same set of RIL was grown in a CSU Plant Sciences greenhouse for DNA extraction, and genotypes were obtained for 18 simple sequence repeat and sequence tagged site markers in three chromosome regions of interest. JoinMap 4.0 was used to construct linkage maps from the molecular marker data. Marker-trait associations (MTA) were detected by single-factor analysis of variance (ANOVA). Linkage maps constructed in the CO940610/Platte RIL and DH populations were mostly consistent. Most of the grain quality traits investigated were associated with the three chromosome regions on 1B, 6B, and 7B in at least one environment, confirming findings in the CO940610/Platte DH population. Five selected DH lines and the recurrent parent Platte were used during MABC, resulting in 35 BC3F2 lines for field trials. These lines were classified into 8 allelic combinations at the selective marker loci Glu-B1, Xwmc182a, and Xwmc182b, representing of the regions of interest on chromosomes 1B, 6B, and 7B, respectively. Of these allelic combinations, lines having PL-PL-CO and CO-CO-PL at Glu-B1, Xwmc182a and Xwmc182b, respectively, were hypothesized to have the lowest and highest Gpc. Experiments for the 35 MABC lines were conducted in Fort Collins fully irrigated (sprinkler irrigation), Greeley irrigated (drip irrigation), and Greeley water deficit (severe stress during grain filling) environments. Marker-trait associations for Gpc detected at Xwmc182a and Xwmc182b in the BC3F2 backcross population were consistent with findings in the CO940610/Platte DH population. The MTA for Gpc and Gac at locus Xwmc182a were robust across two of three environments. In the Fort Collins fully irrigated environment, Gpc of the allelic combination CO-CO-PL was significantly higher than the combination PL-PL-CO, confirming the hypothesized results. A collection of 299 hard winter wheat cultivars and breeding lines representative of the U.S. Great Plains germplasm was evaluated for Gy, Gpc, grain protein deviation (Gpd), Gac and Tw. Experiments were designed as side-by-side moisture treatments in Greeley 2011/12 (drip irrigation, stress began pre-flowering) and Fort Collins 2012/13 (sprinkler irrigation, severe stress during grain filling). Each treatment was arranged as an augmented design with two check varieties, each check having 15 replicates. Grain protein concentration and Gpd were highly correlated (0.72 to 0.87, P<0.001) in all four environments. The panel was characterized using a high-density 90,000 gene-associated single nucleotide polymorphism (SNP) genotyping platform. After removing SNP that did not meet data quality criteria, 16,052 filtered SNP were used to perform the genome-wide association studies (GWAS) conducted in the R programming environment using the 'GAPIT' package. Principal components and a kinship matrix were incorporated to correct for population structure and relatedness among individuals. A total of 40 significant MTA (according to the significance threshold of P<1.67x10-4, suggested by Gao et al. 2008) were detected for the five evaluated traits (Gy, Gpc, Gpd, Gac, and Tw). Of these, two SNP (BS00021704_51 and Excalibur_c4518_2931) on chromosome 6A were associated with Gy. The same SNP (BS00064369_51) on 4A was associated with both Gpc and Gpd. Test weight had the most MTA (17). In particular, two SNP, BS00047114_51 and BS00065934_51, both associated with Tw on chromosome 3B, were robust across three of four environments investigated. In conclusion, two narrow regions (~2 cM each) around Xwmc182a on 6B and Xwmc182b on 7B are of potential value for breeding programs. The incorporation of favorable allele combinations into a uniform background (Platte) was successful, but further investigation is needed for the MABC lines. Grain protein deviation appears to be a useful metric for increasing both Gpc and Gy. Five SNP (BS00021704_51, Excalibur_c4518_2931, BS00064369_51, BS00047114_51, and BS00065934_5) should be investigated further to detect candidate genes in their respective chromosome regions.