Association Mapping for 24 Traits Related to Protein Content, Gluten Strength, Color, Cooking, and Milling Quality Using Balanced and Unbalanced Data in Durum Wheat [ Triticum turgidum L. var. durum (Desf).]

Abstract

Durum wheat [Triticum durum (Desf).] is mostly used to produce pasta, couscous, and bulgur. The quality of the grain and end-use products determine its market value. However, quality tests are highly resource intensive and almost impossible to conduct in the early generations in the breeding program. Modern genomics-based tools provide an excellent opportunity to genetically dissect complex quality traits to expedite cultivar development using molecular breeding approaches. This study used a panel of 243 cultivars and advanced breeding lines developed during the last 20 years to identify SNPs associated with 24 traits related to nutritional value and quality. Genome-wide association study (GWAS) identified a total of 179 marker-trait associations (MTAs), located in 95 genomic regions belonging to all 14 durum wheat chromosomes. Major and stable QTLs were identified for gluten strength on chromosomes 1A and 1B, and for PPO activity on chromosomes 1A, 2B, 3A, and 3B. As a large amount of unbalance phenotypic data are generated every year on advanced lines in all the breeding programs, the applicability of such a dataset for identification of MTAs remains unclear. We observed that ∼84% of the MTAs identified using a historic unbalanced dataset (belonging to a total of 80 environments collected over a period of 16 years) were also identified in a balanced dataset. This suggests the suitability of historic unbalanced phenotypic data to identify beneficial MTAs to facilitate local-knowledge-based breeding. In addition to providing extensive knowledge about the genetics of quality traits, association mapping identified several candidate markers to assist durum wheat quality improvement through molecular breeding. The molecular markers associated with important traits could be extremely useful in the development of improved quality durum wheat cultivars using marker-assisted selection (MAS).

Keywords: Infinium iSelect 90k; durum wheat; genome wide association mapping; gluten strength; grain and pasta color; pasta; protein content; unbalanced data.

Figure 1

Correlation between traits and locations based on adjusted means. Data showing the relationship between quality traits in (A) Prosper, (B) Langdon, and (C) unbalanced combined data. WPROT, whole-wheat protein; SPROT, semolina protein; SDS, sedimentation test; GI, gluten index; WG, wet gluten; GLUT, glutork; VIT, vitreousness; CLOSS, cooking loss; FIRM, firmness; CWT, cooked weight; PPO, polyphenol oxidase; TYP, total yellow pigment; Color_L, semolina color (Hunter lab value); Color_a, semolina color (Hunter lab value a); Color_b, semolina color (Hunter lab value b); Dif_L, difference in semolina dough sheet color L after 24 h; dif_a, difference in semolina dough sheet color a after 24 h; dif_b, difference in in semolina dough sheet color b after 24 h; Color, spaghetti color; TEXT, total extraction; SEXT, semolina extraction; SASH, semolina ash; MIXO, mixogram score. Cells with correlation values not significant at P value < 0.01 have a white background. ## GLUT, WTS, Color_L, Color_a, color_b, Dif_L, Dif_a, Dif_b, PPO, and TYP were only measured in balanced dataset, while TEXT, SEXT, SASH, MIXO, and Color were only measured in historic unbalanced dataset.

Figure 2

Scatter plot showing the linkage disequilibrium (LD) decay across the chromosomes (Chr) for 243 durum wheat genotypes. The genetic distance in centimorgan (cM) is plotted against the LD estimate (R ²) for pairs of SNPs. Smoothing spline fit, lambda = 338,064.8, R ² = 0.56902, and sum of squares error = 6,804.7.

Figure 3

Principal component (PC) analysis obtained from 4,196 polymorphic SNPs, indicating the population structure in 243 durum wheat accessions. PC1, PC2, and PC3 explain 6.8%, 4.5%, and 4.1% of the variation, respectively. The colors represent three different clusters.

Figure 4

Heat map displaying the relationship matrix among durum wheat genotypes. The red diagonal represents a perfect relationship of each accession with itself. The symmetric off-diagonal elements represent the relationship measures (identity-by-state) for pairs of genotypes. The blocks of warmer colors on the diagonal show clusters of closely related genotypes.