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Genetic Mapping and Phenotypic Characterization of Wheat for Yield, Yield Components and Agronomic Traits
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Defining genetic architecture of complex traits is a fundamental step towards marker-assisted selection. The objective of this study was to use a saturated genetic map derived from 90K single nucleotide polymorphic (SNP) array to map quantitative trait loci (QTL) associated with grain yield (GY), yield components, agronomic and end-use quality traits. A population of 217 recombinant inbred lines (RIL), parents and checks were phenotyped across six dryland and two well-watered environments in the United States. In a separate study, the RIL were evaluated for resistance to wheat streak mosaic virus (WSMV) disease. The objective of this study was to map Wsm2, a gene that confers resistance to WSMV disease. GY QTL were detected on chromosome 2B, 5A, and 5B with significant QTL-by-environment interactions (QEI) observed for the QTL on 2B and 5A. Three QTL for GY were mapped on 2B with additive effect ranging from 0.23-0.38, 0.13-0.46 and 0.06- 0.19 t ha^-1, respectively. The maximum coefficient of determination (R^2) corresponding to the three QTL on 2B was 31.2%, 46.7% and 27.2%, respectively. Chromosome 5A and 5B had a single QTL each for GY with maximal additive effect of 0.25 t ha^-1 and 0.27 t ha^-1, respectively. Yield components were mapped on different chromosomes with some QTL showing QEI. Chromosome 2B was a hotspot for many QTL associated with multiple traits. Multi-trait QTL analysis revealed significant QTL-by-trait interactions (QTI) for all QTL detected. The additive effect for GY QTL detected using multi-trait model was 0.19 t ha^-1 and 0.33 t ha^-1 for the QTL detected on chromosome 5A.1 and 5B, respectively. The genetic connectivity among QTL and traits revealed that GY and biomass were enhanced by QTL detected on 2B, 5A and 5B. End-use quality analysis revealed QTL for 10 rheological parameters co-located on chromosome 1A. The co-location was supported by results from the multi-trait QTL mapping. Chromosome 1D.1 had QTL for midline right time and midline peak integral located within 12 cM whereas midline time_X value and midline time_X width were located within 13.6 cM. The QTL for kernel hardness index (HDI) were detected on chromosome 1A, 2B and 2D. The additive effect for HDI QTL was 1.8 and 2.1 for the QTL on 1A and 2D, respectively, whereas the QTL on 2B had an additive effect range of 1.5-2.5. The corresponding R^2 was 13.4%, 7.8-23.2%, and 14.9% for the QTL on 1A, 2B and 2D, respectively. Flour protein content QTL were detected on chromosome 3B and 5B with an R^2 range of 4.2-11.5% and 4.5-11.8%, respectively. NCBI search of markers linked to end-use quality revealed that the SNP M11264 was linked to gliadin/avenin-like mRNA. Genetic mapping for Wsm2 revealed that the gene is located on chromosome 3BS. Nine SNP flanking the gene were detected within 2.0 cM. The markers linked to Wsm2 will be important in development of resistant varieties and protection of yield in wheat.
SubjectQuantitative trait loci
multi-trait QTL analysis
Single nucleotide polymorphism
90K SNP array
Ocheya, Silvano Assanga (2016). Genetic Mapping and Phenotypic Characterization of Wheat for Yield, Yield Components and Agronomic Traits. Doctoral dissertation, Texas A & M University. Available electronically from