Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat

Abstract

Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome-wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA-ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty-five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping-by-sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker-trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding.

Genetic characterization of flour quality and bread‐making traits in a spring wheat nested association mapping population

“…We did not find any SNP marker close to the Glu‐B1 locus, unlike Sallam et al. (2020) who detected a QTL ( S1B_6474022 ) associated with grain protein content on chromosome 1B in the overall SWMIP. As all four parents have functional Glu‐A1 alleles (Table 2), no segregation at that locus was expected, which was later confirmed during mapping as regions in proximity to Glu‐A1 were not detected by either of our GWAS models.…”

“…The SNP marker S4B_38624956 , significantly associated with grain protein content in our study, was observed to be associated with plant height, test weight, and grain protein content in the overall SWMIP population by Sallam et al. (2020), who also established that this SNP represents the dwarfing allele Rht‐B1 . All three core parents have the wild‐type allele Rht‐B1a , whereas RB07 has the dwarfing allele Rht‐B1b .…”

“…Core parents P03 and P08 had higher protein content, whereas P04 and RB07 had lower grain protein content. Although we do not have enough evidence to discuss the effect of Rht‐B1b on grain protein content, P03 and P08 are similar in height (84 cm), whereas P04 is tall (92 cm) and RB07 is short (75 cm) compared with other SWMIP parents (Sallam et al., 2020). No other markers for grain protein content were in common between our study and the SWMIP.…”

“…Out of 257 lines, 230 were used in QTL mapping after discarding lines with insufficient phenotypic and genotypic data. This population is a subset of the larger SWMIP (Sallam et al., 2020). The SWMIP was created by crossing 25 parents that represent the USDA‐ARS spring wheat core collection with RB07, a University of Minnesota‐developed hard red spring wheat variety (Anderson et al., 2009).…”

“…The steps taken to genotype the SWMIP population as well as to create a consensus linkage map have been described in detail by Sallam et al. (2020). Here, we give a brief description of the process.…”