Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits

Authors: GILL, HARSIMARDEEP - South Dakota State University; HALDER, JYOTIRMOY - South Dakota State University; ZHANG, JINFENG - South Dakota State University; RANA, ANSHUL - South Dakota State University; KLIENJAN, JONATHAN - South Dakota State University; St Amand, Paul; Bernardo, Amy; Bai, Guihua; SEHGAL, SUNISH - South Dakota State University

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2022
Publication Date: 8/8/2022
Citation: Gill, H., Halder, J., Zhang, J., Rana, A., Klienjan, J., St Amand, P.C., Bernardo, A.E., Bai, G., Sehgal, S. 2022. Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-022-04160-6.
DOI: https://doi.org/10.1007/s00122-022-04160-6

Interpretive Summary: Wheat yields can be dissected into various yield components such spike number, spikelet number per spike, kernel number per spikelet, and individual kernel size and weight. In this study, we analyzed a population of advanced elite breeding lines and well-adapted cultivars for spike and kernel traits. We identified 12 quantitative trait loci (QTLs) associated with these traits. Seven QTLs had been previously reported and were therefore validated by this study. Four QTLs, on chromosomes 1A, 5B, and 7A, are likely new QTLs for spike length, spikelet number per spike, and kernel length. The new QTLs need to be validated by further investigations. DNA markers were identified to facilitate marker-assisted selection of these QTLs for yield components in wheat breeding.

Technical Abstract: Genetic dissection of yield component traits is essential for the continuous improvement of wheat yield to meet the projected food demand by 2050. Genome-wide association studies (GWAS) have been frequently used to identify genetic determinants for spike and kernel-related traits in wheat, though none have been employed in hard winter wheat which represents a major class in U.S. wheat acreage. Further, most of these studies relied on assembled diversity panels instead of adapted breeding lines, limiting the transferability of results to practical breeding. Here we assembled a population of advanced/elite breeding lines and well-adapted cultivars that was genotyped with genotyping-by-sequencing (GBS) and evaluated over four environments for phenotypic and genetic analysis of spike and kernel traits. We identified 17 significant and multi-environment marker-trait associations (MTAs) for various traits, representing 12 putative quantitative trait loci (QTLs), with five QTLs affecting multiple traits. Comparison with previous studies resulted in the validation of seven QTLs identified in different backgrounds, suggesting four QTLs on three chromosomes 1A, 5B, and 7A for spike length, spikelet number per spike (SNPS), and kernel length are likely novel. Further, a highly significant QTL was detected on chromosome 7AS that has not been previously associated with SNPS and putative candidate genes in this region were identified for further investigation of this region. The allelic frequencies of important MTAs were deduced in a larger panel of 1,124 accessions which revealed the importance of different QTLs in the U.S. hard winter wheat breeding programs. The results from this study could be directly used by the breeders to select the lines with favorable alleles for making crosses and the reported markers will facilitate marker-assisted selection of stable QTLs for yield components in wheat breeding.