Abstract
Genetic dissection of yield component traits including spike and kernel characteristics is essential for the continuous improvement in wheat yield. 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 (HWW) which represents a major class in US wheat acreage. Further, most of these studies relied on assembled diversity panels instead of adapted breeding lines, limiting the transferability of results to practical wheat breeding. Here we assembled a population of advanced/elite breeding lines and well-adapted cultivars and evaluated over four environments for phenotypic analysis of spike and kernel traits. GWAS identified 17 significant multi-environment marker–trait associations (MTAs) for various traits, representing 12 putative quantitative trait loci (QTLs), with five QTLs affecting multiple traits. Four of these QTLs mapped on three chromosomes 1A, 5B, and 7A for spike length, number of spikelets per spike (NSPS), and kernel length are likely novel. Further, a highly significant QTL was detected on chromosome 7AS that has not been previously associated with NSPS and putative candidate genes were identified in this region. The allelic frequencies of important quantitative trait nucleotides (QTNs) were deduced in a larger set of 1,124 accessions which revealed the importance of identified MTAs in the US HWW 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 reported markers will facilitate marker-assisted selection of stable QTLs for yield components in wheat breeding.
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Data availability
The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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Publicly available statistical tools were used in this study.
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Acknowledgements
The authors would like to thank the South Dakota Agriculture Experimental Station (Brookings, SD, USA) for providing the resources to conduct the experiments. The authors are also thankful to Cody Hall and Navreet Brar for their efforts in planting and harvesting of the trials. The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture. The USDA is an equal opportunity provider and employer.
Funding
This project was collectively funded by the USDA hatch projects SD00H695-20, and the USDA Agriculture and Food Research Initiative Competitive Grants 2022–68013-36439 (Wheat-CAP) from the USDA National Institute of Food and Agriculture and South Dakota Wheat Commission grant 3X1340. The funders had no role in the study design, data collection, analysis, decision to publish, or manuscript preparation.
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Gill, H.S., Halder, J., Zhang, J. et al. Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. Theor Appl Genet 135, 2953–2967 (2022). https://doi.org/10.1007/s00122-022-04160-6
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DOI: https://doi.org/10.1007/s00122-022-04160-6