Genome-wide association mapping of bread wheat genotypes using yield and grain morphology-related traits under different environments

Hafiz Ghulam Muhu-Din Ahmed; Yawen Zeng; Muhammad Ahsan Khan; Muhammad Abdul Rehman Rashid; Muhammad Ameen; Ahmed Akrem; Amjad Saeed

doi:10.3389/fgene.2022.1008024

Genome-wide association mapping of bread wheat genotypes using yield and grain morphology-related traits under different environments

Front Genet. 2023 Jan 17:13:1008024. doi: 10.3389/fgene.2022.1008024. eCollection 2022.

Authors

Hafiz Ghulam Muhu-Din Ahmed¹, Yawen Zeng², Muhammad Ahsan Khan³, Muhammad Abdul Rehman Rashid^{4

5}, Muhammad Ameen⁶, Ahmed Akrem⁷, Amjad Saeed⁸

Affiliations

¹ Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
² Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.
³ Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
⁴ Department of Agricultural Sciences, Government College University Faisalabad, Faisalabad, Pakistan.
⁵ Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
⁶ Department of Soil Science, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
⁷ Institute of Botany, Bahauddin Zakariya University, Multan, Pakistan.
⁸ Institute of Forest Sciences Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.

Abstract

Depleting water resources and increasing global temperature due to climate change are major challenges to agriculture and food security worldwide. Deciphering the underlying mechanisms of traits contributing to grain development and yield is essential for the development of climate-resilient cultivars. Therefore, this study assessed 105 bread wheat genotypes grown under control, drought, and heat-stress conditions for two crop seasons and performed a genome-wide association study (GWAS) using a 90k SNP array. The genotypes showed significant trait differences under all environmental conditions. Highly significant variation was observed, with moderate (50.09%) to high (76.19%) heritability in the studied germplasms. The studied traits were all also significantly positively correlated. A total of 541 significant associations (p ≤ 10^-3) between marker and trait (MTAs) were observed after crossing the FDR <0.05 threshold for all traits. Among these, 195, 179, and 167 significant MTAs were detected under control, drought, and heat-stress conditions, respectively. Under the control and drought conditions, pleiotropic loci BS00010616_51 and BS00010868_51 were observed on chromosomes 7B and 1B situated at 186.24 cM and 35.47 cM, respectively. Pleiotropic loci BS00010868_51, Kukri_c11154_1723, and Ex_c10068_1509 were identified on chromosomes 1B, 5B, and 2A, respectively, under control and heat stress conditions. A stable and consistent locus (Excalibur_c20796_395) on chromosome 7A, located at 372.34 cM, was also linked to grain morphology and yield-related attributes in control, drought, and heat-stress conditions. The results of the current study confirmed several previously reported MTAs for the traits under consideration and identified new MTAs under harsh climatic conditions. These SNPs will aid in the discovery of novel genes in wheat. SNPs showing significant associations may be used in marker-assisted selection and allow the development of drought- and heat-tolerant genotypes with high yields to address global food security concerns.

Keywords: breeding; chromosome; drought; genome; genotypes; heat; wheat; yield.