Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat

S Srinatha Reddy; Dinesh Kumar Saini; G Mahendra Singh; Sandeep Sharma; Vinod Kumar Mishra; Arun Kumar Joshi

doi:10.3389/fpls.2023.1166439

Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat

Front Plant Sci. 2023 May 12:14:1166439. doi: 10.3389/fpls.2023.1166439. eCollection 2023.

Authors

S Srinatha Reddy¹, Dinesh Kumar Saini², G Mahendra Singh¹, Sandeep Sharma¹, Vinod Kumar Mishra¹, Arun Kumar Joshi^{3

4}

Affiliations

¹ Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India.
² Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
³ Borlaug Institute of South Asia (BISA), NASC Complex, DPS Marg, New Delhi, India.
⁴ CIMMYT, NASC Complex, DPS Marg, New Delhi, India.

Abstract

Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.

Keywords: GWAS; drought; haplotype; hydroponics; reproductive; seedling; wheat.

Grants and funding

SS is thankful to the Department of Science and Technology, Govt. of India (M14/73) and Institute of Eminence, BHU for financial assistance. VKM thanks Institute of Eminence, BHU for financial support. SR thanks DST for Junior Research Fellowship.