Abstract
With progressive climate change and the associated increase in mean temperature, heat stress tolerance has emerged as one of the key traits in the product profile of the maize breeding pipeline for lowland tropics. The present study aims to identify the genomic regions associated with heat stress tolerance in tropical maize. An association mapping panel, called the heat tolerant association mapping (HTAM) panel, was constituted by involving a total of 543 tropical maize inbred lines from diverse genetic backgrounds, test-crossed and phenotyped across nine locations in South Asia under natural heat stress. The panel was genotyped using a genotyping-by-sequencing (GBS) platform. Considering the large variations in vapor pressure deficit (VPD) at high temperature (Tmax) across different phenotyping locations, genome-wide association study (GWAS) was conducted separately for each location. The individual location GWAS identified a total of 269 novel significant single nucleotide polymorphisms (SNPs) for grain yield under heat stress at a p value of < 10–5. A total of 175 SNPs were found in 140 unique gene models implicated in various biological pathway responses to different abiotic stresses. Haplotype trend regression (HTR) analysis of the significant SNPs identified 26 haplotype blocks and 96 single SNP variants significant across one to five locations. The genomic regions identified based on GWAS and HTR analysis considering genomic region x environment interactions are useful for breeding efforts aimed at developing heat stress resilient maize cultivars for current and future climatic conditions through marker-assisted introgression into elite genetic backgrounds and/or genome-wide selection.
Highlights
With progressive climate change and the associated increase in mean temperature, heat stress tolerance has emerged as one of the key traits in the product profile of the maize breeding pipeline for lowland tropics
The present study aims to identify superior alleles associated with heat stress tolerance using genome-wide association studies (GWAS) and haplotype trend regression (HTR) analysis, in tropical working germplasm maintained in the breeding program
Maximum grain yield ranged from 3.22 t ha−1 (NG) to 8.06 t h a−1 (JA-2), whereas minimum grain yield ranged from 1.15 t ha−1 (BJ) to 5.42 t h a−1 (JA-2) (Table 1)
Summary
With progressive climate change and the associated increase in mean temperature, heat stress tolerance has emerged as one of the key traits in the product profile of the maize breeding pipeline for lowland tropics. Varying degree of VPD results in strong genotype × environment interaction effects and maize crops exposed to heat stress at different locations may respond differently, depending on the level of VPD at T max[13] These studies highlight the need to incorporate heat stress resilience into maize cultivars grown in lowland tropics. Another mapping study for heat stress tolerance in sub-tropical maize[18] identified 12 significant SNP associations for grain yield under heat stress on a panel of 662 DH lines with tropical origin These SNPS were localized on chromosomes 1, 3, 6, 7 and 10 accounting for about 18% of the phenotypic variation. The present study aims to identify superior alleles associated with heat stress tolerance using genome-wide association studies (GWAS) and haplotype trend regression (HTR) analysis, in tropical working germplasm maintained in the breeding program
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