Genome wide association mapping for heat tolerance in sub-tropical maize

Abstract

Background Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program. Results An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. Conclusions The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.

Genomic regions associated with heat stress tolerance in tropical maize (Zea mays L.)

“…The study also identified significant hot-spots for grain yield exclusively under heat stress on chromosome 8 (bin 8.05 and 10.03) and on chromosome 4 for combined heat and drought stress (bin 4.02–4.03 and bin4.04). 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.…”

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm

“…Although maize is well adapted and substantially produced and utilized in the savannas of SSA, the simultaneous incidence of abiotic stresses such as drought and high temperature during the maize flowering period could reduce the photosynthetic rate, accelerate leaf senescence, induce kernel abortion, and ultimately result in drastic yield losses [ 9 , 10 ]. The combination of the two stresses could lead to a grain yield loss of more than 90% during the flowering and grain filling period in maize [ 4 , 11 , 12 , 13 , 14 ]. Thus, the available evidence from climate projections indicates decreasing precipitation, increasing temperatures, and high intensity and frequency of heat and drought stresses [ 15 , 16 , 17 ].…”

“…Heat stress is reported to prolong the anthesis–silking interval, reduce kernel set [ 9 , 10 , 19 , 20 ], decrease photosynthetic rate and chlorophyll content [ 14 , 19 , 21 ], and lead to damaged cellular membrane [ 22 ]. Conversely, drought and or terminal drought at seedling stage has deleterious impacts on seedling establishment, vegetative growth, photosynthesis, root growth, anthesis, anthesis–silking interval, pollination, and grain formation in maize [ 23 , 24 ].…”

“…Several QTLs have been identified via GWAS in maize including QTLs associated with drought or heat tolerance [ 12 , 13 , 14 , 43 , 44 , 45 , 46 , 47 ]. However, reports of QTLs linked to both heat tolerance and combined heat and drought tolerance are limited [ 11 ].…”

“…However, reports of QTLs linked to both heat tolerance and combined heat and drought tolerance are limited [ 11 ]. Longmei et al [ 14 ] detected a total of 30 SNPs strongly associated with grain yield (GY), anthesis–silking interval (ASI), and days to 50% anthesis (AD) under heat stress conditions. Yuan et al [ 11 ] detected 549 SNPs that were significantly associated with 12 traits under one or combined environments (well-watered, drought and heat stress conditions).…”