Abstract
Heat stress among the abiotic stresses is one of the major problems hindering crop production
worldwide due to rapid changing in environmental components. The negative impact of heat
stress on different crops, especially on tropical maize are well studied; however specific stress
adaptive traits along with their interaction to grain yield and genetic basis underlying heat
tolerance, still poorly understood. This study is an attempt to identify key stress adaptive
secondary traits and understanding the molecular mechanism of heat stress tolerance in tropical
maize using genome wide association study (GWAS) and quantitative trait loci (QTL) mapping
with a large diverse maize germplasm. To assess the impact of heat stress and to identify key
stress-adaptive secondary traits and their relation with grain yield we evaluated a sub-set of
germplasm in two field trials during 2014 and 2015 under natural heat stress condition. In
addition, to dissect the genetic basis of heat tolerance, four sets of test cross hybrids (TC's) from
an association mapping panel termed heat tolerance association mapping (HTAM) and a
double haploid (DH) lines were evaluated in several trials across environment under optimal
and heat stress conditions. The HTAM panels and DH population were genotyped and
generated955,690 SNPs through GBS v2.7 using Illumina Hi-seq 2000/2500 at Institute for
Genomic Diversity, Cornell University, Ithaca, NY, USA. Results indicated that an anthesissilking interval (ASI) of 2 - 4 days and pollen shedding duration (PSD) more than two days
showed advantageous to grain yield under heat stress. Stigma receptivity was less affected
under heat stress compared to pollen viability; stigma initiation delayed under heat stress and
resulted in prolongs ASI. Grain yield (GY) under stress was negatively associated with leaf
firing (LF), tassel blast (TB), tassel sterility (TS), ASI and senescence; while positively associated
with chlorophyll content (CHL). Overall effect of heat stress expressed in terms of SSP_OP (seed
setting percentage under open pollination), which explained yield variation of 78.5 and 57.8%
for experiment 1 and 2, respectively. Thus, traits that are indicative to reproductive success
under heat stress (ASI, TB, TS, pollen viability, stigma receptivity and SSP_OP) and other
morpho-physiological traits (LF, SEN and CHL) may be used along with grain yield in selection
of suitable germplasm for heat stress tolerance. Phenotypic evaluation of HTAM panels and DH
population showed moderate to high heritability and significant variation for different traits.
We detected 1,569 significant SNPs associated with three important traits viz., GY, AD and ASI
from a number of GWAS analysis using ~250 - 300K filtered SNPs. QTL mapping with 1,790
high quality polymorphic SNPs were identified 136 traits associated with QTLs of the same
traits. A total of 29 SNPs were associated with multiple traits identified from GWAS using DH
populations. Total 54 GWAS identified SNPs overlapped within the flanking region of detected
QTL. Many of the detected genomic regions from both GWAS and QTL were located within or
nearest to the reported QTL intervals/genes in previous studies. Identified SNPs and QTLs were
mined for candidate genes followed by annotation of biological and molecular functions and/or
pathways. By studying with three most important traits GY, AD and ASI showed that genetic
control of complex polygenic trait heat stress tolerance involved a number of biological and
molecular components. The genomic regions in this study could be used in maize breeding
program for yield improvement and heat tolerance. These findings could be further validated
through functional analysis and re-sequencing/cloning of high-value candidate genes in maize
for adapting in high temperature regions.