Importance of mega-environments in evaluation and identification of climate resilient maize hybrids (Zea mays L.).

Multi-location experiments on maize were conducted from 2016 to 2019 at ten locations distributed across two agro-climatic zones (ACZ) i.e., ACZ-3 and ACZ-8 of Karnataka, India. Individual analysis of variance for each location-year combination showed significant differences among the hybrids; similarly, combined analysis showed a higher proportion of GE interaction variance than due to genotype. Mega-environments were identified using biplot approaches such as AMMI, GGE, and WAASB methodologies for the years 2016 to 2019. The BLUP method revealed a high correlation between grain yield and stability indices ranging from 0.67 to 1.0. Considering all three methods together, the three location pairs Arabhavi-Belavatagi, Bailhongal-Belavatagi, and Hagari-Sirguppa had three occurrences in the same mega-environment with a value of 0.67, and these location combinations consistently produced winning genotypes. Among the common winning genotypes identified, it was G7 during 2016 and 2017 and G10 during 2018 and 2019, based on WAASBY. The likelihood of Arabhavi-Nippani, Hagari-Mudhol, and Dharwad-Hagari occurring in the same mega-environment is minimal because they did not share the same winning genotype, with the exception of a small number of events. Despite being in the same agro-climatic zone, Arabhavi, Hagari, and Mudhol rarely had a winning genotype in common. An agro-climatic zone is grouped based on climatic and soil conditions which doesn't consider GE interaction of cultivars thus, releasing the cultivars for commercial cultivation considering mega environments pattern would enhance the yield for the given target region.

Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping.

Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10-06 to 4.80 × 10-05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.

Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight.

Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.