Abstract
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.
Highlights
Maize is cultivated on more than 180 million hectares (M ha) globally, contributing ∼50% [1,117 million metric tons (MMTs)] to the global grain production (Prasanna, 2018)
A set of 396 lines from the CIMMYT Asia association mapping (CAAM) panel that were developed and adapted in Asian environments, involving inbred lines with tolerance to abiotic stresses like drought, high temperature, and excess moisture, besides quality protein maize (QPM) lines, and inbred lines derived from downy mildew-resistant populations in Asia, was used in genome-wide association study (GWAS)
The CAAM panel consisting of 396 inbred lines was screened for charcoal rot resistance across three locations/years in India
Summary
Maize is cultivated on more than 180 million hectares (M ha) globally, contributing ∼50% [1,117 million metric tons (MMTs)] to the global grain production (Prasanna, 2018). Asian countries have shown rapid progress in maize production and productivity and are the second largest maize producers in the world with 31% share in global maize production (Zaidi et al, 2018). China produced nearly 260.95 MMT of maize by cultivating the maize area of 41.30 M ha during 2019 (FAO., 2021). The second prime maize producing country among Asian countries is India with an estimated maize area of ∼9.03 M ha in 2019 with the maize production of 27.72 M Mt at a productivity of 3.07 t/ha (FAO., 2021). Apart from feed, maize is increasingly used in industries especially in food processing industry for making additives and sweeteners (Prasanna, 2018)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
