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

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.

Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize

“…A few CIMMYT maize lines (CMLs) released from different CIMMYT regional centres across geographies were also the part of panel. In Asian environments, CAAM panel was earlier used in mapping for resistance to diseases like Sorghum downy mildew, Northern corn leaf blight & Charcoal rot (Rashid et al 2018 , Rashid et al 2020 and Rashid et al 2021 ) and root traits under drought conditions (Zaidi et al 2016 ). Two mapping populations were developed by crossing the resistant parents CML578 and CML329/MBRc2amF14-2-B*7 with a common elite, but susceptible parent CML474.…”

“…One of the flanking markers, PHM3466_69 at 167 Mb on chromosome 6 was found to be common between these QTLs identified in the two different mapping populations. This region could be of major significance for this trait as it is infrequent to detect stable QTL for complex traits in genetically unrelated populations (Rashid et al 2021 ). Further studies are required to dissect this important region to identify the causal variation responsible for this trait.…”

“…Similarly, Hap_8.2 and Hap_8.3 identified at 159 Mb in this study were detected within the physical coordinates of the confidence interval of a QTL (146.4-158.9 Mb) for GSR resistance reported by Ma et al 2017 on chromosomal bin 8.06. Similarly, QTLs/SNPs were identified on chromosomal bin 8.06 for resistance to another PFSR pathogen Macrophomina phaseolina , causing Charcoal rot in maize (Rashid et al 2021 ). Hence, this region on chromosome 8 could be considered as a region of interest for resistance to multiple stalk rot pathogens as it has been identified for at least three different PFSR diseases.…”

“…The first population FSR-1 developed from a cross between the resistant parent CML578, is an orange flint line derived from waterlogging stress-tolerant population in Asia. This line was also used as a resistant parent for QTL mapping for charcoal rot resistance (Rashid et al 2021 ). In the second population FSR-2, the resistant parent CML329/MBRc2amF14-2-B*7 is a flint yellow line originated from insect-resistant population from Mexico.…”

“…Identification and fine-mapping of moderate to high effect genes/QTL also increase the accuracy of selection in marker-based breeding (Nair et al 2015 ). QTLs have been mapped for resistance to PFSRs like Charcoal rot (Rashid et al 2021 ), GSR (Yang 2010 ; Zhang et al 2012 ; Ma et al 2017 ) and ASR (Jung et al 1994 ; Abad et al 2006 ; Broglie et al 2011 ). A study that mapped QTL for resistance to FSR in maize was reported by Salah et al ( 2016 ), they studied the trait at vegetative stage and not at post-flowering stage.…”