Abstract
Common rust is one of the major foliar diseases in maize, leading to significant grain yield losses and poor grain quality. To dissect the genetic architecture of common rust resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid (DH) population, DH1, were used to perform GWAS and linkage mapping analyses. The GWAS results revealed six single-nucleotide polymorphisms (SNPs) significantly associated with quantitative resistance of common rust at a very stringent threshold of P-value 3.70 × 10–6 at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04. Linkage mapping identified five quantitative trait loci (QTL) at bins 1.03, 2.06, 4.08, 7.03, and 9.00. The phenotypic variation explained (PVE) value of each QTL ranged from 5.40 to 12.45%, accounting for the total PVE value of 40.67%. Joint GWAS and linkage mapping analyses identified a stable genomic region located at bin 4.08. Five significant SNPs were only identified by GWAS, and four QTL were only detected by linkage mapping. The significantly associated SNP of S10_95231291 detected in the GWAS analysis was first reported. The linkage mapping analysis detected two new QTL on chromosomes 7 and 10. The major QTL on chromosome 7 in the region between 144,567,253 and 149,717,562 bp had the largest PVE value of 12.45%. Four candidate genes of GRMZM2G328500, GRMZM2G162250, GRMZM2G114893, and GRMZM2G138949 were identified, which played important roles in the response of stress resilience and the regulation of plant growth and development. Genomic prediction (GP) accuracies observed in the GWAS panel and DH1 population were 0.61 and 0.51, respectively. This study provided new insight into the genetic architecture of quantitative resistance of common rust. In tropical maize, common rust could be improved by pyramiding the new sources of quantitative resistance through marker-assisted selection (MAS) or genomic selection (GS), rather than the implementation of MAS for the single dominant race-specific resistance gene.
Highlights
Common rust, caused by Puccinia sorghi, is one of the major foliar diseases in maize, which can cause up to 49% grain yield loss in susceptible varieties (Groth et al, 1983)
Some quantitative trait loci (QTL) were overlapped in different studies and were consistent in different genetic backgrounds. These results suggest that major QTL associated with partial resistance from various elite backgrounds are possible to be pyramided for improving common rust resistance in temperate maize germplasm, and selection for multiple partial resistance alleles seems to be more promising than the marker-assisted selection (MAS) of the Rp genes
The population structure analysis showed that the delta K value reached a peak when the K value was 4, indicating that the Drought Tolerant Maize for Africa (DTMA) panel can be divided into four subgroups (Figures 1B,C)
Summary
Common rust, caused by Puccinia sorghi, is one of the major foliar diseases in maize, which can cause up to 49% grain yield loss in susceptible varieties (Groth et al, 1983). Tropical maize germplasm is an important source of resistance for improving common rust in temperate maize, and the six inbred lines developed by CIMMYT were identified as novel donors in Argentina for incorporating resistance to the local germplasm (Rossi et al, 2020). Those studies indicated the presence of genetic resistance to common rust in tropical maize germplasm. The donor lines identified in these studies are valuable donors for improving common rust resistance through breeding, which are novel resistance sources for providing a better understanding of the genetic basis and architecture of common rust resistance
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