Genome Wide Association Mapping of Foliar Blast Resistance Genes in Pearl Millet Using SNP Markers
(2021)Abstract
Background: Foliar blast (FB), aka leaf spot, caused by Magnaporthe grisea became major threat to pearl millet growing areas affecting both forage and grain production of pearl millet hybrids, and parental lines. Even though there exists a huge genetic variability in pearl millet against FB, no systematic efforts were undertaken to identify new resistance genes or map them. Identifying novel alleles and gene associated with FB resistance will help to deploy various resistance genes over large geographical area.
Methods: A panel of 250 genotypes was evaluated at five environments under natural epiphytic conditions. The disease score for each genotype at five environments was assessed following the 0-9 progressive scale and their SNP genotyping was carried out using Genotype-by-sequencing (GBS) protocol. A set of 74K SNP genotyping data of these genotypes were used for Genome-wide association study (GWAS) to identify genes/alleles for FB resistance in pearl millet.
Results: The relative magnitude of each association was represented by the R value as the portion of variation explained by the marker at the threshold -log 10 p-value $5.00. Forty six most significant marker trait associations for foliar blast resistance were identified on pseudo molecules 1, 2, 3, 5 and 7 using MLM analysis. Moreover analysis of the upstream and downstream in a window +2 kb of the SNP loci detected a total of 10 putative candidate genes at the target regions.
Conclusion: The present work reports the resistance genes and its chromosomal locations which are associated with Pearl millet- Magnaporthe interaction for first time in the world.