Deciphering the genomic regions governing major agronomic traits and blast resistance using genome wide association mapping in finger millet

Abstract

Finger millet (Eleusine coracana L.) is climate resilient minor millet of Asia and Africa with wide adaptation and unparallel nutritional profile. To date, genomic resources available in finger millet are scanty and genetic control of agronomic traits remains elusive. Here, a collection of eco-geographically diverse 186 genotypes was quantified for variation in 13 agronomic traits and reaction to blast to identify marker-trait associations (MTAs) using genotyping-by-sequencing (GBS) and genome-wide association study (GWAS). GBS generated 2977 high quality single nucleotide polymorphism (SNPs) markers and identified three subpopulations with varying admixture levels. General linear and mixed model approaches of GWAS to correct for population structure and genetic relatedness identified 132 common MTAs for agronomic traits across the years. The phenotypic variance explained by the makers varied from 4.8% (TP692389-flag leaf width) to 20% (TP714446-green fodder weight). Of these, 26 MTAs showed homology with candidate genes having role in plant growth, development and photosynthesis in the genomes of foxtail millet, rice, maize, wheat and barley. We also found 4 common MTAs for neck blast resistance, which explained 5.9-15.1% phenotypic variance. Three MTAs for neck blast resistance showed orthologues in related genera having putative functions in pathogen defense in plants. The results of this work lay a foundation for understanding the genetic architecture of agronomic traits and blast resistance in finger millet and provide a framework for genomics assisted breeding.

Keywords: Blast resistance; Finger millet; Genome wide association study; Single nucleotide polymorphism.