Journal of Agronomy and Field Innovations

Background: Traditional millets hold great significance in terms of nutrition and climate resilience but still have insufficient genetic variation in comparison to other major cereals and this limits their role in genomic breeding for food and nutrition security.
Objective: The aim of this research was to study the genetic diversity population structure and the loci associated with agronomic traits of traditional millet gene banks by utilizing whole-genome resequencing.
Methods: A total of 96 germplasm of traditional millets from different agricultural/ecological zones were sequenced utilizing the Illumina NovaSeq technology at an average coverage of 15. The quality of sequence reads was assessed by filtering them and aligning them to the reference sequence. The population structure was analyzed by applying a variety of techniques such as PCA and ADMIXTURE along with different genetic metrics that included nucleotide diversity, heterozygosity, linkage disequilibrium, FST.
Results: High rates of genome coverage and mapping were achieved by sequencing that produced 4.82 million reliably-detected SNPs, 812,340 InDels, and 6,124 structural variants. Three genetically distinct subpopulations, generally corresponding to geographical origins, were revealed, showing moderate differentiation across the genome (mean FST = 0.18) and substantial nucleotide diversity among landraces as compared to breeding populations. Candidate genes for traits like drought resistance, grain weight and size, lipid content, and flowering time were found in regions of high density of variants.
Conclusion: WGRS provided an efficient, fine-scale resolution of genetic diversity and population structure of traditional millet accessions, pinpointing candidate genomic segments important for breeding and offering data for the effective selection of accessions in conservation and genetic improvement programs.