Genome-wide SSR markers validated in 73 barnyard millet genotypes

A genome-wide study has developed and experimentally validated simple sequence repeat (SSR) markers for genetic analysis in cultivated barnyard millet, identifying four principal subpopulations among 73 Echinochloa genotypes with negligible admixture. The research, published in BMC Plant Biology, screened a 132,420,621-base-pair barnyard millet genome sequence, designed 21,655 primer pairs and selected 228 hypervariable SSR loci for further assessment. Of 100 randomly chosen markers tested experimentally, 58 amplified efficiently and 42 were polymorphic, providing a validated subset for analyzing genetic relationships in the diversity panel examined.

The study addressed the limited characterization of genomic resources for domesticated Echinochloa species and the early stage of research involving extensive diversity panels and trait mapping. Its computational screen detected 25,108 perfect SSRs and 271,509 imperfect SSRs, corresponding to a relative density of 3,249.39 base pairs per megabase. Trinucleotide repeats were the principal microsatellite category, representing 89.81% of the identified SSRs, and were predominantly associated with GC-rich motifs. Based on repeat length and motif characteristics, the researchers selected 228 hypervariable loci from the 21,655 primer pairs.

Chromosome-level analysis found that SSR loci were unevenly distributed across the barnyard millet genome and showed distinct patterns among subgenomes. The CH subgenome had the highest SSR density. This chromosomal analysis characterized the location and regional variation of the newly identified marker resource; it did not itself establish functional differences among the subgenomes. The distinction is important because the genome-wide catalogue was substantially larger than the subset subsequently evaluated in the laboratory.

For validation, the researchers randomly selected 100 of the 228 candidate markers and tested them across 73 barnyard millet genotypes. Population-structure analysis, neighbor-joining clustering and principal coordinate analysis consistently classified the genotypes into four principal subpopulations with negligible admixture. Together, the results show that the tested SSR markers resolved genetic relationships within this cultivated Echinochloa panel. The experimental validation was nevertheless focused: 100 markers were assessed in 73 genotypes, rather than the complete set of 21,655 designed primer pairs. The authors describe the work as the first comprehensive genome-wide development and validation of SSR markers in cultivated barnyard millet, combining extensive computational discovery with a focused test of amplification, polymorphism and population classification.

Subject of Research: Genome-wide SSR marker development and validation in cultivated barnyard millet

Article Title: Development and validation of genome-wide simple sequence repeat markers for large scale genotyping applications in barnyard millet (Echinochloa spp.)

Article References: Joshi, D. C., Kumar, S., Hasan, N., Rani, V., Bhinda, M. S., & Kant, L. (2026). Development and validation of genome-wide simple sequence repeat markers for large scale genotyping applications in barnyard millet (Echinochloa spp.). BMC Plant Biology. https://doi.org/10.1186/s12870-026-09913-9

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09913-9

Keywords: barnyard millet, Echinochloa, simple sequence repeats, genome-wide markers, genotyping, genetic diversity, population structure, crop genomics, Development, validation, genome-wide, simple