Exploring the Genetic Diversity of the Waxy Gene in Selected Foxtail Millet (Setaria italica (L.) P. Beauv.) Accessions from Sri Lanka

Purpose: Foxtail millet is an ancient cereal crop and a model species used for studying C4 photosynthesis and stress resilience. The composition of its seed starch is primarily determined by the waxy gene, which encodes granule-bound starch synthase1 (GBSS1). Polymorphisms in the first intron of GBSS1 are known to influence allelic diversification in cereals; However, Sri Lankan foxtail millet germplasm has not yet been characterized at the molecular level. This study aimed to evaluate endosperm type and apparent amylose content (AAC) of Sri Lankan accessions, analyze the first intron polymorphism of the GBSS1 gene, and assess their phylogenetic relationships with reported haplotypes.
Research Method: Six accessions collected from diverse agro-ecological regions were evaluated using I₂–KI staining, AAC and sequencing the first intron of GBSS1 gene.
Findings and Values: All accessions displayed a dark blue color in I2–KI staining and 17.7–31.5%, AAC values conformed non-waxy phenotypes. Sequence comparison with the reference non-waxy genotype (AB089142.1) revealed 152 polymorphic sites (SNPs and indels). Moreover, a novel 4bp deletion was identified across all local accessions, representing the first report of this mutation in foxtail millet. Phylogenetic analysis confirmed that all accessions belong to the Type 1-1 non-waxy haplotype but exhibit considerable intra-type diversity. These findings provide new insights into the regional diversification of GBSS1 alleles in Sri Lankan foxtail millet and highlight the potential of this germplasm as a resource for molecular marker development and breeding programs aiming at improving grain quality.