Nutritional and genetic variations within foxtail millet (Setaria italica) landraces collected from indigenous communities across the Philippines

Unknown to many, the Philippines is host to a few remaining accessions of the underutilized and understudied cereal foxtail millet (Setaria italica (L.) P. Beauv.). We collected together accessions from different eco-geographical locations within the Philippines, along with a few accessions from Lanyu, Taiwan, to undertake a study of the nutritional value and genetic diversity within accessions of foxtail millet grown in the Philippines. All accessions were field grown in 2022, dry season (DS) at the Institute of Plant Breeding (IPB) Experiment Station, Los Banos, Laguna, Philippines. The accessions were tested for micronutrients, including Zn and Fe, nitrogen as a proxy for protein, {beta}-carotene and a number of phenolic compounds with known nutritional potential. Of the 20 accessions tested, the accessions Bayaras and GB61438 had the highest level of Zn (107.1 mg/kg) and Fe (70.52 mg/kg), respectively, higher than levels found in traditional rice varieties. For {beta}-carotene the highest concentration was found in the accession Balles ([~]10{micro}g/g). Twelve phenolic compounds were detected, with catechin, syringic acid, ferulic acid and kaempferol having the highest concentrations and greatest variation between accessions. To assess the genetic diversity of these local foxtail millet accessions, we sequenced a core set of eight accessions to a depth of at least 25-fold. Analysis of the population structure, using genome-wide, high-quality SNPs, showed modest diversity among the accession, with two unadmixed groups. The accessions are monophyletic relative to their earliest common ancestor, with the very light brown accessions emerging earlier than the light brown and reddish-brown varieties. Analysis of Zinc/Iron permease (ZIP) transporters within the foxtail millet reference sequence, var. Yugu1 identified 17 putative ZIP transporters. Variant calling identified SNPs primarily within 3 and 5 regions, and introns, indicating variation between foxtail millet accessions within regulatory gene regions rather than in structural proteins. The local foxtail millet accessions found across the Philippines, therefore, represent a potential alternative source of nutrition that would help to address the problems of the double-burden of malnutrition found in the Philippines.