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. 2023 Dec 1;9(12):e22964.
doi: 10.1016/j.heliyon.2023.e22964. eCollection 2023 Dec.

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

Nelzo C Ereful  1 , Jose Arnel O Reyes  1 , Don Emanuel M Cardona  2 , Roneil Christian S Alonday  1 , Nel Oliver B Mateo  1 , Huw Jones  3 , Lesley Boyd  3 , Evelyn F Delfin  1
Affiliations

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

Nelzo C Ereful et al. Heliyon. .

Abstract

Unknown to many, the Philippines is host to a few remaining accessions of the underutilised and understudied cereal foxtail millet (Setaria italica (L.) P. Beauv.). We collected together accessions of this crop from different eco-geographical locations within the Philippines, along with a few accessions from Lanyu, Taiwan, to undertake a study of their nutritional value and genetic diversity. All accessions were field-grown in 2022, dry season (DS) at the Institute of Plant Breeding (IPB) Experiment Station, Los Baños, Laguna, Philippines. The accessions were tested for micronutrients, including Zn and Fe, nitrogen as a proxy for protein, β-carotene, phytic acid, 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 β-carotene the highest concentration was found in the accession Balles (∼10 μg/g). Twelve phenolic compounds were detected, with catechin, syringic acid, ferulic acid and kaempferol having the highest concentrations. To assess the genetic diversity, we sequenced a set of eight samples selected from among the accessions to a depth of at least 25-fold using whole-genome re-sequencing. Analysis of the population structure, using genome-wide, high-quality SNPs, showed modest diversity among the accessions, 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-regulated, iron-regulated transporter-like protein (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, therefore, represent a potential alternative source of nutrients which may help in addressing malnutrition in the Philippines.

Keywords: Foxtail millet; Iron; Nutrient composition; Whole genome re-sequencing; Zinc; β-carotene.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Eco-geographical locations of the foxtail millet accessions collected in this study: (i) Batanes (circled blue), located at the northernmost tip of the Philippines; (ii) Cagayan (filled blue); (iii) Bukidnon, highlighted in red, and (iv) Orchid Is. (circled purple). Also shown is Laguna (green), the site of greenhouse and field experimentation trials. Accessions from Orchid Is. were shipped from USDA and were originally collected by the Germplasm Resource Information Network (GRIN). Map taken from https://simplemaps.com. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2
Fig. 2
Philippine and Taiwanese foxtail millet accessions planted at the field experimentation site of the Institute of Plant Breeding (IPB) during the 2022 DS.
Fig. 3
Fig. 3
Variation in Nitrogen content in 20 foxtail millet accessions.
Fig. 4
Fig. 4
Variation in Zn (mg/kg) content in 20 foxtail millet accessions.
Fig. 5
Fig. 5
Variation in Fe (mg/kg) content in 20 foxtail millet accessions.
Fig. 6
Fig. 6
β-carotene concentrations of 20 foxtail millet accessions (in μg/g).
Fig. 7
Fig. 7
Variation in Phytic acid levels of 20 foxtail millet accessions (in mg/g).
Fig. 8
Fig. 8
Pearson correlations among the micronutrients. Colour intensity indicate degree of correlations based on the colour scale bar (right); numbers indicate P-values. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 9
Fig. 9
Variations in the content of 12 phenolic compounds detected across all foxtail millet accessions.
Fig. 10
Fig. 10
(A) Biochemical pathway relationship between phenolic compounds assessed in this study [adapted from [[47], [48]]]. Dashed lines indicate multi-step reactions. (B) Correlations between the levels of phenolic compounds detected in this study. Legend, similar to Fig. 8.
Fig. 11
Fig. 11
(A) Structure analysis assuming K = 2; (B) PCA; (C) Phylogenetic tree implementing Neighbor–Joining algorithm in VCF kit.
Fig. 12
Fig. 12
Phylogenetic tree of ZIP transporter of foxtail millet (Setaria italica; prefixed with SETIT), rice (Oryza sativa; prefixed with Os), and Arabidopsis thaliana; prefixed with AT). Figure generated using VCF-kit in R. Blue arrows indicate location of foxtail ZIP protein paralogs. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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