Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing

Abstract

Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping‐by‐sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet−green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515‐SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.

The place of millet in food globalization during Late Prehistory as evidenced by new bioarchaeological data from the Caucasus

“…For Setaria , we have a different pattern: the wild progenitor of foxtail millet— Setaria viridis— is widespread across Eurasia. If genetic analyses indicate a single domestication center for foxtail millet in China 76 , 77 then more research is needed to understand its early presence in the Caucasus. Currently, foxtail millet does not appear in Central Asia before 1500 BC.…”

“…Whether this was a localized and shortlived cultivation of Setaria in the Western Caucasus or if foxtail millet spread from here to nearby regions is still hypothetical. The early presence of Setaria in the Caucasus opens a new avenue which needs to be investigated with further ethnobotanical 79 , archaeobotanical and genetic studies 76 , 77 .…”

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

“…Owing to the innovative sequencing technologies, several cost-effective genotyping by sequencing and RNA-seq have been carried out in this era ( Supplementary Table 2 ). Such genotyping by sequencing 328 foxtail millet landraces and 12 green foxtail accessions presented a total of 5,677 single nucleotide polymorphisms for phylogenetic construction ( Hunt et al, 2021 ). Another deep sequencing of long non-coding RNAs (lnRNA) in foxtail millet revealed their responses toward herbicides.…”

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

“…Targeted enrichment approaches have generally not been the method of choice for population genomics studies, which usually favor techniques such as RADseq or genotyping‐by‐sequencing (e.g., Schley et al, 2020; Hunt et al, 2021). Taxon‐specific probe sets have been shown to be suitable at various taxonomic levels (e.g., Nicholls et al, 2015; Villaverde et al, 2018; Soto Gomez et al, 2019; Christe et al, 2021) and might be expected to perform somewhat better at resolving relationships at lower taxonomic levels than a universal one (but see Larridon et al, 2020; Siniscalchi et al, 2021; Ufimov et al, 2021).…”