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Population Sequencing Study Provides Fodder for Foxtail Millet GWAS, Haplotype Map, and More

NEW YORK (GenomeWeb News) – In a study appearing online yesterday in Nature Genetics, a Chinese team presented findings from a population genetic study of foxtail millet, Setaria italica.

The researchers did low-coverage genome sequencing on almost 1,000 varieties of foxtail millet in their quest to put together a haplotype map for the crop plant and find telltale genetic markers for its traits of interest. By combining field data from five different environments with information on SNPs found in the newly generate genome sequences, for instance, they closed in on 512 loci with apparent ties to almost four dozen such traits.

Through more in-depth genome sequencing on one foxtail millet variety and on green foxtail (S. viridis) — believed to be foxtail millet's wild progenitor — the group tallied up even more genetic variation within and between the two related species. Comparisons between the plants also pointed to selective sweeps suspected of having their roots in foxtail millet's domestication.

"Taken together, our large dataset of loci that are associated with numerous agronomic traits in multiple environments along with the identification of loci bearing signatures of recent selection provide a foundation for further genetic improvement of foxtail millet through genomic selection," the study's authors argued.

Foxtail millet has a long history as a grain crop plant, they noted, especially in parts of the world with arid environments, where the plant's drought tolerance and water use efficiency come in handy.

With its modest genome size, diploid genome content, and other favorable features, the plant has also been gaining popularity amongst those interested in studying genomic patterns within a range of related grass plants that have agricultural, economic, or other significance.

To get a first glimpse at the allele diversity that exists in S. italica, the investigators performed genome sequencing on plants from 916 foxtail millet varieties, using Illumina GAIIx and HiSeq 2000 platforms to generate 0.7-fold coverage of each variety, on average.

The team sequenced two genomes to a far greater depth, again using Illumina instruments. Sequences generated for those experiments covered the genome of the green foxtail (S. viridis) accession N10 to a depth of 45-fold, on average, and led to 39-fold average coverage of foxtail millet from a variety known as Daqingjie.

Within the large set of sequenced genomes, researchers found nearly 2.6 million SNPs. Of those, around 846,000 relatively common variants were then used to cobble together a foxtail millet haplotype map.

With data from widespread populations, the team looked not only at foxtail millet's genetic diversity in general, but also at the phylogenetic relationships and genetic differentiation present between different varieties.

The latter analysis offered a glimpse at past domestication patterns, study authors said, noting that patterns so far point to a one main domestication event followed by progressive foxtail millet introductions to other parts of the world.

The researchers also took a first crack at a genome-wide association study using the SNP data available so far and phenotypic data for foxtail millet crops grown under five environmental conditions.

By focusing on 47 traits of interest, they found hundreds of loci with apparent ties to morphological traits, crop yield, disease resistance patterns, and more. At least some of those variants fell in parts of the foxtail millet genome showing evidence of past selective sweeps, study authors noted.

"Of the 36 selective sweeps," they wrote, "16 were located around loci identified in the GWAS, including loci associated with [agronomic traits like] tiller number, total panicle number per plant, and hull color."

The current analysis is expected to pave the way for more extensive studies on foxtail millet traits, domestication, and history. Those involved in the study noted that there are ongoing efforts to sequence large sets of the wild green foxtail plant to get a better sense of the variability in foxtail millet's wild relative.