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Foxtail Millet Pangenome, Graph-Based Reference Genome

Researchers from China and the US have generated a pangenome for foxtail millet (Setaria italica), a grain crop domesticated about 11,000 years ago that is thought to have enabled the establishment of early Chinese civilization. As they report in Nature Genetics, the researchers generated the pangenome from reference-grade genomes for 35 wild, 40 landrace, and 35 modern cultivated Setaria accessions from across the world. Within the pangenome, they identified more than 73,000 gene families, nearly of quarter of which they estimated to be core genes, and found about 203,000 nonredundant structural variants, many of which were associated with transposable elements. They further developed a graph-based Setaria reference genome, which enabled them to examine 68 traits across 13 growing environments to tease out genes for millet improvement. "Understanding the genetic basis underlying the domestication and improvement of foxtail millet, along with these important agricultural characteristics, holds significant potential for its enhancement," first author Qiang He, a postdoc at the Chinese Academy of Agricultural Sciences' Institute of Crop Sciences, says in a statement. "With our graph-based genome, we can estimate grain quality-related traits and potential yield, providing avenues for foxtail millet breeding for climate change adaptation."

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