A graph-based Genome and Pan-genome Variation of the Model plant Setaria
Published:18 Jul.2023 Source:Nature Genetics
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected.
The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.
Foxtail millet (Setaria italica), one of the oldest domesticated grain crops in the world, is considered to have provided the foundation for the formation of early Chinese civilization. Recent archeological evidence suggests that this species was domesticated starting ~11,000 years ago from its progenitor, green foxtail (Setaria viridis), making it contemporaneous with barley and wheat in the early agricultural transitions of human Neolithic societies. Foxtail millet is the only present-day crop species in the genus Setaria and has excellent drought and low soil-nutrient tolerance. Since its domestication, foxtail millet has spread across Eurasia and Africa, and more recently to the Americas, and grows in temperate, tropical and arid environments.