Skip to main content
ARS Home » Pacific West Area » Wapato, Washington » Temperate Tree Fruit and Vegetable Research » Research » Publications at this Location » Publication #367076
Research Project: Developing New Potatoes with Improved Quality, Disease Resistance, and Nutritional Content

Location: Temperate Tree Fruit and Vegetable Research

Title: The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene.

Author
item HUANG, PU - Danforth Plant Science Center
item JENKINS, JERRY - Department Of Energy Joint Genome
item GRIMWOOD, JANE - Department Of Energy Joint Genome
item BARRY, KERRIE - Department Of Energy Joint Genome
item HEALEY, ADAM - Hudsonalpha Institute For Biotechnology
item MAMIDI, SUJAN - Hudsonalpha Institute For Biotechnology
item AVINASH, SREEDASYAM - Department Of Energy Joint Genome
item SHU, SHENGIANG - Department Of Energy Joint Genome
item Feldman, Max
item WU, JINXIA - Danforth Plant Science Center
item YU, YUNGGING - Danforth Plant Science Center
item CHEN, CINDY - Department Of Energy Joint Genome
item JOHNSON, JENIFER - Department Of Energy Joint Genome
item ROKHSAR, DANIEL - Department Of Energy Joint Genome
item BAXTER, IVAN - Danforth Plant Science Center
item SCHMUTZ, JEREMY - Department Of Energy Joint Genome
item BRUTNELL, THOMAS - Danforth Plant Science Center
item KELLOGG, ELIZABETH - Danforth Plant Science Center

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2020
Publication Date: 10/5/2020
Citation: Huang, P., Jenkins, J., Grimwood, J., Barry, K., Healey, A., Mamidi, S., Avinash, S., Shu, S., Feldman, M.J., Wu, J., Yu, Y., Chen, C., Johnson, J., Rokhsar, D., Baxter, I., Schmutz, J., Brutnell, T., Kellogg, E. 2020. The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene.. Nature Biotechnology. 38:1203-1210. https://doi.org/10.1038/s41587-020-0681-2.
DOI: https://doi.org/10.1038/s41587-020-0681-2

Interpretive Summary: Technological innovations in DNA sequencing, computational genomics, and genome editing promise to substantially accelerate our ability to discover genetic variants responsible for important agronomic traits. Scientists at Donald Danforth Plant Science Center in collaboration with researchers at the Department of Energy Joint Genome Institute, The HudsonAlpha Institute of Biotechnology, BASF, and USDA-ARS laboratory in Wapato, WA have leveraged a natural diversity panel, genome sequencing, and gene editing to identify and validate causal variants associated with domestication. This study characterizes the genetic diversity present within North American green foxtail populations and identified genes responsible for variation in seed shattering and leaf angle. The locus responsible for variation of the seed shattering phenotype was found to be under selection during the domestication of foxtail millet and its function was validated using gene editing. The results and methods presented in this study provide a roadmap to identify and validate novel genetic variants associated with domestication and crop productivity.

Technical Abstract: We present a platinum-quality genome assembly for Setaria viridis, a model for complex trait dissection in the panicoid grasses, plus sequences of a panel of 600+ wild accessions (average 42.6x coverage). Presence-absence variation (PAV) and single-nucleotide polymorphisms (SNPs) identify three clear subpopulations plus a fourth admixed population of North American S. viridis. Using genome-wide association mapping plus CRISPR-Cas9 technology, we identified and validated Less Shattering1 (SvLES1), a gene for seed shattering central to crop domestication. A retrotransposon insertion in SiLES1 was under selection during domestication of S. italica (foxtail millet). We also identified a candidate gene for erect leaves, orthologous to the maize gene liguleless2.