Shattering expectations: Novel seed dispersal gene found in green millet
Road trips result in the first shattering gene found in a wild population


Date:
October 5, 2020
Source:
Donald Danforth Plant Science Center
Summary:
Researchers generated genome sequences for nearly 600 green millet
plants and released a very high-quality reference S. viridis genome
sequence and also identified a gene related to seed dispersal in
wild populations for the first time.



FULL STORY ==========================================================================
For years, Elizabeth (Toby) Kellogg, PhD, member and Robert E. King Distinguished Investigator and other researchers at the Donald Danforth
Plant Science Center (Danforth Center) drove up and down the highways
of the continental United States, occasionally pulling over to the side
of the road to collect small weedy plants and bring them back to the
lab. The weedy grass was green millet (Setaria viridis), a small model
grass with a short lifecycle that uses a carbon fixation process known
as the C4 pathway, which particularly helps plants thrive in warm, arid environments. Corn and sugarcane are among the major high-yield C4 crops,
as are the candidate biofuel feedstocks Miscanthus and switchgrass.


========================================================================== Innumerable road trips and hundreds of plants have resulted in a paper,
"A genome resource for green millet Setaria viridis enables discovery
of agronomically valuable loci," in Nature Biotechnology. Kellogg and
her colleagues, along with researchers at the HudsonAlpha Institute
for Biotechnology and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at
Lawrence Berkeley National Laboratory (Berkeley Lab), generated genome sequences for nearly 600 green millet plants and released a very high
quality reference S. viridis genome sequence. Analysis of these plant
genome sequences also led researchers to identify a gene related to seed dispersal in wild populations for the first time.

"To our knowledge, nobody has ever discovered a dispersal gene that
way," said Kellogg, a senior author of the paper. "This paper is the
first one to survey a huge amount of natural diversity and say, 'Yeah,
there are genes out there that affect this phenotype.'" Results from A "Massive Amount" of Sequencing Seed dispersal is critical for plants
in the wild, but it is an undesirable trait for domesticated crops
because it leads to reduced harvest yields. Over thousands of years,
farmers have selected for cereal plants without this shattering trait
-- referring to the moment when the cluster of seeds at the tip of each
branch breaks apart so the seeds can disperse -- so that the seeds remain
atop the plant to be collected.

Association mapping led the team to identify a gene called Less Shattering
1 (SvLes1); gene editing studies led by co-first author Pu Huang
confirmed that it was involved in shattering by turning it off. "It's
a new shattering gene variant identified in a natural population. Not
very many of these shattering genes have been discovered that let a
plant go all the way to seed but prevent the seeds from falling," said
JGI Plant Program head Jeremy Schmutz, who is also a HudsonAlpha Faculty Investigator. "This could be another mechanism to turn off shattering and domesticate crops." How shattering occurs varies widely between crops,
Kellogg added, and shattering genes may be specific to species or groups
of species.



==========================================================================
The genome data also revealed that green millet was introduced into the
United States multiple times from Eurasia. The team also identified a
gene associated with leaf angle, which determines how much sunlight
leaves can get and in turn serves as a predictor of yield. The gene
is an ortholog of known genes, "The gene has now been mapped back in
maize as involved in leaf angle," noted Schmutz. "It's a nice example of
de novo discovery and then mapping back to identify candidate genes."
Through JGI's Community Science Program, sequences of several hundred
green millet plant genomes were generated, though the final analyses
focused on 598 individuals. Schmutz and his team assembled and annotated
the genomes at HudsonAlpha. Sujan Mamidi and Adam Healey, two of the
co-first authors, led the data analyses and assembled the green millet "pan-genome" (a set of 51,000 genes that represent all the genes that
are present in a given species).

"This is a great example of developing a large-scale genome infrastructure
with a reasonably accessible system," said Schmutz. "Building the
pan-genome and accessions allow us to see presence/absence variation
easily and to find genes missing in particular accessions, and to confirm phenotypes, which validate traits." "The number of lines sequenced is
not trivial, and they were all assembled de novo, which let the team
look at presence/absence of whole genes," Kellogg agreed. "Getting that information is hard. There's a good reason nobody's done it; it's a heck
of a lot of work. I wouldn't have done it without the contribution of
Jeremy's group. It's just a massive amount of sequencing." A Resource
for Many Applications Kellogg noted that C4 crops have gotten a lot
of interest because they're very productive even in high heat while C3
crops have become less efficient at photosynthesis, a concern as extreme weather events become more frequent. "A big part of the Danforth Center's mission is to feed the hungry and improve human health. So there's
a major question: how to turn a C3 crop into a C4 crop. There should
be a master regulator but no one has found it," Kellogg mused. "[The
S. viridis genome] is a resource for many different applications.

The JGI group has been wonderful to collaborate with, and this [project] wouldn't have been possible without their involvement; it's something
we wouldn't have even started." Researchers from the RIKEN Center for Sustainable Resource Science (Japan) and Chinese Academy of Agricultural Sciences (China) were also involved in this work.


========================================================================== Story Source: Materials provided by
Donald_Danforth_Plant_Science_Center. Note: Content may be edited for
style and length.


========================================================================== Journal Reference:
1. Sujan Mamidi, Adam Healey, Pu Huang, Jane Grimwood, Jerry Jenkins,
Kerrie
Barry, Avinash Sreedasyam, Shengqiang Shu, John T. Lovell,
Maximilian Feldman, Jinxia Wu, Yunqing Yu, Cindy Chen, Jenifer
Johnson, Hitoshi Sakakibara, Takatoshi Kiba, Tetsuya Sakurai,
Rachel Tavares, Dmitri A.

Nusinow, Ivan Baxter, Jeremy Schmutz, Thomas P. Brutnell,
Elizabeth A.

Kellogg. A genome resource for green millet Setaria viridis enables
discovery of agronomically valuable loci. Nature Biotechnology,
2020; 38 (10): 1203 DOI: 10.1038/s41587-020-0681-2 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/10/201005122131.htm

--- up 6 weeks, 6 hours, 50 minutes
* Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1337:3/111)