Research Report 2019_20

Jane Grimwood, PhD & Jeremy Schmutz / HudsonAlpha Genome Sequencing Center

Because of its hybrid origin, A. hypogaea has a poly- ploid genome, carrying two separate genomes from its ancestral “parents”, referred to as the A and B subge- nomes. Although peanuts have been cultivated for thou- sands of years, relatively little was known about their complex genetic structure until recently. The A and B subgenomes were previously deter- mined to have more than 98 percent DNA identity be- tween corresponding genes. Because of this similarity, the research team decided to use longer read data ob- tained using PacBio technology to construct the pea- nut genome. The published, high-quality reference se- quence makes it easier to trace the history of the crop and breed peanuts for desirable traits like resistance to diseases and pests that may have been lost over time. The study also proves the usefulness of long-read sequencing in agricultural genomics. The A. hypogaea reference genome has already contributed to several interesting discoveries about the peanut. First, researchers determined the geograph- ic origin of A. duranensis , one of the two “parents” of A. hypogaea . In addition, by recreating the genomic merger of the two ancient peanuts species, the researchers also discovered an interesting pattern of DNA swapping and deletions taking place in the offspring plants that likely explains the diverse seed size, shape, color and other traits seen in commercial peanuts today.

shattering gene variant could be targeted as a mecha- nism to turn off shattering in other plants, thus improv- ing their yield. Using a model organism such as S. viridi s to find genes linked to beneficial traits is a promising method of improving crop domestication. Climate change and environmental conditions can greatly influence the success of a crop harvest. Oftentimes, crops domesticated in one geographic loca- tion have vastly different traits than those domesticat- ed elsewhere. One such crop, called switchgrass, is a promising biofuel candidate that exists in several variet- ies adapted to different geographic regions. For exam- ple, the southern lowland switchgrass grow quickly and are tall and thick-stemmed, while the northern upland switchgrass are short and thin-stemmed. The southern switchgrass is the most desirable for biofuel because they produce the most biomass per plant. However, this variety will not survive well in northern climates. Researchers desire to create a switchgrass plant variety that produces the biomass of the southern variety but can thrive in northern climates. In order to determine what genetic loci cause differences between the two varieties, the group took advantage of community switchgrass gardens across the United States 4 . They produced hybrid plants rep- resenting a cross between the southern and northern varieties, and planted them at established community gardens in 10 different field sites across multiple states on a north-south gradient. Having the same plants growing at these community gardens allowed research- ers to consider how the plant’s genes interact with the environment, and look at the genes involved in specif- ic fitness traits such as biomass production and cold tolerance. Results from these large-scale field tests conducted over two years reveal fewer tradeoffs in plant fitness and adaptation than expected. Locally advantageous alleles could potential- ly be combined across multiple loci through breeding to create high-yielding regionally adapted plants. By field-testing the adaptability of switchgrass hybrids in a wide range of environmental conditions, researchers hope to eventually develop a “generalist” switchgrass that would thrive and produce high levels of biomass in various regions. As exemplified here, a central goal of Grimwood and Schmutz’s research is to use genomics to improve crops for use as food, energy, and fiber. They are con- stantly asking ‘How do we apply what we have learned from sequencing hundreds of plant genomes to

Setaria viridis grass

Through the assembly of a high-quality reference genome for the grass Setaria viridis , Grimwood, Schmutz, and colleagues identified a gene related to seed disper- sal in wild plant populations for the first time 3 . They generated genome sequences for nearly 600 S. viridis plants to create the reference genome sequence. Asso- ciation mapping led the team to identify a gene called Less Shattering 1 ( SvLes1 ) which is involved in a process called shattering, or seed dispersal. Shattering is crit- ical for plants in the wild to create offspring, but it is an undesirable trait for domesticated crops because it leads to reduced harvest yields. This newly discovered


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