Location: Corn Insects and Crop Genetics Research
2022 Annual Report
Accomplishments
1. Incorporated genome assemblies and annotations for peanut, bean, cowpea and alfalfa into SoyBase and the Legume Information System (LIS). Genome sequences describe the order and content of the DNA in all of the chromosomes of an organism, and serves as a common framework or backbone for much of the work done by breeders and other researchers. This framework identifies genes, genetic markers, and traits and their chromosomal locations. ARS researchers in Ames, Iowa, have collected 24 new full genome assemblies, across 15 legume species, and incorporated these into the Data Store that is used by SoyBase and LIS and available for use by researchers. The new genome assemblies include three peanut and its wild relatives, six wild relatives of soybean, four bean and its wild relatives, diverse cowpea varieties, three alfalfa and its relatives, and one savannah tree, the apple ring Acacia, that is an important component of agroforestry systems in Africa. These data will be of interest both to plant breeders, and to biologists working to understand the genes involved in adaptation to the various physical environments that these species occupy. This information may be used, for example, to identify genetic markers for traits such as tolerance to increased heat, drought, or salinization. Breeding and research on legume crops impact people worldwide, as legumes provide protein and other nutrients for a large portion of the global population.
2. Published a report describing important contributions of crop wild relatives to cultivated peanut. The small number of crop species and their generally narrow genetics is a fundamental vulnerability to food security. Wild crop relatives are strategic sources of genetic diversity for the breeding of resistance to pests, diseases and environmental stresses. ARS researchers in Ames, Iowa, participated in a consortium that incorporated a wild peanut relative, Arachis cardenasii, into domesticated peanut, Arachis hypogaea. This genetic incorporation, initiated by scientists beginning in 1967, involved complex and challenging genetic crosses. Subsequent breeding cycles substantially obscured this contribution from the wild relative. However, the genetic legacy from this breeding work can now be seen in enhanced peanut cultivars in at least 30 countries. This work has improved food security and provided economic and environmental benefits.
3. Published a study describing the newly assembled genome sequences of six perennial relatives of soybean. Soybean, one of the most important crops globally for its protein and oil content, faces numerous challenges from insects, pathogens, and environmental stresses. A group of wild relatives of soybean, from Australia, may provide information to researchers to better understand how to improve soybean resilience to various stresses. ARS researchers in Ames, Iowa, participated in an international consortium that reported the genome assemblies of six soybean relatives. All six of the newly sequenced species are perennial, and all survive in challenging environments in their native ranges in Australia. This work also identified genes that are highly conserved, as well as genes that are specific to one or several species. A gene involved in the transition between the perennial and annual varieties of soybean was also described. These results provide basic information that may be used by breeders for soybean improvement, particularly in mitigating environmental challenges due to climate change.
4. Incorporated variety trial and pedigree data for soybean, spanning the last 30 years of trials from the northern U.S. For all major crops, variety trials and pedigree data are used to determine which new varieties are most suited to a particular region or to meeting grower and consumer objectives. Traits that are typically assessed in soybean variety trials include yield, tolerance against adverse field conditions such as nutrient deficiencies or pathogens, seed characteristics such as protein and oil concentration and quality, and growth harvest characteristics such as germination rate and plant architecture at harvest. ARS researchers in Ames, Iowa, have added soybean measurements for these traits for more than 1,900 test strains submitted to the Northern Uniform Soybean Tests (NUST). Incorporating trait data on these strains into SoyBase allows breeders access to performance data of test strains from 1989 to the present. This will allow breeders to easily see the results of breeding activity across programs, evaluate any increase in grain yield and other seed quality measurements and incorporate strains with superior genetics into their breeding programs.
Review Publications
Brown, A.V., Grant, D.M., Nelson, R. 2021. Using crop databases to explore phenotypes: from QTL to candidate genes. Plants. 10(11). Article 2494. https://doi.org/10.3390/plants10112494.
Chiteri, K.O., Zaki Jubery, T., Dutta, S., Ganapathysubramanian, B., Cannon, S.B., Singh, A. 2022. Dissecting the root phenotypic and genotypic variability of the Iowa mung bean diversity panel. Frontiers in Plant Science. 12:808001. https://doi.org/10.3389/fpls.2021.808001.
Zhuang, Y., Wang, X., Li, X., Hu, J., Fan, L., Landis, J.B., Cannon, S.B., Grimwood, J., Schmutz, J., Jackson, S.A., Doyle, J.J., Zhang, X., Zhang, D., Ma, J. 2022. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nature Plants. 8: 233-244. https://doi.org/10.1038/s41477-022-01102-4.
Bertioli, D.J., Clevenger, J., Godoy, I., Stalker, T., Wood, S., Santos, J., Ballen-Taborda, C., Abernathy, B., Azevedo, V., Campbell, J.D., Chavarro, C., Chu, Y., Farmer, A.D., Fonceka, D., Gao, D., Grimwood, J., Halpin, N., Korani, W., Michelotto, M.D., Ozias-Akins, P., Vaughn, J.N., Youngblood, R., Moretzsohn, M.C., Wright, G.C., Jackson, S.A., Cannon, S.B., Scheffler, B.E., Leal-Bertioli, S.M. 2021. Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange. Proceedings of the National Academy of Sciences(PNAS). 118(38). Article e2104899118. https://doi.org/10.1073/pnas.2104899118.
Li, J., Singh, U., Bhandary, P., Campbell, J.D., Arendsee, Z., Seetharam, A., Wurtele, E. 2021. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Research. 50(7):e37. https://doi.org/10.1093/nar/gkab1238.
Redsun, S., Hokin, S., Cameron, C.T., Cleary, A.M., Berendzen, J., Dash, S., Brown, A.V., Wilkey, A., Campbell, J.D., Huang, W., Kalberer, S.R., Weeks, N.T., Cannon, S.B., Farmer, A.D. 2022. Doing genetic and genomic biology using the Legume Information System and associated resources. Methods in Molecular Biology. 2443. https://doi.org/10.1007/978-1-0716-2067-0_4.
