Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial

Authors: AGHA, HUSAIN - University Of Minnesota; ENDELMAN, JEFFREY - University Of Wisconsin; CHITWOOD-BROWN, JESSICA - Colorado State University; CLOUGH, MARK - North Carolina State University; COOMBS, JOE - Michigan State University; DE JONG, WALTER - Cornell University; DOUCHES, DAVID - Michigan State University; HIGGINS, CHARLES - Potatoes Usa; HOLM, DAVID - Colorado State University; Novy, Richard; RESENDE, MARCIO - University Of Florida; SATHUVALLI, VIDYASAGAR - Oregon State University; THOMPSON, ASUNTA - North Dakota State University; YENCHO, G. - North Carolina State University; ZOTARELLI, LINCOLN - University Of Florida; SHANNON, LAURA - University Of Minnesota

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2024
Publication Date: 4/10/2024
Citation: Agha, H.I., Endelman, J.B., Chitwood-Brown, J., Clough, M., Coombs, J., De Jong, W.S., Douches, D.S., Higgins, C., Holm, D., Novy, R.G., Resende, M.F., Sathuvalli, V., Thompson, A.L., Yencho, G.C., Zotarelli, L., Shannon, L.M. 2024. Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial. Theoretical and Applied Genetics. 137. Article 99. https://doi.org/10.1007/s00122-024-04610-3.
DOI: https://doi.org/10.1007/s00122-024-04610-3

Interpretive Summary: Interaction between the genetics of an individual and the environment (GxE) it is grown in, is important in potato breeding to help predict the stability of traits when grown in different locations. Some traits are controlled solely by their genetics, others are controlled mainly by their environment, while others are influenced by an interplay between the two. Yield data collected on breeding clones submitted by breeders from ten institutions across multiple sites in the USA over a period of years was analyzed to better understand the GxE interaction in potato breeding. This work demonstrated regions of the DNA associated with yield from specific breeding program environments, as well as genetic regions not at all impacted by the selection environment. Genetic regions were also found that appeared to be associated with GxE for yield. These results will be of benefit to potato breeders in helping to increase and understand yield components across varied environments.

Technical Abstract: We present a novel method for dissecting the interplay between selection, local adaptation and environmental response in plant breeding schemes. Balancing local adaptation and the desire for widely adapted cultivars is challenging for plant breeders and makes genotype-by-environment interactions (GxE) an important target of selection. Selecting for GxE requires plant breeders to evaluate plants across multiple environments. One way breeders have accomplished this is to test advanced materials across many locations. Public potato breeders in the US partake in such a partnership, the National Chip Processing Trial (NCPT), where breeders from ten institutions submit advanced chip lines to be evaluated in up to ten locations across the country. These clones are genotyped and phenotyped for important agronomic traits. We used these data to interrogate the NCPT for GxE. Further, because breeders submitting clones to the NCPT select in a relatively small geographic range for the first three years of selection, we examined the data for evidence of incidental selection for local adaptation, and the alleles underlying it, using environmental genome-wide association study (envGWAS). We found genomic regions associated with continuous environmental variables and discrete breeding programs, as well as regions of the genome potentially underlying GxE for yield.