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

• Published in: Theoretical and applied genetics Vol. 137; no. 5; p. 99
• Main Authors: Agha, Husain I., Endelman, Jeffrey B., Chitwood-Brown, Jessica, Clough, Mark, Coombs, Joseph, De Jong, Walter S., Douches, David S., Higgins, Charles R., Holm, David G., Novy, Richard, Resende, Marcio F. R., Sathuvalli, Vidyasagar, Thompson, Asunta L., Yencho, G. Craig, Zotarelli, Lincoln, Shannon, Laura M.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-05-2024; Springer Nature B.V
• Subjects: Adaptation; Agriculture; Biochemistry; Biomedical and Life Sciences; Biotechnology; Cloning; Cultivars; Gene-Environment Interaction; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genotype; Genotype & phenotype; Genotype-environment interactions; Genotypes; Life Sciences; Original; Original Article; Phenotype; Plant Biochemistry; Plant Breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-024-04610-3

Key message
We find evidence of selection for local adaptation and extensive genotype-by-environment interaction in the potato National Chip Processing Trial (NCPT).
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 test advanced breeding material in the National Chip Processing Trial (NCPT), a public–private partnership 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 3 years of selection, we examined these data for evidence of incidental selection for local adaptation, and the alleles underlying it, using an 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.