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

Area of Science:

• Plant breeding
• Genetics
• Agricultural science

Background:

• Balancing local adaptation and broad adaptability is a key challenge in developing new crop cultivars.
• Genotype-by-environment interactions (GxE) are critical for understanding how genetic material performs across diverse conditions.
• The National Chip Processing Trial (NCPT) provides a valuable dataset for studying GxE and local adaptation in potato.

Purpose of the Study:

• To investigate evidence of selection for local adaptation and GxE within the NCPT.
• To introduce a novel analytical method for dissecting selection, local adaptation, and environmental response in breeding programs.
• To identify genomic regions associated with local adaptation and GxE in potato breeding lines.

Main Methods:

• Utilized data from the National Chip Processing Trial (NCPT), including genotypic and phenotypic information from advanced potato clones.
• Applied an environmental genome-wide association study (envGWAS) to detect associations between genomic regions and environmental variables.
• Analyzed data to identify genomic regions potentially underlying GxE for yield and local adaptation.

Main Results:

• Found significant evidence for selection related to local adaptation and substantial GxE in the NCPT.
• Identified specific genomic regions associated with continuous environmental variables and distinct breeding programs.
• Discovered genomic regions potentially responsible for GxE related to potato yield.

Conclusions:

• The NCPT data reveals complex interactions between potato genotypes, environments, and breeding selection strategies.
• The developed method offers a new approach for breeders to dissect GxE and local adaptation.
• Understanding these genetic underpinnings can improve the development of both locally adapted and widely adapted potato cultivars.