Environmental genomic selection to leverage polygenic local adaptation in barley landraces

Authors: HALPIN-MCCORMICK, ANNA - University Of Hawaii; CAMPBELL, QUINN - University Of Hawaii; NEGRAO, SONIA - University College Dublin; MORRELL, PETER - University Of Minnesota; HUBNER, SARIEL - Migal Galilee Research Institute; Neyhart, Jeffrey; KANTAR, MICHAEL - University Of Hawaii

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/4/2025
Publication Date: 4/16/2025
Citation: Halpin-Mccormick, A., Campbell, Q., Negrao, S., Morrell, P., Hubner, S., Neyhart, J.L., Kantar, M. 2025. Environmental genomic selection to leverage polygenic local adaptation in barley landraces. Communications Biology. https://doi.org/10.1038/s42003-025-08045-4.
DOI: https://doi.org/10.1038/s42003-025-08045-4

Interpretive Summary: Breeding crops that can thrive in different environments is a major challenge in agriculture. Traditional methods often struggle to pinpoint the best plants for breeding or conservation, particularly when it comes to adapting to specific environmental conditions. We studied locally adapted selections of barley, a cereal crop known for its ability to grow in diverse environments, and developed a new method combining genomic selection and novel modeling of crop distribution across diverse growing locations. Using genetic data from 753 locally adapted selections of barley, we identified key plants that are best suited for adapting to specific environmental factors. This approach used a whole-genome analysis to account for the complex ways plants adapt to their surroundings. This research builds on previous approaches and provides a more intuitive method for selecting parents to breed for stress tolerance.

Technical Abstract: Environmental association analysis (EAA) and allele frequency comparisons in genomic environmental association (GEA) have become standard approaches for investigating the genetic basis of adaptation. While these analyses provide insight into local adaptation, they have not been widely adopted in breeding or conservation programs. This may be attributable to the difficulty in identifying the best individuals for conservation efforts or the best parents in breeding programs. To explore the use of EAA and GEA for future breeding programs, we used a cereal crop - barley (Hordeum vulgare L.) as a case-study due to its wide adaptability to different environments and agro-ecologies, ranging from marginal and low input fields to high-productive farms. We use publicly available data to conduct environmental genomic selection (EGS) on 753 landrace barley accessions using a mini-core of 31 accessions and a de-novo core of 100 as the training populations. Since local adaptation to the environment is polygenic, a whole-genome approach is likely to be more accurate for selecting for environmental adaptation. Here we show distinct genetic background and population differences and how an integrative approach coupling environmental genomic selection and species distribution modelling can help identify key parents for breeding for adaptation to specific environmental variables.