Managing the genetic diversity of Dioscorea yams for adaptation to climate change

Abstract

Understanding adaptation to environmental variation is fundamental to climate-resilient agriculture. Here, we analyzed a georeferenced collection of 167 Dioscorea accessions spanning a wide range of bioclimatic and biophysical variation, from dry sahelian environment to rainforest environment. Genome-wide association analyses revealed that the genetic architecture of environmental adaptation is largely driven by large-effect loci, although precipitation-related traits were associated with many small-effect loci. This mixed architecture could lead to multiple breeding strategies, including marker-assisted backcrossing and the targeted use of wild and semi-wild relatives. We identified a core collection of accessions that captures much of the genetic and environmental diversity, and highlighted accessions as potential parents for abiotic stress tolerance. Projections under future climate scenarios using genomic offset identified regions and accessions at elevated risk of maladaptation, as well as others with broad adaptive potentiality. Maximizing the use of available material may facilitate the development of climate-resilient cultivars. Plain Language Summary Yam is an ancient staple crop grown across the tropics, but there is still much room for plant breeders to understand how yam species adapt to their environments. We studied 167 wild and cultivated yam samples from West Africa, spanning dry Sahelian conditions to rainforest, exploring the relationship of these samples’ local climate and soil data. Adaptation appears shaped mainly by a handful of strong-effect genes, plus many small-effect genes tied to rainfall. We identified a smaller “core” set of samples capturing most of the genetic and environmental diversity, and flagged accessions especially promising as parents for breeding stress-tolerant yam. We also predicted which populations face the greatest risk under future climate change. Together, these findings give breeders practical tools for developing climate-resilient yam varieties from existing genebank collections.