title: Genome-environment associations in sorghum landraces predict adaptive traits.
abstract: Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.
authors.affiliation: Earth Institute, and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10025, USA.
authors.forename: Jesse R
authors.initials: JR
authors.lastname: Lasky
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India. ; Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA. ; UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India. ; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Punna
authors.initials: P
authors.lastname: Ramu
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India.
authors.forename: Santosh
authors.initials: S
authors.lastname: Deshpande
authors.affiliation: ICRISAT Sahelian Center, BP 12404, Niamey, Niger.
authors.forename: C Tom
authors.initials: CT
authors.lastname: Hash
authors.affiliation: Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Bonnette
authors.affiliation: Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Juenger
authors.affiliation: Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Katie
authors.initials: K
authors.lastname: Hyma
authors.affiliation: Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Acharya
authors.affiliation: Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Mitchell
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA. ; U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Brenton
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Kresovich
authors.affiliation: Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.
authors.forename: Geoffrey P
authors.initials: GP
authors.lastname: Morris
keywords: climate; domestication; genome scan; genomic selection; genotyping-by-sequencing; local adaptation; plant breeding; plasticity; quantitative trait loci; water stress