Data from: Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.SNP Data Set of Senegalese Sorghum in the USDA-NPGS GRINThe file contains 213,916 GBS-SNPs obtained using genotyping-by-sequencing on the Senegalese sorghum accessions in the USDA-NPGS GRIN. Single-end sequence reads obtained from Illumina sequencing HiSeq 2500 were processed with the TASSEL 5 GBS v2 pipeline and sequence tags were aligned to the sorghum reference genome, BTx623 for SNP discovery. Only SNPs with 0.01, and biallelic SNPs are present in this data set.SNP_DataSet_ImpBeag4_SnSorghumGRIN.421_v1.0_MAF01.vcfFaye-Supporting_Information_Data_S1The file contains information about the sorghum accessions used in the present study, local name, the village, the agro-ecological region and the country of origin, and the ADMIXTURE coefficient of membership.Faye-Supporting_Information_Data_S2The file contains information about the candidate genes used in the present study, gene functions, and references.Faye-Supporting_Information_Data_S3The file contains the composite likelihood ratio (CLR) outliers, obtained from the SweeD program, in durra and guinea sorghum accessions.Faye-Supporting_Information_Data_S4The file contains significantly associated SNPs with phenotypes (photoperiod sensitivity and panicle compactness) or environment variables.Faye-Supporting_Information_File_S1The file contains ADMIXTURE population structure at K = 3–7