DOI: 10.5061/dryad.32f5395
title: Data from: Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

description: 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.
description: 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 &lt; 20%
 missing data, minor allele frequency MAF &gt; 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.