DOI: 10.5061/dryad.n02v6wwx0
title: Genotyping-by-sequencing data for a Haitian sorghum breeding program

description: Rapid environmental change can lead to extinction of populations or
 evolutionary rescue via genetic adaptation. In the past several years,
 smallholder and commercial cultivation of sorghum (Sorghum bicolor), a
 global cereal and forage crop, has been threatened by a global outbreak of
 an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari).
 Here we characterized genomic signatures of adaptation in a Haitian
 sorghum breeding population, which had been recently founded from admixed
 global germplasm, extensively intercrossed, and subjected to intense
 selection under SCA infestation. We conducted evolutionary population
 genomics analyses of 296 post-selection Haitian lines compared to 767
 global accessions at 159,683 single nucleotide polymorphisms. Despite
 intense selection, the Haitian population retains high nucleotide
 diversity through much of the genome due to diverse founders and an
 intercrossing strategy. A genome-wide fixation (FST) scan and geographic
 analyses suggests that adaptation to SCA in Haiti is conferred by a
 globally-rare East African allele of RMES1, which has also spread to other
 breeding programs in Africa, Asia, and the Americas. De novo genome
 sequencing data for SCA resistant and susceptible lines revealed putative
 causative variants at RMES1. Convenient low-cost markers were developed
 from the RMES1 selective sweep and successfully predicted resistance in
 independent U.S. × African breeding lines and eight U.S. commercial and
 public breeding programs, demonstrating the global relevance of the
 findings. Together, the findings highlight the potential of evolutionary
 genomics to develop adaptive trait breeding technology and the value of
 global germplasm exchange to facilitate evolutionary rescue.
description: Genotypes for the 296 Haitian breeding lines were generated with
 genotyping-by-sequencing. Genomic DNA digestion, ligation and PCR
 amplification processes were performed according to the methods previously
 described (Morris et
 al. 2013). The libraries were sequenced using the single-end
 100-cycle sequencing by Illumina HiSeq2500 (Illumina, San Diego CA, USA)
 at the University of Kansas Medical Center, Kansas City, MO, USA. A total
 of 220 million reads for the HBP were combined with published data for the
 GDP (Morris et
 al. 2013) for SNP calling. TASSEL 5 GBS v2 pipeline (Glaubitz
 et al. 2014) was used to perform the SNP calling of the sequence
 data obtained from Illumina sequencing. Reads were aligned to the BTx623
 sorghum reference genome v.3.1 (McCormick
 et al. 2018) with the Burrows-Wheeler Alignment (Li and
 Durbin 2009). The SNPs were filtered for 20% missingness, then
 missing data were imputed using BEAGLE 4.0 (Browning
 and Browning 2016)
description: Two files are provided: (1)
 haiti_global_all_together.hmp.txt These are SNP
 genotypes for the Haitian sorghum breeding lines (N=296) and global
 reference lines (N = 767) in hapmap format generated by the TASSEL GBS
 pipeline. More information on hapmap format is availble here
 (https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load). (2) key.csv This the key file for the TASSEL GBS pipeline, which can be used to regenerate the SNP genotype calls from raw sequencing reads. Note, raw sequencing reads are not provided here on Dryad due to the large file sizes, but can be found on the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) under accession PRJNA757369. See Glaubitz et al. 2014 PLOS ONE for more information on the use of key files in the TASSEL GBS pipeline. http://dx.doi.org/10.1371/journal.pone.0090346