Genotyping-by-sequencing data for a Haitian sorghum breeding program

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.