Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum

Abstract

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world's poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

Figure 1. Analysis of the phylogenetic relationship and LD decay of sorghum.

(a) A neighbor-joining tree constructed using SNP data. (b) Principal component analysis of sorghum accessions. (c) LD decay determined by squared correlations of allele frequencies (r²) against distance between polymorphic sites in wild and weedy sorghum genotypes (red), landraces (green) and improved inbreds (blue).

Figure 2. Signatures of selection in two genomic regions.

(a,b) Diversity (θπ) (wild and weedy group in red; landraces in blue, improved inbreds in green) and F_ST values (black line) in 10-kb intervals. (c,d) Predicted gene models in genomic regions with candidate genes under selection highlighted, Sb01g032830 (SbGS3) and Sb04g028060 (SSIIb), respectively. (e,f) LD blocks around candidate genes under selection. Red and white spots indicate strong (r²=1) and weak (r²=0) LD, respectively. (g,h) Gene trees for GS3 and SSIIb, respectively.

Figure 3. Summary of sorghum resequencing data.

Concentric circles show the different features that were drawn using the Circos program. The 10 chromosomes are portrayed along the perimeter of each circle. (a) Gene content density distribution. (b) Genomic diversity (θπ) of wild and weedy genotypes (red), landraces (green) and improved inbreds (blue). (c) Tajima’s D of wild and weedy genotypes (red), landraces (green) and improved inbreds (blue). (d) Number of SNPs in wild and weedy genotypes (red), landraces (green) and improved inbreds (blue). (e) F_ST values of improved inbreds versus landraces. (f) F_ST values of improved inbreds versus wild and weedy genotypes. (g) F_ST values of landraces versus wild and weedy genotypes. (h) A graphical view of duplicated annotated genes is indicated by connections between segments.