Population genomic and genome-wide association analysis of lignin content in a global collection of 206 forage sorghum accessions

Forage sorghum (Sorghum bicolor(L.) Moench) is a wildly cultivated C4 cereal crop in many geographical regions and differs among germplasms in a number of important physiological traits. Lignin is a complex heteropolymer found in plant cell walls that adversely affects economic and environmental benefits of the crop. To understand the genetic basis, we re-sequenced the genomes of 206 sorghum accessions collected around the globe and identified 14,570,430 SNPs and 1,967,033 indels. Based on the SNP markers, we characterized the population structure and identified loci underlying lignin content by genome-wide association studies (GWAS). Analysis of the genetic relationships among the accessions revealed a more diverse spread of sorghum accessions and breeding lines from Asia, America, and their genetically improved variety, but a limited genetic diversity in the European accessions. These findings add new perspectives to the historical processes of crop diffusion within and across agroclimatic zones of America, Asia, and Europe. GWAS revealed 9 quantitative trait loci (QTLs) for lignin content, harboring 184 genes. These genes were significantly enriched into 7 major gene ontology (GO) terms involved in plant-type cell wall organization or bioenergy. The alleles of 9 QTLs in the 206 accessions were geographically distributed. The findings provide us with an understanding of the origin and spread of haplotypes linked to lignin content. The findings will allow improvements to feed quality and adaptation to stresses in sorghum, through the rapid increase of genetic gains for lignin content.