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

Abstract

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 resequenced 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.

Sorghum breeding in the genomic era: opportunities and challenges

“…More recently, a GWAS of 206 forage sorghum accessions further identified 9 QTLs for lignin content, covering 184 genes. Importantly, 13 of 184 sorghum lignin-related loci were found to have high collinearity with previously reported gene families in other crops (Niu et al 2020 ). These studies would facilitate future genetic breeding of sorghum as bioenergy and forage.…”

Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes

“…QTL mapping for fodder quality traits has not been reported so far. The closest study reported is the association study performed in sorghum for 5 fodder quality traits by identifying 42 SNPs ( Li et al, 2018 ) and population genomic study performed for lignin content in forage sorghum ( Niu et al, 2020 ).…”

Mobilizing sorghum genetic diversity: Biochemical and histological‐assisted design of a stem ideotype for biomethane production

“…However, according to the greater yield potential per unit area of structural carbohydrates (cellulose and hemicellulose) compared to soluble sugars, the first one is expected to allow higher ethanol yield per unit area. Jointly with the definition of the target ideotypes, optimized genetic gains will also depend on a better understanding of the genetic determinism of biochemical (Brenton et al, 2016; Burks et al, 2015; Hennet et al, 2020; Niu et al, 2020) and histological related traits as recently reported in maize (Mazaheri et al, 2019).…”

“…Sorghum genotypes with high biomass potentials and suitable to support the development of biomass value chains in temperate (Amaducci et al, 2016) and semi‐arid environments (Oikawa et al, 2015) have already been identified. Sorghum also presents a large phenotypic diversity regarding biomass composition (Brenton et al, 2016; Niu et al, 2020; Trouche et al, 2014) that constitutes a vector of adaptation to diverse biomass value chains.…”