Abstract
BackgroundIn sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study.ResultsLevels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study.ConclusionPromising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.
Highlights
In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality
Based on high-density re-sequencing data and robust statistical analysis, we were able to identify genetic regions previously associated with grain quality traits including homologs of Tannin1, Zm1 and TESTA 16 (TT16) for tannins content, sucrose phosphate synthase (SPS) for starch content and opaque1 and opaque2 for amino acids
We identified novel candidate genes that mapped into various metabolic pathways associated with tannins, starch and amino acids
Summary
In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. With the increasing demand for healthy and nutritious food, developing crop varieties with enhanced grain quality is an important target for many breeding programs. Understanding the natural variation and genetic architecture of grain quality traits in sorghum is a first step towards improvement of the nutritional quality through conventional and molecular breeding. Grain quality is determined by the biochemical and physical characteristics of the grain It varies among cereal crops and diverse germplasm, but in general, cereal grains mainly contain starch, protein and fat. Mutants of waxy gene that encodes GBSS, have little or no amylose, increased protein and starch digestibility [6]. The sugary mutants which contain high water-soluble carbohydrates in the endosperm have been characterized in sorghum [7]
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