Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Genomics. 2020 Jan 31;21(1):112. doi: 10.1186/s12864-020-6538-8.
In 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.
Levels 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.
Promising 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.
在高粱（Sorghum bicolor）中，一个主要的育种目标是提高谷物品质。高粱籽粒的营养品质和最终用途价值主要受单宁、淀粉和蛋白质的比例影响，但这些谷物品质性状的遗传基础在很大程度上仍不清楚。本研究旨在通过全基因组关联研究解析高粱籽粒品质性状的自然变异，并鉴定其潜在的遗传位点。
对 196 个不同的高粱自交系进行了淀粉、单宁和 17 种氨基酸的定量分析，并根据已知的代谢途径和 17 种氨基酸之间的生化相互作用计算了 44 个基于表型的性状。对来自重测序数据的 3512517 个 SNP 进行全基因组关联研究（GWAS），鉴定出 14 个、15 个和 711 个与高粱籽粒中单宁、淀粉和氨基酸水平相关的显著 SNP，分别代表 14、14、492 个与单宁、淀粉和氨基酸水平相关的遗传位点。在这些显著 SNP 中，有两个 SNP 与第 4 号染色体上的单宁含量相关，与之前鉴定的 Tannin1 三个位点以及 Zm1 和 TT16 基因的同源物共定位。一个与淀粉含量相关的 SNP 与蔗糖磷酸合酶基因共定位。此外，还鉴定到与氨基酸含量相关的 opaque1 和 opaque2 基因的同源物。利用 KEGG 途径数据库，将单宁和淀粉的 6 个和 3 个候选基因分别映射到 12 个和 3 个代谢途径中。34 个候选基因映射到 16 个氨基酸的合成和分解代谢途径中。最后，根据本研究中鉴定的 15 个候选基因，重建了天冬氨酸和支链氨基酸的生物合成途径。
本研究鉴定到与籽粒品质性状相关的有希望的候选基因。其中一些与之前鉴定的遗传区域共定位，但也解析了参与影响籽粒品质性状的各种代谢途径的新的候选基因。我们的研究为进一步阐明控制高粱中单宁、淀粉和氨基酸等谷物品质性状的复杂机制的验证研究提供了切入点。
