Ghosh Suprio, Zhang Shengrui, Azam Muhammad, Agyenim-Boateng Kwadwo Gyapong, Qi Jie, Feng Yue, Li Yecheng, Li Jing, Li Bin, Sun Junming
The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China.
Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh.
Plants (Basel). 2022 Jun 27;11(13):1703. doi: 10.3390/plants11131703.
Soybean seeds are primary sources of natural tocopherols used by the food and pharmaceutical industries, owing to their beneficial impacts on human health. Selection for higher tocopherol contents in seeds along with other desirable traits is an important goal in soybean breeding. In order to identify the genomic loci and candidate genes controlling tocopherol content in soybean seeds, the bulked-segregant analysis technique was performed using a natural population of soybean consisting of 1525 accessions. We constructed the bulked-segregant analysis based on 98 soybean accessions that showed extreme phenotypic variation for the target trait, consisting of 49 accessions with extremely-high and 49 accessions with extremely-low tocopherol content. A total of 144 variant sites and 109 predicted genes related to tocopherol content were identified, in which a total of 83 genes were annotated by the gene ontology functions. Furthermore, 13 enriched terms (p < 0.05) were detected, with four of them found to be highly enriched: response to lipid, response to abscisic acid, transition metal ion transmembrane transporter activity, and double-stranded DNA binding. Especially, six candidate genes were detected at 41.8−41.9 Mb genomic hotspots on chromosome 5 based on ANNOtate VARiation analysis. Among the genes, only Glyma.05G243400 carried a non-synonymous mutation that encodes a “translation elongation factor EF1A or initiation factor IF2gamma family protein” was identified. The haplotype analysis confirmed that Glyma.05G243400 exhibited highly significant variations in terms of tocopherol content across multiple experimental locations, suggesting that it can be the key candidate gene regulating soybean seed tocopherols. The present findings provide novel gene resources related to seed tocopherols for further validation by genome editing, functional characterization, and genetic improvement targeting enhanced tocopherol composition in soybean molecular breeding.
大豆种子是食品和制药行业天然生育酚的主要来源，因为它们对人类健康有有益影响。在大豆育种中，选择种子中生育酚含量更高以及具有其他理想性状是一个重要目标。为了鉴定控制大豆种子生育酚含量的基因组位点和候选基因，使用了由1525份材料组成的大豆自然群体进行混合分组分析法。我们基于98份大豆材料构建了混合分组分析，这些材料在目标性状上表现出极端的表型变异，其中49份材料的生育酚含量极高，49份材料的生育酚含量极低。共鉴定出144个变异位点和109个与生育酚含量相关的预测基因，其中共有83个基因通过基因本体功能进行了注释。此外，检测到13个富集术语（p < 0.05），其中4个被发现高度富集：对脂质的反应、对脱落酸的反应、过渡金属离子跨膜转运活性和双链DNA结合。特别是，基于ANNOtate VARiation分析，在5号染色体上41.8−41.9 Mb的基因组热点区域检测到6个候选基因。在这些基因中，仅鉴定出Glyma.05G243400携带一个非同义突变，该突变编码一种“翻译延伸因子EF1A或起始因子IF2γ家族蛋白”。单倍型分析证实，Glyma.05G243400在多个实验地点的生育酚含量方面表现出极显著差异，表明它可能是调节大豆种子生育酚的关键候选基因。本研究结果提供了与种子生育酚相关的新基因资源，可通过基因组编辑、功能表征以及针对大豆分子育种中提高生育酚组成的遗传改良进行进一步验证。
