National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
Theor Appl Genet. 2024 Apr 8;137(5):96. doi: 10.1007/s00122-024-04607-y.
A total of 416 InDels and 112 SNPs were significantly associated with soybean photosynthesis-related traits. GmIWS1 and GmCDC48 might be related to chlorophyll fluorescence and gas-exchange parameters, respectively. Photosynthesis is one of the main factors determining crop yield. A better understanding of the genetic architecture for photosynthesis is of great significance for soybean yield improvement. Our previous studies identified 5,410,112 single nucleotide polymorphisms (SNPs) from the resequencing data of 219 natural soybean accessions. Here, we identified 634,106 insertions and deletions (InDels) from these 219 accessions and used these InDel variations to perform principal component and linkage disequilibrium analysis of this population. The genome-wide association study (GWAS) were conducted on six chlorophyll fluorescence parameters (chlorophyll content, light energy absorbed per reaction center, quantum yield for electron transport, probability that a trapped exciton moves an electron into the electron transport chain beyond primary quinone acceptor, maximum quantum yield of photosystem II primary photochemistry in the dark-adapted state, performance index on absorption basis) and four gas-exchange parameters (intercellular carbon dioxide concentration, stomatal conductance, net photosynthesis rate, transpiration rate) and revealed 416 significant InDels and 112 significant SNPs. Based on GWAS results, GmIWS1 (encoding a transcription elongation factor) and GmCDC48 (encoding a cell division cycle protein) with the highest expression in the mapping region were determined as the candidate genes responsible for chlorophyll fluorescence and gas-exchange parameters, respectively. Further identification of favorable haplotypes with higher photosynthesis, seed weight and seed yield were carried out for GmIWS1 and GmCDC48. Overall, this study revealed the natural variations and candidate genes underlying the photosynthesis-related traits based on abundant phenotypic and genetic data, providing valuable insights into the genetic mechanisms controlling photosynthesis and yield in soybean.
共鉴定到 416 个 InDels 和 112 个 SNPs 与大豆光合作用相关性状显著相关。GmIWS1 和 GmCDC48 可能分别与叶绿素荧光和气体交换参数有关。光合作用是决定作物产量的主要因素之一。更好地了解光合作用的遗传结构对提高大豆产量具有重要意义。我们之前的研究从 219 个自然大豆品系的重测序数据中鉴定了 5410112 个单核苷酸多态性（SNP）。在这里，我们从这 219 个品系中鉴定了 634106 个插入和缺失（InDel），并使用这些 InDel 变异对该群体进行主成分和连锁不平衡分析。对 6 个叶绿素荧光参数（叶绿素含量、每个反应中心吸收的光能、电子传递量子产率、被捕获的激子进入电子传递链的电子转移概率、暗适应状态下光系统 II 初级光化学的最大量子产率、吸收基础上的性能指数）和 4 个气体交换参数（胞间二氧化碳浓度、气孔导度、净光合速率、蒸腾速率）进行全基因组关联研究（GWAS），共鉴定到 416 个显著 InDel 和 112 个显著 SNP。基于 GWAS 结果，确定在图谱区域表达量最高的 GmIWS1（编码转录延伸因子）和 GmCDC48（编码细胞分裂周期蛋白）为负责叶绿素荧光和气体交换参数的候选基因。进一步对 GmIWS1 和 GmCDC48 进行了更高光合作用、种子重量和产量有利单倍型的鉴定。总的来说，这项研究基于丰富的表型和遗传数据，揭示了与光合作用相关性状相关的自然变异和候选基因，为控制大豆光合作用和产量的遗传机制提供了有价值的见解。
