National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
BMC Genomics. 2020 Oct 19;21(1):725. doi: 10.1186/s12864-020-07143-3.
Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and identification of P efficiency genes are important strategies for increasing soybean yield.
Genome-wide association analysis (GWAS) with NJAU 355 K SoySNP array was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with three shoot P efficiency-related traits of a natural population of 211 cultivated soybeans and relative values of these traits under normal P (+P) condition and P deficiency (-P) condition. A total of 155 SNPs were identified significantly associated with P efficiency-related traits. SNPs that were significantly associated with shoot dry weight formed a SNP cluster on chromosome 11, while SNPs that were significantly associated with shoot P concentration formed a SNP cluster on chromosome 10. Thirteen haplotypes were identified based on 12 SNPs, and Hap9 was considered as the optimal haplotype. Four SNPs (AX-93636685, AX-93636692, AX-93932863, and AX-93932874) located on chromosome 10 were identified to be significantly associated with shoot P concentration under +P condition in two hydroponic experiments. Among these four SNPs, two of them (AX-93636685 and AX-93932874) were also significantly associated with the relative values of shoot P concentration under two P conditions. One SNP AX-93932874 was detected within 5'-untranslated region of Glyma.10 g018800, which contained SPX and RING domains and was named as GmSPX-RING1. Furthermore, the function research of GmSPX-RING1 was carried out in soybean hairy root transformation. Compared with their respective controls, P concentration in GmSPX-RING1 overexpressing transgenic hairy roots was significantly reduced by 32.75% under +P condition; In contrast, P concentration in RNA interference of GmSPX-RING1 transgenic hairy roots was increased by 38.90 and 14.51% under +P and -P conditions, respectively.
This study shows that the candidate gene GmSPX-RING1 affects soybean phosphorus efficiency by negatively regulating soybean phosphorus concentration in soybean hairy roots. The SNPs and candidate genes identified should be potential for improvement of P efficiency in future soybean breeding programs.
磷（P）是维持作物高生物量和产量的必需元素。大豆（Glycine max（L.）Merr.）在生长和发育过程中需要大量的 P。提高 P 效率和鉴定 P 效率基因是提高大豆产量的重要策略。
利用 NJAU 355K SoySNP 阵列进行全基因组关联分析（GWAS），以鉴定与 211 个栽培大豆自然群体的三个地上部 P 效率相关性状及其在正常 P（+P）和 P 缺乏（-P）条件下的相对值显著相关的单核苷酸多态性（SNP）。共鉴定出 155 个与 P 效率相关性状显著相关的 SNP。与地上部干重显著相关的 SNP 形成了 11 号染色体上的 SNP 簇，而与地上部 P 浓度显著相关的 SNP 形成了 10 号染色体上的 SNP 簇。基于 12 个 SNP 鉴定出 13 个单倍型，其中 Hap9 被认为是最佳单倍型。在两个水培实验中，鉴定出位于 10 号染色体上的 4 个 SNP（AX-93636685、AX-93636692、AX-93932863 和 AX-93932874）与+P 条件下地上部 P 浓度显著相关。在这 4 个 SNP 中，有 2 个（AX-93636685 和 AX-93932874）也与两种 P 条件下地上部 P 浓度的相对值显著相关。一个 SNP AX-93932874 位于 Glyma.10g018800 的 5'-非翻译区，该基因含有 SPX 和 RING 结构域，被命名为 GmSPX-RING1。此外，在大豆毛状根转化中对 GmSPX-RING1 进行了功能研究。与各自的对照相比，+P 条件下 GmSPX-RING1 过表达转基因毛状根中的 P 浓度显著降低了 32.75%；相比之下，在+P 和-P 条件下，GmSPX-RING1 RNA 干扰转基因毛状根中的 P 浓度分别增加了 38.90%和 14.51%。
本研究表明候选基因 GmSPX-RING1 通过负调控大豆毛状根中的大豆磷浓度来影响大豆的磷效率。鉴定出的 SNP 和候选基因在未来的大豆育种计划中可能有助于提高 P 效率。
