Identification of loci and candidate gene GmSPX-RING1 responsible for phosphorus efficiency in soybean via genome-wide association analysis.
Identification of loci and candidate gene GmSPX-RING1 responsible for phosphorus efficiency in soybean via genome-wide association analysis.
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DOI：
10.1186/s12864-020-07143-3
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发表时间：
2020-10-19
期刊：
影响因子：
4.4
通讯作者：
Yu D
中科院分区：
文献类型：
--
作者：
Du W;Ning L;Liu Y;Zhang S;Yang Y;Wang Q;Chao S;Yang H;Huang F;Cheng H;Yu D
磷（P）是维持作物高生物量和产量的重要元素。大豆 [Glycine max (L.) Merr.] 在生长和发育过程中需要大量的磷。提高磷效率和鉴定磷效率基因是提高大豆产量的重要策略。使用 NJAU 355 K SoySNP 阵列进行全基因组关联分析 (GWAS)，以确定与 211 个栽培大豆自然群体的三个芽磷效率相关性状显着相关的单核苷酸多态性 (SNP)，以及这些性状在正常磷 (+P) 条件和磷缺乏 (-P) 条件下的相对值。总共鉴定出 155 个 SNP 与 P 效率相关性状显着相关。与地上部干重显着相关的SNP在11号染色体上形成SNP簇，而与地上部磷浓度显着相关的SNP在10号染色体上形成SNP簇。基于12个SNP鉴定出13个单倍型，并认为Hap9是最佳单倍型。在两次水培实验中，位于 10 号染色体上的四个 SNP（AX-93636685、AX-93636692、AX-93932863 和 AX-93932874）被鉴定与 +P 条件下芽磷浓度显着相关。在这四个SNP中，其中两个（AX-93636685和AX-93932874）也与两种磷条件下地上部磷浓度的相对值显着相关。在Glyma.10 g018800的5'非翻译区内检测到1个SNP AX-93932874，其含有SPX和RING结构域，命名为GmSPX-RING1。此外，还开展了GmSPX-RING1在大豆毛状根转化中的功能研究。与对照相比，+P条件下过表达GmSPX-RING1转基因毛状根的P浓度显着降低了32.75%；相比之下，GmSPX-RING1转基因毛状根的RNA干扰中的P浓度在+P和-P条件下分别增加了38.90和14.51%。本研究表明候选基因GmSPX-RING1通过负向调节大豆毛状根中大豆磷浓度影响大豆磷效率。所确定的 SNP 和候选基因应该有可能提高未来大豆育种计划中的磷效率。
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.
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