Dataset Information

Genome-Wide Association Studies of Photosynthetic Traits Related to Phosphorus Efficiency in Soybean.

ABSTRACT: Photosynthesis is the basis of plant growth and development, and is seriously affected by low phosphorus (P) stress. However, few studies have reported for the genetic foundation of photosynthetic response to low P stress in soybean. To address this issue, 219 soybean accessions were genotyped by 292,035 high-quality single nucleotide polymorphisms (SNPs) and phenotyped under normal and low P conditions in 2015 and 2016. These datasets were used to identify quantitative trait nucleotides (QTNs) for photosynthesis-related traits using mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA, and pKWmEB methods. As a result, 159 QTNs within 31 genomic regions were found to be associated with four photosynthesis-related traits under different P stress conditions. Among the 31 associated regions, five (q7-2, q8-1, q9, q13-1, and q20-2) were detected commonly under both normal and low P conditions, indicating the insensitivity of these candidate genes to low P stress; five were detected only under normal P condition, indicating the sensitivity of these candidate genes to low P stress; six were detected only under low P condition, indicating the tolerantness of these candidate genes to low P stress; 20 were reported in previous studies. Around the 159 QTNs, 52 candidate genes were mined. These results provide the important information for marker-assisted breeding in soybean and further reveal the basis for the application of P tolerance to photosynthetic capacity.

SUBMITTER: Lu H

PROVIDER: S-EPMC6122521 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Genome-Wide Association Studies of Photosynthetic Traits Related to Phosphorus Efficiency in Soybean.

Lü Haiyan H Yang Yuming Y Li Haiwang H Liu Qijia Q Zhang Jianjun J Yin Junyi J Chu Shanshan S Zhang Xiangqian X Yu Kaiye K Lv Lingling L Chen Xi X Zhang Dan D

Frontiers in plant science 20180828

Photosynthesis is the basis of plant growth and development, and is seriously affected by low phosphorus (P) stress. However, few studies have reported for the genetic foundation of photosynthetic response to low P stress in soybean. To address this issue, 219 soybean accessions were genotyped by 292,035 high-quality single nucleotide polymorphisms (SNPs) and phenotyped under normal and low P conditions in 2015 and 2016. These datasets were used to identify quantitative trait nucleotides (QTNs) ...[more]

PMID: 30210514

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Project description:BackgroundPhosphorus (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.ResultsGenome-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.ConclusionsThis 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.

Dataset Information

Genome-Wide Association Studies of Photosynthetic Traits Related to Phosphorus Efficiency in Soybean.

Publications

Genome-Wide Association Studies of Photosynthetic Traits Related to Phosphorus Efficiency in Soybean.

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