Identification of loci and candidate gene GmSPX-RING1 responsible for phosphorus efficiency in soybean via genome-wide association analysis

Abstract Background 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. Results 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. Conclusions 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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A genome-wide association analysis implicates SOX6 as a candidate gene for wrist bone mass

Science China Life Sciences ◽

10.1007/s11427-010-4056-7 ◽

2010 ◽

Vol 53 (9) ◽

pp. 1065-1072 ◽

Cited By ~ 10

Author(s):

LiJun Tan ◽

Rong Liu ◽

ShuFeng Lei ◽

Rong Pan ◽

TieLin Yang ◽

...

Keyword(s):

Bone Mass ◽

Candidate Gene ◽

Association Analysis ◽

Genome Wide Association ◽

Genome Wide Association Analysis ◽

Genome Wide ◽

A Genome

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An Integrated Approach of QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame (Sesamum indicum L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.604709 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sovetgul Asekova ◽

Eunyoung Oh ◽

Krishnanand P. Kulkarni ◽

Muhammad Irfan Siddique ◽

Myoung Hee Lee ◽

...

Keyword(s):

Qtl Mapping ◽

Candidate Gene ◽

Candidate Genes ◽

Sesamum Indicum ◽

Genome Wide Association ◽

Phytophthora Blight ◽

Chromosome 10 ◽

Resistant Parent ◽

Exon 2 ◽

Genome Wide

Phytophthora blight (PB) caused by Phytophthora nicotianae is a highly destructive disease in sesame (Sesamum indicum L.). In this study, we used linkage mapping and genome-wide association study (GWAS) to identify quantitative trait loci (QTL) and candidate genes associated with PB resistance. The QTL mapping in 90 RILs of the Goenbaek × Osan cross using genotyping-by-sequencing detected significant QTLs for PB resistance on chromosome 10, explaining 12.79%–13.34% of phenotypic variation. Association of this locus to PB resistance was also revealed through bulked segregant analysis in second RIL population (Goenbaek × Milsung cross) comprising 188 RILs. The GWAS of 87 sesame accessions evaluated against three P. nicotianae isolates identified 29 SNPs on chromosome 10 significantly associated with PB resistance. These SNPs were located within a 0.79 Mb region, which co-located with the QTL intervals identified in RIL populations, and hence scanned for identifying candidate genes. This region contained several defense-related candidate R genes, five of which were selected for quantitative expression analysis. One of these genes, SIN_1019016 was found to show significantly higher expression in the resistant parent compared to that in the susceptible parents and selected RILs. Paired-end sequencing of the gene SIN_1019016 in parental cultivars revealed two synonymous SNPs between Goenbaek and Osan in exon 2 of coding DNA sequence. These results suggested SIN_1019016 as one of the candidate gene conferring PB resistance in sesame. The findings from this study will be useful in the marker-assisted selection as well as the functional analysis of PB resistance candidate gene(s) in sesame.

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PLXNA2 identified as a candidate gene by genome-wide association analysis for mandibular prognathism in human chondrocytes

Biomedical Reports ◽

10.3892/br.2018.1128 ◽

2018 ◽

Author(s):

Takashi Kajii ◽

Akira Oka ◽

Mitsutoki Hatta ◽

Jun Yamazaki ◽

Junro Yamashita ◽

...

Keyword(s):

Candidate Gene ◽

Association Analysis ◽

Genome Wide Association ◽

Human Chondrocytes ◽

Mandibular Prognathism ◽

Genome Wide Association Analysis ◽

Genome Wide

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Population structure and genome-wide association studies in bread wheat for phosphorus efficiency traits using 35 K Wheat Breeder’s Affymetrix array

Scientific Reports ◽

10.1038/s41598-021-87182-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Preman R. Soumya ◽

Amanda J. Burridge ◽

Nisha Singh ◽

Ritu Batra ◽

Renu Pandey ◽

...

Keyword(s):

Bread Wheat ◽

Genome Wide Association Study ◽

Polymorphic Information Content ◽

Association Studies ◽

Snp Array ◽

Genome Wide Association ◽

Phosphorus Efficiency ◽

Genome Wide Association Studies ◽

P Efficiency ◽

Genome Wide

AbstractSoil bioavailability of phosphorus (P) is a major concern for crop productivity worldwide. As phosphatic fertilizers are a non-renewable resource associated with economic and environmental issues so, the sustainable option is to develop P use efficient crop varieties. We phenotyped 82 diverse wheat (Triticum aestivum L.) accessions in soil and hydroponics at low and sufficient P. To identify the genic regions for P efficiency traits, the accessions were genotyped using the 35 K-SNP array and genome-wide association study (GWAS) was performed. The high-quality SNPs across the genomes were evenly distributed with polymorphic information content values varying between 0.090 and 0.375. Structure analysis revealed three subpopulations (C1, C2, C3) and the phenotypic responses of these subpopulations were assessed for P efficiency traits. The C2 subpopulation showed the highest genetic variance and heritability values for numerous agronomically important traits as well as strong correlation under both P levels in soil and hydroponics. GWAS revealed 78 marker-trait associations (MTAs) but only 35 MTAs passed Bonferroni Correction. A total of 297 candidate genes were identified for these MTAs and their annotation suggested their involvement in several biological process. Out of 35, nine (9) MTAs were controlling polygenic trait (two controlling four traits, one controlling three traits and six controlling two traits). These multi-trait MTAs (each controlling two or more than two correlated traits) could be utilized for improving bread wheat to tolerate low P stress through marker-assisted selection (MAS).

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Faculty Opinions recommendation of Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1083881.536824 ◽

2007 ◽

Cited By ~ 1

Author(s):

Terri Beaty

Keyword(s):

Type 2 Diabetes ◽

Association Analysis ◽

Genome Wide Association ◽

Genome Wide Association Analysis ◽

Genome Wide

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Faculty Opinions recommendation of Alpha-T-catenin (CTNNA3) gene was identified as a risk variant for toluene diisocyanate-induced asthma by genome-wide association analysis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1157877.619129 ◽

2009 ◽

Author(s):

Francine Kauffmann ◽

Lidwien Smit

Keyword(s):

Association Analysis ◽

Toluene Diisocyanate ◽

Genome Wide Association ◽

Risk Variant ◽

Genome Wide Association Analysis ◽

Genome Wide

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A Caution in Association of ABO Blood Group with COVID-19

Global Clinical and Translational Research ◽

10.36316/02.0031 ◽

2020 ◽

Cited By ~ 2

Keyword(s):

Gene Cluster ◽

Clinical Outcomes ◽

Blood Group ◽

Association Analysis ◽

Blood Type ◽

Genome Wide Association ◽

Chromosome 3 ◽

Abo Blood Group ◽

Genome Wide Association Analysis ◽

Genome Wide

A comment on Zhao J, Yang Y, Huang H, Li D, Gu D, Lu X, et al. Association of ABO blood group and Covid19 susceptability. medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.03.11.20031096. Zeng X, Fan H, Lu D, Huang F, Meng X, Li Z, et al. Association between ABO blood group and clinical outcomes of Covid19. medRxiv[PREPRINT].2020; https://doi.org/10.1101/2020.04.15.20063107. Zietz M, Tatonetti N. Testing the association between blood type and COVID-19 infection, intubation, and death medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.04.08.20058073. Ellinghaus D, Degenhardt F, Bujanda L, al. e. The ABO blood group and a chromosome 3 gene cluster associate with SRAS-CoV2 respitarory failure in an Italy-Spain genome-wide association analysis. medRxiv. 2020; https://doi.org/10.1101/2020.05.31.20114991.

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