Genome-wide association study for biomass accumulation traits in soybean

Wang, Xin; Zhou, Shaodong; Wang, Jie; Lin, Wenxin; Yao, Xiaolei; Su, Jiaqing; Li, Haiyang; Fang, Chao; Kong, Fanjiang; Guan, Yuefeng

doi:10.1007/s11032-023-01380-6

Cited by 5 publications

(2 citation statements)

References 65 publications

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“…Within these genetic loci, seven instances of domestication sweep and six improvement sweeps have been identified. Notably, Glyma.05G047900, encoding a purple acid phosphatase, has emerged as a robust candidate gene for enhancing biomass, offering promising prospects for the future of soybean breeding efforts [42]. Previous research on mungbean identified a total of 71 protein-coding genes.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

Hakla,

Sharma,

Urfan

et al. 2024

Plants

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Phosphate (P) is a crucial macronutrient for normal plant growth and development. The P availability in soils is a limitation factor, and understanding genetic factors playing roles in plant adaptation for improving P uptake is of great biological importance. Genome-wide association studies (GWAS) have become indispensable tools in unraveling the genetic basis of complex traits in various plant species. In this study, a comprehensive GWAS was conducted on diverse tomato (Solanum lycopersicum L.) accessions grown under normal and low P conditions for two weeks. Plant traits such as shoot height, primary root length, plant biomass, shoot inorganic content (SiP), and root inorganic content (RiP) were measured. Among several models of GWAS tested, the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) models were used for the identification of single nucleotide polymorphisms (SNPs). Among all the traits analyzed, significantly associated SNPs were recorded for PB, i.e., 1 SNP (SSL4.0CH10_49261145) under control P, SiP, i.e., 1 SNP (SSL4.0CH08_58433186) under control P and 1 SNP (SSL4.0CH08_51271168) under low P and RiP i.e., 2 SNPs (SSL4.0CH04_37267952 and SSL4.0CH09_4609062) under control P and 1 SNP (SSL4.0CH09_3930922) under low P condition. The identified SNPs served as genetic markers pinpointing regions of the tomato genome linked to P-responsive traits. The novel candidate genes associated with the identified SNPs were further analyzed for their protein-protein interactions using STRING. The study provided novel candidate genes, viz. Solyc10g050370 for PB under control, Solyc08g062490, and Solyc08g062500 for SiP and Solyc09g010450, Solyc09g010460, Solyc09g010690, and Solyc09g010710 for RiP under low P condition. These findings offer a glimpse into the genetic diversity of tomato accessions’ responses to P uptake, highlighting the potential for tailored breeding programs to develop P-efficient tomato varieties that could adapt to varying soil conditions, making them crucial for sustainable agriculture and addressing global challenges, such as soil depletion and food security.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

Hakla,

Sharma,

Urfan

et al. 2024

Plants

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show abstract

“…For example, twenty significant SNPs associated with PN have been identified from 211 germplasm by GWAS, and three stable QTL regions were on chromosomes 4, 18 and 20 ( Bhat et al., 2022 ). Wang et al. (2023) used a diverse panel, including 121 wild soybeans, 207 landraces, and 231 improved cultivars to perform GWAS on BM and identified ten important loci, encompassing 47 putative candidate genes.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association mapping for yield-related traits in soybean (Glycine max) under well-watered and drought-stressed conditions

Li,

Cao,

Wang

et al. 2023

Front. Plant Sci.

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Soybean (Glycine max) productivity is significantly reduced by drought stress. Breeders are aiming to improve soybean grain yields both under well-watered (WW) and drought-stressed (DS) conditions, however, little is known about the genetic architecture of yield-related traits. Here, a panel of 188 soybean germplasm was used in a genome wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers linked to yield-related traits including pod number per plant (PN), biomass per plant (BM) and seed weight per plant (SW). The SLAF-seq genotyping was conducted on the population and three phenotype traits were examined in WW and DS conditions in four environments. Based on best linear unbiased prediction (BLUP) data and individual environmental analyses, 39 SNPs were significantly associated with three soybean traits under two conditions, which were tagged to 26 genomic regions by linkage disequilibrium (LD) analysis. Of these, six QTLs qPN-WW19.1, qPN-DS8.8, qBM-WW1, qBM-DS17.4, qSW-WW4 and qSW-DS8 were identified controlling PN, BM and SW of soybean. There were larger proportions of favorable haplotypes for locus qPN-WW19.1 and qSW-WW4 rather than qBM-WW1, qBM-DS17.4, qPN-DS8.8 and qSW-DS8 in both landraces and improved cultivars. In addition, several putative candidate genes such as Glyma.19G211300, Glyma.17G057100 and Glyma.04G124800, encoding E3 ubiquitin-protein ligase BAH1, WRKY transcription factor 11 and protein zinc induced facilitator-like 1, respectively, were predicted. We propose that the further exploration of these locus will facilitate accelerating breeding for high-yield soybean cultivars.

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Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean

Li,

Zhao,

Tang

et al. 2024

Theor Appl Genet

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Genome-wide association study for biomass accumulation traits in soybean

Cited by 5 publications

References 65 publications

Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

Genome-wide association mapping for yield-related traits in soybean (Glycine max) under well-watered and drought-stressed conditions

Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean

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