ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2022
Identification of closely associated SNPs and candidate genes with seed size and shape via deep re-sequencing GWAS in soybean.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Integrative genomics and zero-shot deep learning-based phenotyping reveal the genetic architecture of seed traits in mungbean (Vigna radiata L.).The plant genome · 2026Article
- Identification of candidate loci regulating seed-associated traits in soybean using genome-wide association study and image-based high-throughput phenotyping.Frontiers in plant science · 2026Article
- Genome-wide detection of superior haplotypes for seed oil and protein content in Northeast China soybean (Frontiers in plant science · 2026Article
- Integrative genome-wide association and haplotype-based analyses reveal genetic structure and local adaptation in Korean landrace soybeans.BMC plant biology · 2025Article
- Image-based GWAS identifies the genetic architecture of seed-related traits in a soybean mutant population.Molecular breeding : new strategies in plant improvement · 2025Article
- Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Molecular breeding : new strategies in plant improvement · 2025Article
- Genome-wide association study and fine-mapping identify a major quantitative trait locus controlling hundred-seed weight in soybean.Frontiers in plant science · 2025Article
- Exploring novel SNPs and candidate genes associated with seed allometry inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum).Plant biotechnology journal · 2024Article
- Genome resequencing reveals genetic loci and genes conferring resistance to SMV-SC8 in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.Frontiers in plant science · 2023Review
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
key messageA soybean natural population was genotyped by deep re-sequencing and phenotyped for six seed size- and shape-related traits under six environments to identify closely associated SNPs and candidate genes. Seed size and shape are important determining factors for soybean yield formation, while their genetic basis and molecular mechanism are still largely unknown, which seriously constrains the increasing of soybean yield at present. In view of this, a natural population was genotyped via the deep re-sequencing technique (~ 20 ×) and phenotyped for six related traits under six environments. In total, 154 SNPs were closely associated with seed length across diverse environments, and 323, 483, 565, 394 and 2038 SNPs were closely associated with seed width, seed diameter, seed circumference, seed area and ratio of length to width under multiple environments. Moreover, 98.70%, 96.28%, 48.24%, 85.13%, 97.21% and 98.58% of them were further demonstrated by the BLUP and mean values of the related traits. Furthermore, 218 genes flanking the associated SNPs on chromosomes 6 and 10 were analyzed for DNA mutations and RNA expressions through SNP alleles and transcriptome data, simultaneously. The candidate genes, Glyma.10G035200 (Sn1-specific diacylglycerol lipase), Glyma.10G035400 (transcription factor) and Glyma.10G058200 (phenylalanine ammonia-lyase), were discovered to relate with the seed size and shape for their different DNA sequences or differential RNA expressions among soybean varieties at five seed developmental stages. Thus, these closely associated SNPs and related genes provide novel insights and useful information for the seed size and shape genetic basis dissection and breeding improvement in soybean.
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