ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max).
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Dissecting genetic architecture of flowering and maturity traits in soybean using GWAS in Indian environment.BMC plant biology · 2025Article
- Identification of novel candidate genes for regulating oil composition in soybean seeds under environmental stresses.Frontiers in plant science · 2025Article
- Identification of major QTLs for seed vigor and growth-related traits using a biparental population in soybean.Frontiers in genetics · 2025Article
- A single-nucleotide insertion in Rxp confers durable resistance to bacterial pustule in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Identification of quantitative trait loci for lodging and related agronomic traits in soybean (Glycine max [L.] Merr.).BMC genomics · 2024Article
- V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data.Breeding science · 2023Article
- Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat.Nature plants · 2023Article
- The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.BMC genomics · 2023Article
- Deciphering the roles of unknown/uncharacterized genes in plant development and stress responses.Frontiers in plant science · 2023Review
- Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- PhenGenVar: A User-Friendly Genetic Variant Detection and Visualization Tool for Precision Medicine.Journal of personalized medicine · 2022Article
- Validation of AmpliSeq NGS Panel forLife (Basel, Switzerland) · 2022Article
- Genetic control and allele variation among soybean maturity groups 000 through IX.The plant genome · 2021Article
- Rapid excavating aMolecular breeding : new strategies in plant improvement · 2021Article
- Evolutionary QTL-allele changes in main stem node number among geographic and seasonal subpopulations of Chinese cultivated soybeans.Molecular genetics and genomics : MGG · 2021Article
- Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Targeted amplicon sequencing + next-generation sequencing-based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum).BMC plant biology · 2021Article
- Impacts of genomic research on soybean improvement in East Asia.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication.Nature genetics · 2020Article
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5 authors.
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Abstract
Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci-E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes-E2, E3, Dt1, and two-component response regulator-can explain 51.1-52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.
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