ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2015
Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 90 citations in OpenAlex.
- A near-complete genome assembly of onion resolves its genomic architecture, origin, and evolution.Plant communications · 2026Article
- Mitochondrial-Nuclear Interactions, Co-Transcription, and Adaptive Evolution in Cytoplasmic Male Sterility.Plant, cell & environment · 2026Review
- Integration of bulked segregant analysis and transcriptome sequencing reveals an interaction network associated with cluster buds trait in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Identification of a gene coding for a pentatricopeptide repeat protein as a candidate responsible for theMolecular breeding : new strategies in plant improvement · 2025Article
- Fertility restorer geneHorticulture research · 2024Article
- Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (International journal of molecular sciences · 2023Article
- Genetic Mechanisms for Hybrid Breeding in Vegetable Crops.Plants (Basel, Switzerland) · 2023Review
- Fine mapping and causal gene identification of a novel QTL for early flowering by QTL-seq, Target-seq and RNA-seq in spring oilseed rape.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Two-Step Identification of N-, S-, R- and T-Cytoplasm Types in Onion Breeding Lines Using High-Resolution Melting (HRM)-Based Markers.International journal of molecular sciences · 2023Article
- Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion.Frontiers in plant science · 2023Article
- Molecular marker-based characterization of cytoplasm and restorer of male sterility (Ms) locus in commercially grown onions in India.Molecular biology reports · 2022Article
- Article
- Comparative phylogenomic analyses and co-expression gene network reveal insights in flowering time and aborted meiosis in woody bamboo,Frontiers in plant science · 2022Article
- Development and application of KASP markers associated withPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- The loss of function of HEL, which encodes a cellulose synthase interactive protein, causes helical and vine-like growth of tomato.Horticulture research · 2020Article
- Fine-mapping of the BjPur gene for purple leaf color in Brassica juncea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq.Rice (New York, N.Y.) · 2020Article
- Omics approaches inPeerJ · 2020Article
- A predicted NEDD8 conjugating enzyme gene identified as aHorticulture research · 2020Article
- Rapid identification of a candidate nicosulfuron sensitivity gene (Nss) in maize (Zea mays L.) via combining bulked segregant analysis and RNA-seq.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageA combination of BSA and RNA-seq was performed to identify candidates for the restorer-of-fertility gene in onion. The AcPMS1 involved in DNA mismatch repair was identified as the best candidate. To identify candidate genes of the restorer-of-fertility gene (Ms) responsible for fertility restoration of onion cytoplasmic male-sterility, a combined approach of bulked segregant analysis and RNA-seq was employed. From 32,674 de novo assembled contigs, 430 perfectly homozygous SNPs between male-fertile (MF) and male-sterile (MS) bulks were identified in 141 contigs. After verifying the homozygosity of the SNPs by PCR amplification and sequencing, the SNPs on 139 of the contigs were genotypes for the two recombinants which contained crossover events between the Ms locus and two tightly linked molecular markers. As a result, 30 contigs showing perfect linkage with the Ms locus in the large-sized segregating population were identified. Among them, 14 showed perfect linkage disequilibrium (LD) with the Ms locus, as determined by genotyping 251 domestic breeding lines. Furthermore, molecular markers tagging the 14 contigs also showed almost perfect LD with each other in 124 exotic accessions introduced from 21 countries, except for one accession which contained a crossover event by which the 14 markers were divided into two groups. After sequencing of the full-length cDNA of the 14 contigs showing perfect LD, the deduced amino acids sequences of the MF and MS alleles were compared. Four genes were shown to harbor putative critical amino acid changes in the known domains. Among them, the gene encoding PMS1, involved in the DNA mismatch repair pathway, was assumed to be the best candidate gene responsible for fertility restoration of male-sterility in onion.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.