ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016
Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 27 citations in OpenAlex.
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- Characterization and genetic differences analysis in adventitious roots development of 38 Populus germplasm resources.Plant molecular biology · 2024Article
- Comprehensive Evaluation of 24 Red Raspberry Varieties in Northeast China Based on Nutrition and Taste.Foods (Basel, Switzerland) · 2022Article
- High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait inInternational journal of molecular sciences · 2021Article
- Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Frontiers in plant science · 2021Article
- Fine Mapping to Identify the Functional Genetic Locus for Red Coloration inFrontiers in plant science · 2020Article
- Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research.BMC genomics · 2019Article
- Article
- Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina).Plant molecular biology · 2018Article
- Mapping and screening of the tomato Stemphylium lycopersici resistance gene, Sm, based on bulked segregant analysis in combination with genome resequencing.BMC plant biology · 2017Article
- Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.).BMC genomics · 2017Article
- Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.).Scientific reports · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (Poncirus trifoliata L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes annotation revealed that the transcripts containing the mutant- and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three genera of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.
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