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Jia X, Zhang Y, Zhang Q, Zhao Q, Traw MB, Wang L, Tian D, Wang C, Yang S. High-resolution insight into recombination events at the SD1 locus in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:683-692. [PMID: 30417595 DOI: 10.1111/tpj.14154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/28/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Recombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semi-dwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F2 progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of ~3.3 × 10-4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotype-related functional genes, which are abundant in other plant genomes.
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Affiliation(s)
- Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qijun Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants. Int J Mol Sci 2018; 19:ijms19123758. [PMID: 30486351 PMCID: PMC6320998 DOI: 10.3390/ijms19123758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022] Open
Abstract
Hybridization has been routinely practiced in agriculture to enhance the crop yield. Principally, it can cause hybrid vigor where hybrid plants display increased size, biomass, fertility, and resistance to diseases, when compared to their parents. During hybridization, hybrid offspring receive a genomic shock due to mixing of distant parental genomes, which triggers a myriad of genomic rearrangements, e.g., transpositions, genome size changes, chromosomal rearrangements, and other effects on the chromatin. Recently, it has been reported that, besides genomic rearrangements, hybridization can also alter the somatic mutation rates in plants. In this review, we provide in-depth insights about hybridization triggered genomic rearrangements and somatic mutations in plants.
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Zhang Y, Li S, Xue S, Yang S, Huang J, Wang L. Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes. FRONTIERS IN PLANT SCIENCE 2018; 9:473. [PMID: 29692796 PMCID: PMC5902711 DOI: 10.3389/fpls.2018.00473] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 03/26/2018] [Indexed: 05/03/2023]
Abstract
The ERECTA family genes (ERfs) have been found to play diverse functions in Arabidopsis, including controlling cell proliferation and cell growth, regulating stomata patterning, and responding to various stresses. This wide range of functions has rendered them as a potential candidate for crop improvement. However, information on their functional roles, particularly their morphological impact, in crop genomes, such as rice, is limited. Here, through evolutionary prediction, we first depict the evolutionary trajectory of the ER family, and show that the ER family is actually highly conserved across different species, suggesting that most of their functions may also be observed in other plant species. We then take advantage of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats-associated nuclease 9) system to assess their morphological impact on one of the most important crops, rice. Loss-of-function mutants of OsER1 and OsER2 display shortened plant stature and reduced panicle size, suggesting they possibly also functioned in regulating cell proliferation and cell growth in rice. In addition to functions similar to that in Arabidopsis, we also find clues that rice ERfs may play unique functional roles. The OsER2 displayed more severe phenotypic changes than OsER1, indicating putative differentiation in their functions. The OsERL might be of essential in its function, and the proper function of all three rice ER genes might be dependent of their genetic background. Future investigations relating to these functions are key to exploiting ERfs in crop development.
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Affiliation(s)
| | | | | | | | - Ju Huang
- *Correspondence: Ju Huang, Long Wang,
| | - Long Wang
- *Correspondence: Ju Huang, Long Wang,
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