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Xie YN, Qi QQ, Li WH, Li YL, Zhang Y, Wang HM, Zhang YF, Ye ZH, Guo DP, Qian Q, Zhang ZF, Yan N. Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris. FRONTIERS IN PLANT SCIENCE 2023; 14:1183739. [PMID: 37324716 PMCID: PMC10266587 DOI: 10.3389/fpls.2023.1183739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Wild rice (Zizania spp.), an aquatic grass belonging to the subfamily Gramineae, has a high economic value. Zizania provides food (such as grains and vegetables), a habitat for wild animals, and paper-making pulps, possesses certain medicinal values, and helps control water eutrophication. Zizania is an ideal resource for expanding and enriching a rice breeding gene bank to naturally preserve valuable characteristics lost during domestication. With the Z. latifolia and Z. palustris genomes completely sequenced, fundamental achievements have been made toward understanding the origin and domestication, as well as the genetic basis of important agronomic traits of this genus, substantially accelerating the domestication of this wild plant. The present review summarizes the research results on the edible history, economic value, domestication, breeding, omics research, and important genes of Z. latifolia and Z. palustris over the past decades. These findings broaden the collective understanding of Zizania domestication and breeding, furthering human domestication, improvement, and long-term sustainability of wild plant cultivation.
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Affiliation(s)
- Yan-Ning Xie
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian-Qian Qi
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wan-Hong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ya-Li Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yu Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Hui-Mei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Fen Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Zi-Hong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - De-Ping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Fukai E, Yoshikawa M, Shah N, Sandal N, Miyao A, Ono S, Hirakawa H, Akyol TY, Umehara Y, Nonomura KI, Stougaard J, Hirochika H, Hayashi M, Sato S, Andersen SU, Okazaki K. Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1397-1410. [PMID: 35792830 DOI: 10.1111/tpj.15896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.
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Affiliation(s)
- Eigo Fukai
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Manabu Yoshikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Niraj Shah
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Akio Miyao
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Seijiro Ono
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hideki Hirakawa
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Yosuke Umehara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Ken-Ichi Nonomura
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Hirohiko Hirochika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Makoto Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Shusei Sato
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | | | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
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Hu Y, Mao B, Xia Y, Peng Y, Zhang D, Tang L, Shao Y, Li Y, Zhao B. Spike-Stalk Injection Method Causes Extensive Phenotypic and Genotypic Variations for Rice Germplasm. FRONTIERS IN PLANT SCIENCE 2020; 11:575373. [PMID: 33101344 PMCID: PMC7546333 DOI: 10.3389/fpls.2020.575373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Genetic diversities or favorable genes within distantly related species are the important resources for crop genetic improvement and germplasm innovation. Spike-Stalk injection method (SSI) has long been applied in rice genetic improvement by directly introducing genetic materials from non-mating donor species, while its inheritance patterns and the underlying mechanisms are poorly elucidated. In this study, a rice variant ERV1 with improved yield-related traits was screened out in the way of introducing genomic DNA of Oryza eichingeri (2n=24, CC genome) into RH78 (Oryza sativa L. 2n=24, AA genome) using SSI method. Genome-wide comparison revealed that the genomic heterozygosity of ERV1 was approximately 8-fold higher than RH78. Restriction-site associated DNA sequencing technology (RAD-seq) and association analysis of the ERV1 inbred F2 population identified 5 quantitative trait loci (QTLs) regions responsible for these yield-related traits, and found that genomic heterozygosity of ERV1 inbred lines was significantly lower than ERV1, while spontaneous mutation rate of the ERV1 inbred lines was significantly higher than ERV1. Our results preliminarily uncovered the inheritance patterns of SSI variant rice, and the potential genomic regions for traits changes, which yielded novel insights into the mechanisms of SSI method, and may accelerate our understanding of plant genome evolution, domestication, and speciation in nature.
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Affiliation(s)
- Yuanyi Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Molecular Breeding Laboratory, National Innovation Center of Saline-Alkali Tolerant Rice in Sanya, Sanya, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Yumei Xia
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Yan Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Dan Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Yaokui Li
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
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Meng WL, Zhao MJ, Yang XB, Zhang AX, Wang NN, Xu ZS, Ma J. Examination of Genomic and Transcriptomic Alterations in a Morphologically Stable Line, MU1, Generated by Intergeneric Pollination. Genes (Basel) 2020; 11:genes11020199. [PMID: 32075264 PMCID: PMC7073617 DOI: 10.3390/genes11020199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
Interspecific hybridization creates genetic variation useful for crop improvement. However, whether pollen from a different genus affects the genomic stability and/or transcriptome of the recipient species during intergeneric pollination has not been investigated. Here, we crossed japonica rice cv. Z12 with the maize accession B73 (pollen donor) and obtained a morphologically stable line, MU1, exhibiting moderate dwarfism, higher tiller number, and increased grain weight compared with Z12. To reveal the genetic basis of these morphological changes in MU1, we performed whole-genome resequencing of MU1 and Z12. Compared with Z12, MU1 showed 107,250 single nucleotide polymorphisms (SNPs) and 23,278 insertion/deletions (InDels). Additionally, 5'-upstream regulatory regions (5'UTRs) of 429 and 309 differentially expressed genes (DEGs) in MU1 contained SNPs and InDels, respectively, suggesting that a subset of these DEGs account for the variation in 5'UTRs. Transcriptome analysis revealed 2190 DEGs in MU1 compared with Z12. Genes up-regulated in MU1 were mainly involved in photosynthesis, generation of precursor metabolites, and energy and cellular biosynthetic processes; whereas those down-regulated in MU1 were involved in plant hormone signal transduction pathway and response to stimuli and stress processes. Quantitative PCR (qPCR) further identified the expression levels of the up- or down-regulated gene in plant hormone signal transduction pathway. The expression level changes of plant hormone signal transduction pathway may be significant for plant growth and development. These findings suggest that mutations caused by intergeneric pollination could be the important reason for changes of MU1 in agronomic traits.
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Affiliation(s)
- Wei-Long Meng
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Meng-Jie Zhao
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China;
| | - Xiang-Bo Yang
- College of Agronomy, Jilin Agricultural Science and Technology University, Jilin 132101, China;
| | - An-Xing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Ning-Ning Wang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Zhao-Shi Xu
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China;
- Correspondence: (Z.-S.X.); (J.M.)
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
- Correspondence: (Z.-S.X.); (J.M.)
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5
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Cho J, Benoit M, Catoni M, Drost HG, Brestovitsky A, Oosterbeek M, Paszkowski J. Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. NATURE PLANTS 2019; 5:26-33. [PMID: 30531940 PMCID: PMC6366555 DOI: 10.1038/s41477-018-0320-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 11/07/2018] [Indexed: 05/02/2023]
Abstract
Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. Such studies provide important 'snapshots' reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5' LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.
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Affiliation(s)
- Jungnam Cho
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China.
| | - Matthias Benoit
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Matthijs Oosterbeek
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Laboratory of Nematology, Wageningen University, Wageningen, the Netherlands
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Radachowka 37, Kolbiel, Poland.
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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Valliyodan B, Dan Qiu, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, Nguyen HT. Landscape of genomic diversity and trait discovery in soybean. Sci Rep 2016; 6:23598. [PMID: 27029319 PMCID: PMC4814817 DOI: 10.1038/srep23598] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/18/2016] [Indexed: 02/08/2023] Open
Abstract
Cultivated soybean [Glycine max (L.) Merr.] is a primary source of vegetable oil and protein. We report a landscape analysis of genome-wide genetic variation and an association study of major domestication and agronomic traits in soybean. A total of 106 soybean genomes representing wild, landraces, and elite lines were re-sequenced at an average of 17x depth with a 97.5% coverage. Over 10 million high-quality SNPs were discovered, and 35.34% of these have not been previously reported. Additionally, 159 putative domestication sweeps were identified, which includes 54.34 Mbp (4.9%) and 4,414 genes; 146 regions were involved in artificial selection during domestication. A genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Dan Qiu
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Peng Zeng
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiaying Huang
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Lu Dai
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Chengxuan Chen
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Yanjun Li
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Trupti Joshi
- Department of Molecular Microbiology and Immunology and Medical Research Office, School of Medicine, University of Missouri, Columbia, 65212
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, 65211, USA
| | - Li Song
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Tri D. Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Theresa A. Musket
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
| | - Dong Xu
- Department of Molecular Microbiology and Immunology and Medical Research Office, School of Medicine, University of Missouri, Columbia, 65212
| | - J. Grover Shannon
- Division of Plant Sciences and NCSB, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA
| | - Cheng Shifeng
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA
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Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza). PLoS One 2015. [PMID: 26208215 PMCID: PMC4514751 DOI: 10.1371/journal.pone.0132911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica) and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown. Methodology/Principal Findings We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH) and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs) and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i) all three triploid hybrids are stable in both chromosome number and gross structure; (ii) stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii) alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv) transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner. Conclusions/Significance Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might provide a rich resource of genetic and epigenetic diversities for potential utilization in rice genetic improvements.
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Zhang D, Wang Z, Wang N, Gao Y, Liu Y, Wu Y, Bai Y, Zhang Z, Lin X, Dong Y, Ou X, Xu C, Liu B. Tissue culture-induced heritable genomic variation in rice, and their phenotypic implications. PLoS One 2014; 9:e96879. [PMID: 24804838 PMCID: PMC4013045 DOI: 10.1371/journal.pone.0096879] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/12/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Somaclonal variation generally occurs in plants regenerated from tissue culture. However, fundamental issues regarding molecular characteristics, mutation rates and mutation spectra of plant somatic variation as well as their phenotypic relevance have been addressed only recently. Moreover, these studies have reported highly discrepant results in different plant species and even in the same plant genotype. METHODOLOGY/PRINCIPAL FINDINGS We investigated heritable genomic variation induced by tissue culture in rice by whole genome re-sequencing of an extensively selfed somaclonal line (TC-reg-2008) and its wild type (WT) donor (cv. Hitomebore). We computed the overall mutation rate, single nucleotide polymorphisms (SNPs), small scale insertions/deletions (Indels) and mobilization of transposable elements (TEs). We assessed chromosomal distribution of the various types of genomic variations, tested correlations between SNPs and Indels, and examined concomitancy between TE activity and its cytosine methylation states. We also performed gene ontology (GO) analysis of genes containing nonsynonymous mutations and large-effect mutations, and assayed effects of the genomic variations on phenotypes under both normal growing condition and several abiotic stresses. We found that heritable somaclonal genomic variation occurred extensively in rice. The genomic variations distributed non-randomly across each of the 12 rice chromosomes, and affected a large number of functional genes. The phenotypic penetrance of the genomic variations was condition-dependent. CONCLUSIONS/SIGNIFICANCE Tissue culture is a potent means to generate heritable genetic variations in rice, which bear distinct difference at least in space (chromosomal distribution) from those occurred under natural settings. Our findings have provided new information regarding the mutation rate and spectrum as well as chromosomal distribution pattern of somaclonal variation in rice. Our data also suggest that rice possesses a strong capacity to canalize genetic variations under normal growing conditions to maintain phenotypic robustness, which however can be released by certain abiotic stresses to generate variable phenotypes.
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Affiliation(s)
- Di Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Yang Gao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuzhu Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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