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Bhattacharya J, Nitnavare RB, Bhatnagar-Mathur P, Reddy PS. Cytoplasmic male sterility-based hybrids: mechanistic insights. PLANTA 2024; 260:100. [PMID: 39302508 DOI: 10.1007/s00425-024-04532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 09/15/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION A comprehensive understanding of the nucleocytoplasmic interactions that occur between genes related to the restoration of fertility and cytoplasmic male sterility (CMS) provides insight into the development of hybrids of important crop species. Modern biotechnological techniques allow this to be achieved in an efficient and quick manner. Heterosis is paramount for increasing the yield and quality of a crop. The development of hybrids for achieving heterosis has been well-studied and proven to be robust and efficient. Cytoplasmic male sterility (CMS) has been explored extensively in the production of hybrids. The underlying mechanisms of CMS include the role of cytotoxic proteins, PCD of tapetal cells, and improper RNA editing of restoration factors. On the other hand, the restoration of fertility is caused by the presence of restorer-of-fertility (Rf) genes or restorer genes, which inhibit the effects of sterility-causing genes. The interaction between mitochondria and the nuclear genome is crucial for several regulatory pathways, as observed in the CMS-Rf system and occurs at the genomic, transcriptional, post-transcriptional, translational, and post-translational levels. These CMS-Rf mechanisms have been validated in several crop systems. This review aims to summarize the nucleo-mitochondrial interaction mechanism of the CMS-Rf system. It also sheds light on biotechnological interventions, such as genetic engineering and genome editing, to achieve CMS-based hybrids.
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Affiliation(s)
- Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, 500007, India
| | - Rahul B Nitnavare
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, Nottingham, LE12 5RD, UK
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
- Plant Breeding & Genetics Laboratory of United Nation, International Atomic Energy Agency, 1400, Vienna, Austria.
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
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Dehaene N, Boussardon C, Andrey P, Charif D, Brandt D, Gilouppe Taillefer C, Nietzel T, Ricou A, Simon M, Tran J, Vezon D, Camilleri C, Arimura SI, Schwarzländer M, Budar F. The mitochondrial orf117Sha gene desynchronizes pollen development and causes pollen abortion in Arabidopsis Sha cytoplasmic male sterility. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4851-4872. [PMID: 38733289 DOI: 10.1093/jxb/erae214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024]
Abstract
Cytoplasmic male sterility (CMS) is of major agronomical relevance in hybrid breeding. In gametophytic CMS, abortion of pollen is determined by the grain genotype, while in sporophytic CMS, it is determined by the mother plant genotype. While several CMS mechanisms have been dissected at the molecular level, gametophytic CMS has not been straightforwardly accessible. We used the gametophytic Sha-CMS in Arabidopsis to characterize the cause and process of pollen abortion by implementing in vivo biosensing in single pollen and mitoTALEN mutagenesis. We obtained conclusive evidence that orf117Sha is the CMS-causing gene, despite distinct characteristics from other CMS genes. We measured the in vivo cytosolic ATP content in single pollen, followed pollen development, and analyzed pollen mitochondrial volume in two genotypes that differed only by the presence of the orf117Sha locus. Our results showed that the Sha-CMS is not triggered by ATP deficiency. Instead, we observed desynchronization of a pollen developmental program. Pollen death occurred independently in pollen grains at diverse stages and was preceded by mitochondrial swelling. We conclude that pollen death is grain-autonomous in Sha-CMS and propose that mitochondrial permeability transition, which was previously described as a hallmark of developmental and environmental-triggered cell death programs, precedes pollen death in Sha-CMS.
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Affiliation(s)
- Noémie Dehaene
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Clément Boussardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Delphine Charif
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Dennis Brandt
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Clémence Gilouppe Taillefer
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Thomas Nietzel
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Anthony Ricou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Matthieu Simon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Joseph Tran
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Daniel Vezon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Christine Camilleri
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Françoise Budar
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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3
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Wang M, Yu W, Yang J, Hou Z, Li C, Niu Z, Zhang B, Xue Q, Liu W, Ding X. Mitochondrial genome comparison and phylogenetic analysis of Dendrobium (Orchidaceae) based on whole mitogenomes. BMC PLANT BIOLOGY 2023; 23:586. [PMID: 37993773 PMCID: PMC10666434 DOI: 10.1186/s12870-023-04618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Mitochondrial genomes are essential for deciphering the unique evolutionary history of seed plants. However, the rules of their extreme variation in genomic size, multi-chromosomal structure, and foreign sequences remain unresolved in most plant lineages, which further hindered the application of mitogenomes in phylogenetic analyses. RESULTS Here, we took Dendrobium (Orchidaceae) which shows the great divergence of morphology and difficulty in species taxonomy as the study focus. We first de novo assembled two complete mitogenomes of Dendrobium wilsonii and Dendrobium henanense that were 763,005 bp and 807,551 bp long with multichromosomal structures. To understand the evolution of Dendrobium mitogenomes, we compared them with those of four other orchid species. The results showed great variations of repetitive and chloroplast-derived sequences in Dendrobium mitogenomes. Moreover, the intergenic content of Dendrobium mitogenomes has undergone expansion during evolution. We also newly sequenced mitogenomes of 26 Dendrobium species and reconstructed phylogenetic relationships of Dendrobium based on genomic mitochondrial and plastid data. The results indicated that the existence of chloroplast-derived sequences made the mitochondrial phylogeny display partial characteristics of the plastid phylogeny. Additionally, the mitochondrial phylogeny provided new insights into the phylogenetic relationships of Dendrobium species. CONCLUSIONS Our study revealed the evolution of Dendrobium mitogenomes and the potential of mitogenomes in deciphering phylogenetic relationships at low taxonomic levels.
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Grants
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
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Affiliation(s)
- Mengting Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, China
| | - Wenhui Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenyu Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chao Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Benhou Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Zhao Z, Ding Z, Huang J, Meng H, Zhang Z, Gou X, Tang H, Xie X, Ping J, Xiao F, Liu YG, Xie Y, Chen L. Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding. Nat Commun 2023; 14:7333. [PMID: 37957162 PMCID: PMC10643609 DOI: 10.1038/s41467-023-43009-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Cytoplasmic male sterility (CMS) lines are important for breeding hybrid crops, and utilization of CMS lines requires strong fertility restorer (Rf) genes. Rf4, a major Rf for Wild-Abortive CMS (CMS-WA), has been cloned in rice. However, the Rf4 evolution and formation of CMS-WA/Rf system remain elusive. Here, we show that the Rf4 locus emerges earlier than the CMS-WA gene WA352 in wild rice, and 69 haplotypes of the Rf4 locus are generated in the Oryza genus through the copy number and sequence variations. Eight of these haplotypes of the Rf4 locus are enriched in modern rice cultivars during natural and human selections, whereas non-functional rf4i is preferentially selected for breeding current CMS-WA lines. We further verify that varieties carrying two-copy Rf4 haplotype have stronger fertility restoration ability and are widely used in three-line hybrid rice breeding. Our findings increase our understanding of CMS/Rf systems and will likely benefit crop breeding.
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Affiliation(s)
- Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zhi Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jingjing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Hengjun Meng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zixu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xin Gou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Huiwu Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jingyao Ping
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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5
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Zhou Q, Ni Y, Li J, Huang L, Li H, Chen H, Liu C. Multiple configurations of the plastid and mitochondrial genomes of Caragana spinosa. PLANTA 2023; 258:98. [PMID: 37831319 DOI: 10.1007/s00425-023-04245-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
MAIN CONCLUSION In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes. Caragana spinosa belongs to the Papilionoidea subfamily and has significant pharmaceutical value. To explore the possible interaction between the organelle genomes, we assembled and analyzed the plastome and mitogenome of C. spinosa using the Illumina and Nanopore DNA sequencing data. The plastome of C. spinosa was 129,995 bp belonging to the inverted repeat lacking clade (IRLC), which contained 77 protein-coding genes, 29 tRNA genes, and four rRNA genes. The mitogenome was 378,373 bp long and encoded 54 unique genes, including 33 protein-coding, three ribosomal RNA (rRNA), and 18 transfer RNA (tRNA) genes. In addition to the single circular conformation, alternative conformations mediated by one and four repetitive sequences in the plastome and mitogenome were identified and validated, respectively. The inverted repeat (PDR12, the 12th dispersed repeat sequence in C. spinosa plastome) of plastome mediating recombinant was conserved in the genus Caragana. Furthermore, we identified 14 homologous fragments by comparing the sequences of mitogenome and plastome, including eight complete tRNA genes. A phylogenetic analysis of protein-coding genes extracted from the plastid and mitochondrial genomes revealed congruent topologies. Analyses of sequence divergence found one intergenic region, trnN-GUU-ycf1, exhibiting a high degree of variation, which can be used to develop novel molecular markers to distinguish the nine Caragana species accurately. This plastome and mitogenome of C. spinosa could provide critical information for the molecular breeding of C. spinosa and be used as a reference genome for other species of Caragana. In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes.
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Affiliation(s)
- Qingqing Zhou
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Jingling Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Husheng Li
- Shenzhou Space Biotechnology Group, Beijing, 100190, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
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Cai W, Li W, Duan L, Chen Y, Zhang F, Hu B, Xie J. Genetic Analysis of Novel Fertility Restoration Genes ( qRf3 and qRf6) in Dongxiang Wild Rice Using GradedPool-Seq Mapping and QTL-Seq Correlation Analysis. Int J Mol Sci 2023; 24:14832. [PMID: 37834281 PMCID: PMC10573815 DOI: 10.3390/ijms241914832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The improvement of grain yield, quality, and resistance can be achieved through the utilization of heterosis. The combination of cytoplasmic male sterility (CMS) and fertility restoration (Rf) gene(s) greatly facilitates the commercial development of three-line hybrid rice based on heterosis. The basis for investigating the relationship between CMS and Rf genes lies in the rapid localization of wild rice fertility restoration genes. A set of the BC4F5 population derived from interspecific crosses between Xieqingzao B (XB) and the BC1F9 XB//Dongxiang wild rice (DWR)/XB line L5339 was used to detect quantitative trait loci (QTL) for fertility restoration. The population was then crossed with two male sterile lines, Zhong9A (Z9A) and DongB11A (DB11A), in order to generate a testcrossing population for investigating spikelet fertility. Based on the linkage mapping, seven QTLs were detected on chromosomes 1, 3, 5, 6, 8, and 10, explaining 2.76 to 12.46% of the phenotypic variation. Of them, two novel fertility restoration QTLs, qRf3 and qRf6, can restore fertility of the CMS-DWR line DB11A by 16.56% and 15.12%, respectively. By employing joint QTL-seq and GradedPool-Seq methods, two novel Rf QTLs for DB11A, qRf3 and qRf6, were identified at the physical locations of 10,900,001-11,700,000 bp and 28,016,785-31,247,556 bp, respectively. These findings are useful for exploring the natural variations of Rf genes in rice. Therefore, rice's new genetic resources for the selection and breeding of rice restorer lines provide promising candidates for QTL fine localization and clarification.
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Affiliation(s)
- Wenshan Cai
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Wanlin Li
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Liuying Duan
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Yaling Chen
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Fantao Zhang
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Biaolin Hu
- Rice Research Institute, National Engineering Laboratory for Rice (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jiankun Xie
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
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7
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Zhang X, Chen S, Zhao Z, Ma C, Liu Y. Investigation of B-atp6-orfH79 distributing in Chinese populations of Oryza rufipogon and analysis of its chimeric structure. BMC PLANT BIOLOGY 2023; 23:81. [PMID: 36750954 PMCID: PMC9903446 DOI: 10.1186/s12870-023-04082-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The cytoplasmic male sterility (CMS) of rice is caused by chimeric mitochondrial DNA (mtDNA) that is maternally inherited in the majority of multicellular organisms. Wild rice (Oryza rufipogon Griff.) has been regarded as the ancestral progenitor of Asian cultivated rice (Oryza sativa L.). To investigate the distribution of original CMS source, and explore the origin of gametophytic CMS gene, a total of 427 individuals with seventeen representative populations of O. rufipogon were collected in from Dongxiang of Jiangxi Province to Sanya of Hainan Province, China, for the PCR amplification of atp6, orfH79 and B-atp6-orfH79, respectively. RESULTS The B-atp6-orfH79 and its variants (B-atp6-GSV) were detected in five among seventeen populations (i.e. HK, GZ, PS, TL and YJ) through PCR amplification, which could be divided into three haplotypes, i.e., BH1, BH2, and BH3. The BH2 haplotype was identical to B-atp6-orfH79, while the BH1 and BH3 were the novel haplotypes of B-atp6-GSV. Combined with the high-homology sequences in GenBank, a total of eighteen haplotypes have been revealed, only with ten haplotypes in orfH79 and its variants (GSV) that belong to three species (i.e. O. rufipogon, Oryza nivara and Oryza sativa). Enough haplotypes clearly demonstrated the uniform structural characteristics of the B-atp6-orfH79 as follows: except for the conserved sequence (671 bp) composed of B-atp6 (619 bp) and the downstream followed the B-atp6 (52 bp, DS), and GSV sequence, a rich variable sequence (VS, 176 bp) lies between the DS and GSV with five insertion or deletion and more than 30 single nucleotide polymorphism. Maximum likelihood analysis showed that eighteen haplotypes formed three clades with high support rate. The hierarchical analysis of molecular variance (AMOVA) indicated the occurrence of variation among all populations (FST = 1; P < 0.001), which implied that the chimeric structure occurred independently. Three haplotypes (i.e., H1, H2 and H3) were detected by the primer of orfH79, which were identical to the GVS in B-atp6-GVS structure, respectively. All seventeen haplotypes of the orfH79, belonged to six species based on our results and the existing references. Seven existed single nucleotide polymorphism in GSV section can be translated into eleven various amino acid sequences. CONCLUSIONS Generally, this study, indicating that orfH79 was always accompanied by the B-atp6, not only provide two original CMS sources for rice breeding, but also confirm the uniform structure of B-atp-orfH79, which contribute to revealing the origin of rice gametophytic CMS genes, and the reason about frequent recombination of mitochondrial DNA.
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Affiliation(s)
- Xuemei Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Shuying Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Zixian Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Cunqiang Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Yating Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- College of Tobacco, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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8
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He W, Xiang K, Chen C, Wang J, Wu Z. Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework. Brief Bioinform 2023; 24:bbac522. [PMID: 36644898 DOI: 10.1093/bib/bbac522] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/03/2022] [Accepted: 11/02/2022] [Indexed: 01/17/2023] Open
Abstract
Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.
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Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kunli Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Caijin Chen
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528200, China
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Zhong Y, Yu R, Chen J, Liu Y, Zhou R. Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica. FRONTIERS IN PLANT SCIENCE 2022; 13:988368. [PMID: 36212306 PMCID: PMC9532969 DOI: 10.3389/fpls.2022.988368] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Mitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, characterization of repeat-mediated recombination should extend to more plant species, including parasitic plants with a distinct heterotrophic lifestyle. Here we assembled the mitogenome of the holoparasitic plant Aeginetia indica (Orobanchaceae) using Illumina sequencing reads. The mitogenome was assembled into a circular chromosome of 420,362 bp, 18,734 bp longer than that of another individual of A. indica which was assembled before as a linear molecule. Synteny analysis between the two mitogenomes revealed numerous rearrangements, unique regions of each individual and 0.2% sequence divergence in their syntenic regions. The A. indica mitogenome contains a gene content typical of flowering plants (33 protein-coding, 3 rRNA, and 17 tRNA genes). Repetitive sequences >30 bp in size totals 57,060 bp, representing 13.6% of the mitogenome. We examined recombination mediated by repeats >100 bp in size and found highly active recombination for all the repeats, including a very large repeat of ~16 kb. Recombination between these repeats can form much smaller subgenomic circular chromosomes, which may lead to rapid replication of mitochondrial DNA and thus be advantageous for A. indica with a parasitic lifestyle. In addition, unlike some other parasitic plants, A. indica shows no evidence for horizontal gene transfer of protein-coding genes in its mitogenome.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Runxian Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Toriyama K. Molecular basis of cytoplasmic male sterility and fertility restoration in rice. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:285-295. [PMID: 34782814 PMCID: PMC8562580 DOI: 10.5511/plantbiotechnology.21.0607a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait that causes dysfunctions in pollen and anther development. CMS is caused by the interaction between nuclear and mitochondrial genomes. A product of a CMS-causing gene encoded by the mitochondrial genome affects mitochondrial function and the regulation of nuclear genes, leading to male sterility. In contrast, the RESTORER OF FERTILITY gene (Rf gene) in the nuclear genome suppresses the expression of the CMS-causing gene and restores male fertility. An alloplasmic CMS line is often bred as a result of nuclear substitution, which causes the removal of functional Rf genes and allows the expression of a CMS-causing gene in mitochondria. The CMS/Rf system is an excellent model for understanding the genetic interactions and cooperative functions of mitochondrial and nuclear genomes in plants, and is also an agronomically important trait for hybrid seed production. In this review article, pollen and anther phenotypes of CMS, CMS-associated mitochondrial genes, Rf genes, and the mechanism that causes pollen abortion and its agronomical application for rice are described.
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Affiliation(s)
- Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
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Hong Z, Liao X, Ye Y, Zhang N, Yang Z, Zhu W, Gao W, Sharbrough J, Tembrock LR, Xu D, Wu Z. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. BMC Genomics 2021; 22:672. [PMID: 34536995 PMCID: PMC8449883 DOI: 10.1186/s12864-021-07967-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. RESULTS We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. CONCLUSION For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.
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Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Weidong Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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Wang H, Xiao Q, Wei C, Chen H, Chen X, Dai C, Wen J, Ma C, Tu J, Fu T, Shen J, Yi B. A mitochondria-localized pentatricopeptide repeat protein is required to restore hau cytoplasmic male sterility in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1377-1386. [PMID: 33725137 DOI: 10.1007/s00122-021-03777-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
A mitochondria-localized pentatricopeptide repeat protein was identified by positional cloning and transferred into the hau CMS line, where it successfully restored fertility Cytoplasmic male sterility (CMS) is a maternally inherited trait that can be controlled by restorer-of-fertility (Rf) genes present in the nucleus. The hau CMS was identified as a new form of CMS associated with the mitochondrial transcript orf288; however, a lack of a restorer gene has limited its utilization in Brassica crops. Here, the combination of Brassica 60 K array with bulk segregant analysis and map-based cloning was used to delimit the Rfh locus to an 82.2-kb region on chromosome A09. A candidate gene encoding a mitochondria-localized pentatricopeptide repeat (PPR) protein was identified and transferred into the hau CMS line, where it successfully restored the fertility of the hau CMS plants. Furthermore, the expression analysis showed that Rfh was highly expressed in the flower buds, and the sequence analysis results implied that functional divergence between RFH and rfh could be due to 59 amino acid residue differences in the deduced protein sequences. In addition, a co-separated molecular marker was developed based on the divergent sequences between the dominant and recessive alleles. These results will help enable the heterosis of Brassica crops in the future.
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Affiliation(s)
- Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Qing Xiao
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chao Wei
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- College of Life Science, Zhaoqing University, Zhaoqing, 526061, People's Republic of China
| | - Hui Chen
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiaohan Chen
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Centre of Rapeseed Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Jin Z, Seo J, Kim B, Lee SY, Koh HJ. Identification of a Candidate Gene for the Novel Cytoplasmic Male Sterility Derived from Inter-Subspecific Crosses in Rice ( Oryza sativa L.). Genes (Basel) 2021; 12:590. [PMID: 33920582 PMCID: PMC8073397 DOI: 10.3390/genes12040590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/09/2023] Open
Abstract
Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies indica and japonica in rice (Oryza sativa L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene orf312, which possesses a transmembrane domain and overlaps with two mitotype-specific sequences (MSSs) that are unique to the Tetep-CMS line. The encoded peptide of orf312 was toxic to Escherichia coli and inhibited cell growth compared to the control under isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The peptide of orf312 contains COX11-interaction domains, which are thought to be a main functional domain for WA352c in the wild abortive (WA-CMS) line of rice. A QTL for Rf-Tetep (restorer-of-fertility gene(s) originating from Tetep) was identified on chromosome 10. In this region, several restorer genes, Rf1a, Rf1b, and Rf4, have previously been reported. Collectively, the interactions of orf312, a candidate gene for Tetep-CMS, and Rf-Tetep, a restorer QTL, confer male sterility and fertility restoration, respectively, which enables a hybrid rice breeding system. Further studies on orf312 and isolation of Rf-Tetep will help to identify the underlying molecular mechanism of mitochondrial ORFs with the COX11-interaction domains.
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Affiliation(s)
- Zhuo Jin
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Jeonghwan Seo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
| | - Backki Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Seung Young Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
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He W, Chen C, Xiang K, Wang J, Zheng P, Tembrock LR, Jin D, Wu Z. The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:781793. [PMID: 34868182 PMCID: PMC8637288 DOI: 10.3389/fpls.2021.781793] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 05/19/2023]
Abstract
The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.
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Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caijin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Kunli Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Luke R. Tembrock,
| | - Deming Jin
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Deming Jin,
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Zhiqiang Wu,
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