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Gong Y, Xie X, Zhou G, Chen M, Chen Z, Li P, Huang H. Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria. BMC Genomics 2024; 25:546. [PMID: 38824587 PMCID: PMC11143693 DOI: 10.1186/s12864-024-10457-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.
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Affiliation(s)
- Yihui Gong
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Xin Xie
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Guihua Zhou
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Meiyu Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Zhiyin Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Peng Li
- Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China
| | - Hua Huang
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Bhattacharya J, Srinivas Reddy D, Prasad K, Nitnavare RB, Bhatnagar-Mathur P, Sudhakar Reddy P. Ectopic expression of pigeonpea Orf147 gene imparts partial sterility in Cicer arietinum. Gene 2023; 868:147372. [PMID: 36933813 DOI: 10.1016/j.gene.2023.147372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
Orf147, a cytotoxic peptide, has been found to cause cytoplasmic male sterility (CMS) in Cajanus cajanifolius (pigeonpea). In our study, Orf147 was introduced into self-pollinating Cicer arietinum (chickpea) using Agrobacterium-mediated transformation for induction of CMS. The stable integration and expression of the transgene has been assessed through PCR and qRT-PCR analysis. In addition, phenotypic sterility analysis has been performed, considering developmental parameters like flower development, pod formation and flower drop. Transgene inheritance analysis demonstrates that out of the five PCR positive events in the T0 generation, two events have segregated according to the Mendelian segregation ratio (3:1) in the T2 generation. Further, pollen viability test using microscopic analysis confirms the induction of partial CMS in transgenic chickpea. The study holds significant value regarding the heterosis of self-pollinating legumes like chickpea. As a part of the prospect, exploring inducible promoters of species-specific or related legumes would be the next step to developing a two-line hybrid system.
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Affiliation(s)
- Joorie Bhattacharya
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India; Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Dumbala Srinivas Reddy
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India; ATGC Biotech Private Limited, ICCI Knowledge Park (IKP), Genome Valley, Hyderabad, 500078 Telangana, India
| | - Kalyani Prasad
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India
| | - Rahul B Nitnavare
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom; Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz 16 Km. 45, El Batán, Texcoco C.P. 56237, Mexico.
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India.
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Ren W, Si J, Chen L, Fang Z, Zhuang M, Lv H, Wang Y, Ji J, Yu H, Zhang Y. Mechanism and Utilization of Ogura Cytoplasmic Male Sterility in Cruciferae Crops. Int J Mol Sci 2022; 23:ijms23169099. [PMID: 36012365 PMCID: PMC9409259 DOI: 10.3390/ijms23169099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 12/11/2022] Open
Abstract
Hybrid production using lines with cytoplasmic male sterility (CMS) has become an important way to utilize heterosis in vegetables. Ogura CMS, with the advantages of complete pollen abortion, ease of transfer and a progeny sterility rate reaching 100%, is widely used in cruciferous crop breeding. The mapping, cloning, mechanism and application of Ogura CMS and fertility restorer genes in Brassica napus, Brassica rapa, Brassica oleracea and other cruciferous crops are reviewed herein, and the existing problems and future research directions in the application of Ogura CMS are discussed.
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Affiliation(s)
- Wenjing Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinchao Si
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
| | - Li Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
| | - Jialei Ji
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
| | - Hailong Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
- Correspondence: (H.Y.); (Y.Z.)
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China
- Correspondence: (H.Y.); (Y.Z.)
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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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Sang SF, Mei DS, Liu J, Zaman QU, Zhang HY, Hao MY, Fu L, Wang H, Cheng HT, Hu Q. Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus. BMC Genomics 2019; 20:813. [PMID: 31694534 PMCID: PMC6836354 DOI: 10.1186/s12864-019-6187-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022] Open
Abstract
Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.
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Affiliation(s)
- Shi-Fei Sang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - De-Sheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Qamar U Zaman
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hai-Yan Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Meng-Yu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hong-Tao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
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Wu Z, Hu K, Yan M, Song L, Wen J, Ma C, Shen J, Fu T, Yi B, Tu J. Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea. BMC Genomics 2019; 20:348. [PMID: 31068124 PMCID: PMC6507029 DOI: 10.1186/s12864-019-5721-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/22/2019] [Indexed: 01/15/2023] Open
Abstract
Background Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea. Results The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes. Conclusions On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengxiang Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjiao Yan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liping Song
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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