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Bishnoi R, Solanki R, Singla D, Mittal A, Chhuneja P, Meena OP, Dhatt AS. Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion. 3 Biotech 2024; 14:6. [PMID: 38074291 PMCID: PMC10700285 DOI: 10.1007/s13205-023-03850-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/08/2023] [Indexed: 01/19/2024] Open
Abstract
Cytoplasmic male sterility (CMS) has been widely exploited for hybrid seed production in onions (Allium cepa L.). In contrast to long-day onion cultivars, short-day onion has not yet been investigated for mitochondrial genome structure and DNA rearrangements associated with CMS activity. Here, we report the 3,16,321 bp complete circular mitochondrial genome of tropical onion CMS line (97A). Due to the substantial number of repetitive regions, the assembled mitochondrial genome of maintainer line (97B) remained linear with 15 scaffolds. Additionally, 13 and 20 chloroplast-derived fragments with a size ranging from 143 to 13,984 bp and 153-17,725 bp were identified in the 97A and 97B genomes, respectively. Genome annotation revealed 24 core protein-coding genes along with 24 and 28 tRNA genes in the mitochondrial genomes of 97A and 97B, respectively. Furthermore, comparative genome analysis of the 97A and 97B mitochondrial genomes showed that gene content was almost similar except for the chimeric ORF725 gene which is the extended form of the COX1 gene. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03850-2.
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Affiliation(s)
- Ritika Bishnoi
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Ravindra Solanki
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Om Prakash Meena
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004 India
| | - Ajmer Singh Dhatt
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004 India
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Gautam R, Shukla P, Kirti PB. Male sterility in plants: an overview of advancements from natural CMS to genetically manipulated systems for hybrid seed production. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:195. [PMID: 37606708 DOI: 10.1007/s00122-023-04444-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE The male sterility system in plants has traditionally been utilized for hybrid seed production. In last three decades, genetic manipulation for male sterility has revolutionized this area of research related to hybrid seed production technology. Here, we have surveyed some of the natural cytoplasmic male sterility (CMS) systems that existed/ were developed in different crop plants for developing male sterility-fertility restoration systems used in hybrid seed production and highlighted some of the recent biotechnological advancements in the development of genetically engineered systems that occurred in this area. We have indicated the possible future directions toward the development of engineered male sterility systems. Cytoplasmic male sterility (CMS) is an important trait that is naturally prevalent in many plant species, which has been used in the development of hybrid varieties. This is associated with the use of appropriate genes for fertility restoration provided by the restorer line that restores fertility on the corresponding CMS line. The development of hybrids based on a CMS system has been demonstrated in several different crops. However, there are examples of species, which do not have usable cytoplasmic male sterility and fertility restoration systems (Cytoplasmic Genetic Male Sterility Systems-CGMS) for hybrid variety development. In such plants, it is necessary to develop usable male sterile lines through genetic engineering with the use of heterologous expression of suitable genes that control the development of male gametophyte and fertile male gamete formation. They can also be developed through gene editing using the recently developed CRISPR-Cas technology to knock out suitable genes that are responsible for the development of male gametes. The present review aims at providing an insight into the development of various technologies for successful production of hybrid varieties and is intended to provide only essential information on male sterility systems starting from naturally occurring ones to the genetically engineered systems obtained through different means.
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Affiliation(s)
- Ranjana Gautam
- Department of Life Sciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, 208024, India
| | - Pawan Shukla
- Seri-Biotech Research Laboratory, Central Silk Board, Carmelram Post, Kodathi, Bangalore, 560035, India.
| | - P B Kirti
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad, Telangana, 500030, India
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3
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Kitazaki K, Oda K, Akazawa A, Iwahori R. Molecular genetics of cytoplasmic male sterility and restorer-of-fertility for the fine tuning of pollen production in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:156. [PMID: 37330934 DOI: 10.1007/s00122-023-04398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/01/2023] [Indexed: 06/20/2023]
Abstract
Cytoplasmic male sterility (CMS) is an increasingly important issue within the context of hybrid seed production. Its genetic framework is simple: S-cytoplasm for male sterility induction and dominant allele of the restorer-of-fertility gene (Rf) for suppression of S. However, breeders sometimes encounter a phenotype of CMS plants too complex to be explained via this simple model. The molecular basis of CMS provides clue to the mechanisms that underlie the expression of CMS. Mitochondria have been associated with S, and several unique ORFs to S-mitochondria are thought to be responsible for the induction of male sterility in various crops. Their functions are still the subject of debate, but they have been hypothesized to emit elements that trigger sterility. Rf suppresses the action of S by various mechanisms. Some Rfs, including those that encode the pentatricopeptide repeat (PPR) protein and other proteins, are now considered members of unique gene families that are specific to certain lineages. Additionally, they are thought to be complex loci in which several genes in a haplotype simultaneously counteract an S-cytoplasm and differences in the suite of genes in a haplotype can lead to multiple allelism including strong and weak Rf at phenotypic level. The stability of CMS is influenced by factors such as the environment, cytoplasm, and genetic background; the interaction of these factors is also important. In contrast, unstable CMS becomes inducible CMS if its expression can be controlled. CMS becomes environmentally sensitive in a genotype-dependent manner, suggesting the feasibility of controlling the expression of CMS.
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Affiliation(s)
- Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan.
| | - Kotoko Oda
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Akiho Akazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryoma Iwahori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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Singh H, Sekhon BS, Kumar P, Dhall RK, Devi R, Dhillon TS, Sharma S, Khar A, Yadav RK, Tomar BS, Ntanasi T, Sabatino L, Ntatsi G. Genetic Mechanisms for Hybrid Breeding in Vegetable Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:2294. [PMID: 37375919 DOI: 10.3390/plants12122294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.
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Affiliation(s)
- Hira Singh
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Bhallan Singh Sekhon
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Pradeep Kumar
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Ruma Devi
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Tarsem Singh Dhillon
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Suman Sharma
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Anil Khar
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | | | | | - Theodora Ntanasi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, IeraOdos 75, 11855 Athens, Greece
| | - Leo Sabatino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, IeraOdos 75, 11855 Athens, Greece
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Comparison of Mitochondrial Genomes between a Cytoplasmic Male-Sterile Line and Its Restorer Line for Identifying Candidate CMS Genes in Gossypium hirsutum. Int J Mol Sci 2022; 23:ijms23169198. [PMID: 36012463 PMCID: PMC9409232 DOI: 10.3390/ijms23169198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton (Gossypium hirsutum), sequencing and de novo assembly were performed on the mitochondrial genome of the G. hirsutum CMS line SI3A, with G. harknessii CMS-D2 cytoplasm, and the corresponding G. hirsutum restorer line 0-613-2R. Remarkable variations in genome structure and gene transcripts were detected. The mitochondrial genome of SI3A has three circle molecules, including one main circle and two sub-circles, while 0-613-2R only has one. RNA-seq and RT-qPCR analysis proved that orf606a and orf109a, which have a chimeric structure and transmembrane domain, were highly expressed in abortive anthers of SI3A. In addition, comparative analysis of RNA-seq and full-length transcripts revealed the complex I gene nad4 to be expressed at a lower level in SI3A than in its restorer and that it featured an intron retention splicing pattern. These two novel chimeric ORFs and nad4 are potential candidates that confer CMS character in SI3A. This study provides new insight into the molecular basis of the nuclear–cytoplasmic interaction mechanism, and that putative CMS genes might be important sources for future precise design cross-breeding of cotton.
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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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7
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Xu F, Yang X, Zhao N, Hu Z, Mackenzie SA, Zhang M, Yang J. Exploiting sterility and fertility variation in cytoplasmic male sterile vegetable crops. HORTICULTURE RESEARCH 2022; 9:uhab039. [PMID: 35039865 PMCID: PMC8807945 DOI: 10.1093/hr/uhab039] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 05/04/2023]
Abstract
Cytoplasmic male sterility (CMS) has long been used to economically produce hybrids that harness growth vigor through heterosis. Yet, how CMS systems operate within commercially viable seed production strategies in various economically important vegetable crops, and their underlying molecular mechanisms, are often overlooked details that could expand the utility of CMS as a cost-effective and stable system. We provide here an update on the nature of cytoplasmic-nuclear interplay for pollen sterility and fertility transitions in vegetable crops, based on the discovery of components of nuclear fertility restoration and reversion determinants. Within plant CMS systems, pollen fertility can be rescued by the introduction of nuclear fertility restorer genes (Rfs), which operate by varied mechanisms to countermand the sterility phenotype. By understanding these systems, it is now becoming feasible to achieve fertility restoration with Rfs designed for programmable CMS-associated open reading frames (ORFs). Likewise, new opportunities exist for targeted disruption of CMS-associated ORFs by mito-TALENs in crops where natural Rfs have not been readily identified, providing an alternative approach to recovering fertility of cytoplasmic male sterile lines in crops. Recent findings show that facultative gynodioecy, as a reproductive strategy, can coordinate the sterility and fertility transition in response to environmental cues and/or metabolic signals that reflect ecological conditions of reproductive isolation. This information is important to devising future systems that are more inherently stable.
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Affiliation(s)
- Fengyuan Xu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiaodong Yang
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Na Zhao
- College of Grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou,
Zhejiang, 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou,
Zhejiang, 310058, China
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Kim S, Kim S. An insertion mutation located on putative enhancer regions of the MYB26-like gene induces inhibition of anther dehiscence resulting in novel genic male sterility in radish ( Raphanus sativus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:67. [PMID: 37309318 PMCID: PMC10236041 DOI: 10.1007/s11032-021-01254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/24/2021] [Indexed: 06/14/2023]
Abstract
A novel male-sterility trait was identified in a radish (Raphanus sativus L.) population. Although the size of male-sterile anthers was comparable to that of normal flowers, no pollen grain was observed during anther dehiscence. However, dissection of male-sterile anthers revealed an abundance of normal pollen grains. Analysis of segregating populations showed that a single recessive locus, designated RsMs1, conferred male sterility. Based on two radish draft genome sequences, molecular markers were developed to delimit the genomic region harboring the RsMs1. The region was narrowed down to approximately 24 kb after analyzing recombinants selected from 7511 individuals of a segregating population. Sequencing of the delimited region yielded six putative genes including four genes expressed in the floral tissue, and one gene with significant differential expression between male-fertile and male-sterile individuals of a segregating population. This differentially expressed gene was orthologous to the Arabidopsis MYB26 gene, which played a critical role in anther dehiscence. Excluding a synonymous single nucleotide polymorphism in exon3, no polymorphism involving coding and putative promoter regions was detected between alleles. A 955-bp insertion was identified 7.5 kb upstream of the recessive allele. Highly conserved motifs among four Brassicaceae species were identified around this insertion site, suggesting the presence of putative enhancer sequences. A functional marker was developed for genotyping of the RsMs1 based on the 955-bp insertion. A total of 120 PI accessions were analyzed using this marker, and 11 accessions were shown to carry the recessive rsms1 allele. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01254-9.
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Affiliation(s)
- Seongjun Kim
- Jeollanamdo Agricultural Research and Extension Service, Naju-si, 58213 Republic of Korea
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186 Republic of Korea
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Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata). BMC Genomics 2021; 22:646. [PMID: 34493212 PMCID: PMC8425178 DOI: 10.1186/s12864-021-07963-x] [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: 12/23/2020] [Accepted: 08/27/2021] [Indexed: 12/29/2022] Open
Abstract
Background Cytoplasmic male sterility (CMS) has been widely used for commercial F1 hybrid seeds production. CMS is primarily caused by chimeric genes in mitochondrial genomes. However, which specific stages of anther development in cabbage are affected by the chimeric genes remain unclear. Results In the present study, the complete mitochondrial genomes were sequenced and assembled for the maintainer and Ogura CMS cabbage lines. The genome size of the maintainer and Ogura CMS cabbage are 219,962 bp and 236,648 bp, respectively. There are 67 and 69 unknown function ORFs identified in the maintainer and Ogura CMS cabbage mitochondrial genomes, respectively. Four orfs, orf102a, orf122b, orf138a and orf154a were specifically identified in the Ogura CMS mitochondrial genome, which were likely generated by recombination with Ogura type radish during breeding process. Among them, ORF138a and ORF154a possessed a transmembrane structure, and orf138a was co-transcribed with the atp8 and trnfM genes. orf154a is partially homologous to the ATP synthase subunit 1 (atpA) gene. Both these genes were likely responsible for the CMS phenotype. In addition, cytological sections showed that the abnormal proliferation of tapetal cells might be the immediate cause of cytoplasmic male-sterility in Ogura CMS cabbage lines. RNA-seq results showed that orf138a and orf154a in Ogura CMS might influence transcript levels of genes in energy metabolic pathways. Conclusions The presence of orf138a and orf154a lead to increased of ATPase activity and ATP content by affecting the transcript levels of genes in energy metabolic pathways, which could provide more energy for the abnormal proliferation of tapetal cells. Our data provides new insights into cytoplasmic male-sterility from whole mitochondrial genomes, cytology of anther development and transcriptome data. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07963-x.
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Cheng Q, Wang P, Li T, Liu J, Zhang Y, Wang Y, Sun L, Shen H. Complete Mitochondrial Genome Sequence and Identification of a Candidate Gene Responsible for Cytoplasmic Male Sterility in Celery ( Apium graveolens L.). Int J Mol Sci 2021; 22:ijms22168584. [PMID: 34445290 PMCID: PMC8395238 DOI: 10.3390/ijms22168584] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/17/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Celery (Apium graveolens L.) is an important leafy vegetable worldwide. The development of F1 hybrids in celery is highly dependent on cytoplasmic male sterility (CMS) because emasculation is difficult. In this study, we first report a celery CMS, which was found in a high-generation inbred line population of the Chinese celery “tanzhixiangqin”. Comparative analysis, following sequencing and assembly of the complete mitochondrial genome sequences for this celery CMS line and its maintainer line, revealed that there are 21 unique regions in the celery CMS line and these unique regions contain 15 ORFs. Among these ORFs, only orf768a is a chimeric gene, consisting of 1497 bp sequences of the cox1 gene and 810 bp unidentified sequences located in the unique region, and the predicted protein product of orf768a possesses 11 transmembrane domains. In summary, the results of this study indicate that orf768a is likely to be a strong candidate gene for CMS induction in celery. In addition, orf768a can be a co-segregate marker, which can be used to screen CMS in celery.
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Affiliation(s)
- Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Tiantian Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
| | - Jinkui Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
| | - Yingxue Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
| | - Yihao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (Q.C.); (T.L.); (J.L.); (Y.Z.); (Y.W.); (L.S.)
- Correspondence:
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11
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Transcriptome and MiRNAomics Analyses Identify Genes Associated with Cytoplasmic Male Sterility in Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2021; 22:ijms22094684. [PMID: 33925234 PMCID: PMC8124215 DOI: 10.3390/ijms22094684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is important for large-scale hybrid seed production. Rearrangements in the mitochondrial DNA (mtDNA) for the cotton (Gossypium hirsutum L.) CMS line J4A were responsible for pollen abortion. However, the expression patterns of nuclear genes associated with pollen abortion and the molecular basis of CMS for J4A are unknown, and were the objectives of this study by comparing J4A with the J4B maintainer line. Cytological evaluation of J4A anthers showed that microspore abortion occurs during meiosis preventing pollen development. Changes in enzyme activity of mitochondrial respiratory chain complex IV and mitochondrial respiratory chain complex V and the content of ribosomal protein and ATP during anther abortion were observed for J4A suggesting insufficient synthesis of ATP hindered pollen production. Additionally, levels of sucrose, starch, soluble sugar, and fructose were significantly altered in J4A during the meiosis stage, suggesting reduced sugar metabolism contributed to sterility. Transcriptome and miRNAomics analyses identified 4461 differentially expressed mRNAs (DEGs) and 26 differentially expressed microRNAs (DEMIs). Pathway enrichment analysis indicated that the DEMIs were associated with starch and sugar metabolism. Six deduced target gene regulatory pairs that may participate in CMS were identified, ghi-MIR7484-10/mitogen-activated protein kinase kinase 6 (MAPKK6), ghi-undef-156/agamous-like MADS-box protein AGL19 (AGL19), ghi-MIR171-1-22/SNF1-related protein kinase regulatory subunit gamma-1 and protein trichome birefringence-like 38, and ghi-MIR156-(8/36)/WRKY transcription factor 28 (WRKY28). Overall, a putative CMS mechanism involving mitochondrial dysfunction, the ghi-MIR7484-10/MAPKK6 network, and reduced glucose metabolism was suggested, and ghi-MIR7484-10/MAPKK6 may be related to abnormal microspore meiosis and induction of excessive sucrose accumulation in anthers.
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Park HS, Lee WK, Lee SC, Lee HO, Joh HJ, Park JY, Kim S, Song K, Yang TJ. Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F 1 hybrid combinations. Sci Rep 2021; 11:2506. [PMID: 33510273 PMCID: PMC7843999 DOI: 10.1038/s41598-021-81988-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.
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Affiliation(s)
- Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Won Kyung Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sang-Choon Lee
- Phyzen Genomics Institute, Seongnam, Gyeonggi-do, 13558, Republic of Korea
| | - Hyun Oh Lee
- Phyzen Genomics Institute, Seongnam, Gyeonggi-do, 13558, Republic of Korea
| | - Ho Jun Joh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kihwan Song
- Department of Bioresources Engineering, College of Life Sciences, Sejong University, Seoul, 05006, Republic of Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Yamagishi H, Hashimoto A, Fukunaga A, Terachi T. Appearance of male sterile and black radishes in the progeny of cross between Raphanus raphanistrum and Raphanus sativus. BREEDING SCIENCE 2020; 70:637-641. [PMID: 33603561 PMCID: PMC7878931 DOI: 10.1270/jsbbs.20081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
In addition to Ogura cytoplasmic male sterility (CMS), which is used extensively for F1 hybrid seed production in Brassicaceae crops, two other CMS systems, NWB CMS and DCGMS, have also been identified. The causal gene for the latter two CMS systems has been identified as a novel chimeric gene, orf463. We previously reported that orf463 is specific to black radish cultivars and that it is present in line 'RS-5' of Raphanus raphanistrum; however, the orf463 sequence in 'RS-5' differed from that of black radish cultivars. Though, R. raphanistrum with an orf463 sequence identical to that found in black radish cultivars was recently identified. We therefore sought to determine whether the orf463 gene in line 'RS-5' induces CMS in radishes. We crossed 'RS-5' as a female parent with a cultivated radish, 'Uchiki-Gensuke', as a male parent, and examined the gross plant morphology and pollen fertility of the resulting progeny. The F2 population contained both male sterile plants and plants with black roots. The findings showed that R. raphanistrum contains two types of orf463 genes that induce CMS, and that the origin of black radishes could be attributed to R. raphanistrum having orf463 gene.
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Affiliation(s)
- Hiroshi Yamagishi
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto 603-8555, Japan
| | - Ayako Hashimoto
- Research Center of Botany, Kyoto Sangyo University, Kamigamo, Kita, Kyoto 603-8555, Japan
| | - Asumi Fukunaga
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto 603-8555, Japan
| | - Toru Terachi
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto 603-8555, Japan
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Palumbo F, Vitulo N, Vannozzi A, Magon G, Barcaccia G. The Mitochondrial Genome Assembly of Fennel ( Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. Int J Mol Sci 2020; 21:E4664. [PMID: 32630002 PMCID: PMC7370444 DOI: 10.3390/ijms21134664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 01/12/2023] Open
Abstract
Cytoplasmic male sterility (CMS) has always aroused interest among researchers and breeders, being a valuable resource widely exploited not only to breed F1 hybrid varieties but also to investigate genes that control stamen and pollen development. With the aim of identifying candidate genes for CMS in fennel, we adopted an effective strategy relying on the comparison between mitochondrial genomes (mtDNA) of both fertile and sterile genotypes. mtDNA raw reads derived from a CMS genotype were assembled in a single molecule (296,483 bp), while a draft mtDNA assembly (166,124 nucleotides, 94 contigs) was performed using male fertile sample (MF) sequences. From their annotation and alignment, two atp6-like sequences were identified. atp6-, the putative mutant copy with a 300 bp truncation at the 5'-end, was found only in the mtDNA of CMS samples, while the wild type copy (atp6+) was detected only in the MF mtDNA. Further analyses (i.e., reads mapping and Sanger sequencing), revealed an atp6+ copy also in CMS samples, probably in the nuclear DNA. However, qPCRs performed on different tissues proved that, despite its availability, atp6+ is expressed only in MF samples, while apt6- mRNA was always detected in CMS individuals. In the light of these findings, the energy deficiency model could explain the pollen deficiency observed in male sterile flower. atp6- could represent a gene whose mRNA is translated into a not-fully functional protein leading to suboptimal ATP production that guarantees essential cellular processes but not a high energy demand process such as pollen development. Our study provides novel insights into the fennel mtDNA genome and its atp6 genes, and paves the way for further studies aimed at understanding their functional roles in the determination of male sterility.
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Affiliation(s)
- Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy;
| | - Alessandro Vannozzi
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
| | - Gabriele Magon
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
| | - Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy; (A.V.); (G.M.); (G.B.)
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Mitochondrial Genome Sequencing Reveals orf463a May Induce Male Sterility in NWB Cytoplasm of Radish. Genes (Basel) 2020; 11:genes11010074. [PMID: 31936663 PMCID: PMC7017215 DOI: 10.3390/genes11010074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Radish (Raphanus sativus L.) is an important root vegetable worldwide. The development of F1 hybrids, which are extensively used for commercial radish production, relies on cytoplasmic male sterility (CMS). To identify candidate genes responsible for CMS in NWB cytoplasm, we sequenced the normal and NWB CMS radish mitochondrial genomes via next-generation sequencing. A comparative analysis revealed 18 syntenic blocks and 11 unique regions in the NWB CMS mitogenome. A detailed examination indicated that orf463a was the most likely causal factor for male sterility in NWB cytoplasm. Interestingly, orf463a was identical to orf463, which is responsible for CMS in Dongbu cytoplasmic and genic male sterility (DCGMS) radish. Moreover, only structural variations were detected between the NWB CMS and DCGMS mitochondrial genomes, with no nucleotide polymorphisms (SNPs) or meaningful indels. Further analyses revealed these two mitochondrial genomes are coexisting isomeric forms belonging to the same mitotype. orf463a was more highly expressed in flower buds than in vegetative organs and its expression was differentially regulated in the presence of restorer of fertility (Rf) genes. orf463a was confirmed to originate from Raphanus raphanistrum. In this study, we identified a candidate gene responsible for the CMS in NWB cytoplasm and clarified the relationship between NWB CMS and DCGMS.
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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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Singh S, Dey SS, Bhatia R, Kumar R, Behera TK. Current understanding of male sterility systems in vegetable Brassicas and their exploitation in hybrid breeding. PLANT REPRODUCTION 2019; 32:231-256. [PMID: 31053901 DOI: 10.1007/s00497-019-00371-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Overview of the current status of GMS and CMS systems available in Brassica vegetables, their molecular mechanism, wild sources of sterile cytoplasm and exploitation of male sterility in hybrid breeding. The predominantly herbaceous family Brassicaceae (crucifers or mustard family) encompasses over 3700 species, and many of them are scientifically and economically important. The genus Brassica is an economically important genus within the tribe Brassicaceae that comprises important vegetable, oilseed and fodder crops. Brassica vegetables display strong hybrid vigor, and heterosis breeding is the integral part in their improvement. Commercial production of F1 hybrid seeds in Brassica vegetables requires an effective male sterility system. Among the available male sterility systems, cytoplasmic male sterility (CMS) is the most widely exploited in Brassica vegetables. This system is maternally inherited and studied intensively. A limited number of reports about the genic male sterility (GMS) are available in Brassica vegetables. The GMS system is reported to be dominant, recessive and trirecessive in nature in different species. In this review, we discuss the available male sterility systems in Brassica vegetables and their potential use in hybrid breeding. The molecular mechanism of mt-CMS and causal mitochondrial genes of CMS has been discussed in detail. Finally, the exploitation of male sterility system in heterosis breeding of Brassica vegetables, future prospects and need for further understanding of these systems are highlighted.
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Affiliation(s)
- Saurabh Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India.
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Raj Kumar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
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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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Kim B, Yang TJ, Kim S. Identification of a gene responsible for cytoplasmic male-sterility in onions (Allium cepa L.) using comparative analysis of mitochondrial genome sequences of two recently diverged cytoplasms. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:313-322. [PMID: 30374528 DOI: 10.1007/s00122-018-3218-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
Almost identical mitochondrial genome sequences of two recently diverged male-fertile normal and male-sterile CMS-T-like cytoplasms were obtained in onions. A chimeric gene, orf725 , was found to be a CMS-inducing gene. In onions (Allium cepa L.), cytoplasmic male-sterility (CMS) has been widely used in hybrid seed production. Two types of CMS (CMS-S and CMS-T) have been reported in onions. A complete mitochondrial genome sequence of the CMS-S cytoplasm has been reported in our previous study. Draft mitochondrial genome sequences of male-fertile normal and CMS-T-like cytoplasms are reported in this study. Raw reads obtained from normal and CMS-T-like cytoplasms were assembled into eight and nine almost identical contigs, respectively. After connection and reorganization of contigs by PCR amplification and genome walking, four scaffold sequences with total length of 339 and 180 bp were produced for the normal cytoplasm. A mitochondrial genome sequence of the CMS-T-like cytoplasm was obtained by mapping trimmed reads of CMS-T onto scaffold sequences of the normal cytoplasm. Compared with the CMS-S mitochondrial genome, the normal mitochondrial genome was highly rearranged with 31 syntenic blocks. A total of 499 single nucleotide polymorphisms (SNPs) or insertions/deletions were identified in these syntenic regions. On the other hand, normal and CMS-T-like mitochondrial genome sequences were almost identical except for orf725, a chimeric gene consisting of cox1 with other sequences. Only three SNPs were identified between normal and CMS-T-like syntenic sequences. These results indicate that orf725 is likely to be the casual gene for CMS induction in onions and that CMS-T-like cytoplasm has recently diverged from the normal cytoplasm by introduction of orf725.
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Affiliation(s)
- Bongju Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper ( Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing. Int J Mol Sci 2019; 20:ijms20030578. [PMID: 30699994 PMCID: PMC6386957 DOI: 10.3390/ijms20030578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 12/14/2022] Open
Abstract
Cytoplasmic male sterility (CMS), which is controlled by mitochondrial genes, is an important trait for commercial hybrid seed production. So far, genes controlling this trait are still not clear in pepper. In this study, complete mitochondrial genomes were sequenced and assembled for the CMS line 138A and its maintainer line 138B. The genome size of 138A is 504,210 bp, which is 8618 bp shorter than that of 138B. Meanwhile, more than 214 and 215 open reading frames longer than 100 amino acids (aas) were identified in 138A and 138B, respectively. Mitochondrial genome structure of 138A was quite different from that of 138B, indicating the existence of recombination and rearrangement events. Based on the mitochondrial genome sequence and structure variations, mitochondrion of 138A and FS4401, a Korean origin CMS line, may have inherited from a common female ancestor, but their CMS traits did originate separately. Candidate gene selection was performed according to the published characteristics of the CMS genes, including the presence SNPs and InDels, located in unique regions, their chimeric structure, co-transcription, and transmembrane domain. A total of 35 ORFs were considered as potential candidate genes and 14 of these were selected, with orf300a and 0rf314a as strong candidates. A new marker, orf300a, was developed which did co-segregate with the CMS trait.
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Zhang B, Zhang X, Liu G, Guo L, Qi T, Zhang M, Li X, Wang H, Tang H, Qiao X, Pei W, Shahzad K, Xing C, Zhang J, Wu J. A combined small RNA and transcriptome sequencing analysis reveal regulatory roles of miRNAs during anther development of Upland cotton carrying cytoplasmic male sterile Gossypium harknessii (D2) cytoplasm. BMC PLANT BIOLOGY 2018; 18:242. [PMID: 30332993 PMCID: PMC6192183 DOI: 10.1186/s12870-018-1446-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/27/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) in flowering plants is usually caused by incompatibility between mitochondrial and nuclear genomes, and can be restored by nuclear genes known as restorer-of-fertility (Rf). Although the CMS/Rf system is useful and convenient for economic production of commercial hybrid seed, the molecular mechanisms of CMS occurrence and fertility restoration in cotton are unclear. RESULTS Here, a combined small RNA and transcriptome sequencing analysis was performed on floral buds at the meiosis stage in three-line hybrid cotton system, and differentially expressed microRNAs (DEMs) and their target genes were identified and further analyzed for a possible involvement in CMS and fertility restoration. Totally 10 and 30 differentially expressed miRNA-target gene pairs were identified in A-B and A-R comparison group, respectively. A putative regulatory network of CMS occurrence and fertility restoration-related miRNA-target pairs during anther development were then constructed. The RLM-RACE analysis showed that gra-miR7505b regulates a PPR gene (Gh_D05G3392) by cleaving precisely at the 643 nt and 748 nt sites. The further analysis indicated that the sequence variation in the binding regions of Gh_D05G3392 and Gh_D05G3356 may cause a lower cleavage efficiency of the PPR genes by miR7505b and miR7505 in R line, respectively, leading to the up-regulation of the PPR genes and fertility restoration. These results have established their genetic involvement in fertility restoration in the CMS-D2 system. CONCLUSION Our combined miRNA and transcriptome analysis in three-line hybrid cotton system provides new insights into the molecular mechanisms of CMS occurrence and fertility restoration, which will contribute to further hybrid breeding in cotton.
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Affiliation(s)
- Bingbing Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Liping Guo
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xue Li
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Huini Tang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003 USA
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, 38 Huanghe Dadao, Anyang, 455000 Henan China
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22
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Arimura SI, Yanase S, Tsutsumi N, Koizuka N. The mitochondrial genome of an asymmetrically cell-fused rapeseed, Brassica napus, containing a radish-derived cytoplasmic male sterility-associated gene. Genes Genet Syst 2018; 93:143-148. [DOI: 10.1266/ggs.18-00005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Shungo Yanase
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
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23
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Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. Sci Rep 2018; 8:7353. [PMID: 29743507 PMCID: PMC5943242 DOI: 10.1038/s41598-018-25585-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/24/2018] [Indexed: 12/31/2022] Open
Abstract
The concept of U's triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2-6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U's triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.
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24
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Kim YJ, Zhang D. Molecular Control of Male Fertility for Crop Hybrid Breeding. TRENDS IN PLANT SCIENCE 2018; 23:53-65. [PMID: 29126789 DOI: 10.1016/j.tplants.2017.10.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 05/22/2023]
Abstract
In many plant species, male-sterile female lines with cytoplasmic male sterility (CMS) or nuclear-controlled environment-sensitive genic male sterility (EGMS) have long been used to efficiently produce hybrids that harness hybrid vigor or heterosis. However, the underlying molecular mechanisms for these applications have only recently been uncovered in a few species. We provide here an update on the understanding of cytoplasmic-nuclear communication based on the discovery of mitochondrial CMS genes and their corresponding nuclear fertility determinants. Recent findings that uncover diverse mechanisms such as epigenetic, transcriptional, and post-transcriptional controls of EGMS by temperature and photoperiod signals are also reviewed. Furthermore, translational research that applies basic knowledge of plant male fertility control to hybrid seed production practice is highlighted.
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Affiliation(s)
- Yu-Jin Kim
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin 446-701, South Korea
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; School of Agriculture, Food, and Wine, University of Adelaide, South Australia 5064, Australia.
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25
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Kim B, Kim K, Yang TJ, Kim S. Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split. Curr Genet 2016; 62:873-885. [PMID: 27016941 DOI: 10.1007/s00294-016-0595-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/16/2023]
Abstract
Cytoplasmic male-sterility (CMS) conferred by the CMS-S cytoplasm has been most commonly used for onion (Allium cepa L.) F1 hybrid seed production. We first report the complete mitochondrial genome sequence containing CMS-S cytoplasm in this study. Initially, seven contigs were de novo assembled from 150-bp paired-end raw reads produced from the total genomic DNA using the Illumina NextSeq500 platform. These contigs were connected into a single circular genome consisting of 316,363 bp (GenBank accession: KU318712) by PCR amplification. Although all 24 core protein-coding genes were present, no ribosomal protein-coding genes, except rps12, were identified in the onion mitochondrial genome. Unusual trans-splicing of the cox2 gene was verified, and the cox1 gene was identified as part of the chimeric orf725 gene, which is a candidate gene responsible for inducing CMS. In addition to orf725, two small chimeric genes were identified, but no transcripts were detected for these two open reading frames. Thirteen chloroplast-derived sequences, with sizes of 126-13,986 bp, were identified in the intergenic regions. Almost 10 % of the onion mitochondrial genome was composed of repeat sequences. The vast majority of repeats were short repeats of <100 base pairs. Interestingly, the gene encoding ccmFN was split into two genes. The ccmF N gene split is first identified outside the Brassicaceae family. The breakpoint in the onion ccmF N gene was different from that of other Brassicaceae species. This split of the ccmF N gene was also present in 30 other Allium species. The complete onion mitochondrial genome sequence reported in this study would be fundamental information for elucidation of onion CMS evolution.
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Affiliation(s)
- Bongju Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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26
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Mei S, Liu T, Wang Z. Comparative Transcriptome Profile of the Cytoplasmic Male Sterile and Fertile Floral Buds of Radish (Raphanus sativus L.). Int J Mol Sci 2016; 17:E42. [PMID: 26751440 PMCID: PMC4730287 DOI: 10.3390/ijms17010042] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 11/16/2022] Open
Abstract
Radish cytoplasmic male sterility (CMS) has been widely used for breeding in Raphanus and Brassica genera. However, the detailed regulation network of the male sterility remains to be determined. Our previous work has shown that the abnormalities in a CMS radish appeared shortly after the tetrad stage when microspores were malformed and the tapetal cells grew abnormally large. In this work, histological analysis shows that anthers are at the tetrad stage when the radish buds are about 1.5 mm in length. Furthermore, a high throughput RNA sequencing technology was employed to characterize the transcriptome of radish buds with length about 1.5 mm from two CMS lines possessing the CMS-inducing orf138 gene and corresponding near-isogenic maintainer lines. A total of 67,140 unigenes were functionally annotated. Functional terms for these genes are significantly enriched in 55 Gene Ontology (GO) groups and 323 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome detected transcripts for 72 out of a total of 79 protein genes encoded in the chloroplast genome from radish. In contrast, the radish mitochondrial genome contains 34 protein genes, but only 16 protein transcripts were detected from the transcriptome. The transcriptome comparison between CMS and near-isogenic maintainer lines revealed 539 differentially expressed genes (DEGs), indicating that the false positive rate for comparative transcriptome profiling was clearly decreased using two groups of CMS/maintainer lines with different nuclear background. The level of 127 transcripts was increased and 412 transcripts were decreased in the CMS lines. No change in levels of transcripts except CMS-inducing orf138 was identified from the mitochondrial and chloroplast genomes. Some DEGs which would be associated with the CMS, encoding MYB and bHLH transcription factors, pentatricopeptide repeat (PPR) proteins, heat shock transcription factors (HSFs) and heat shock proteins (HSPs), are discussed. The transcriptome dataset and comparative analysis will provide an important resource for further understanding anther development, the CMS mechanism and to improve molecular breeding in radish.
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Affiliation(s)
- Shiyong Mei
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Zhiwei Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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27
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Kim S, Kim CW, Park M, Choi D. Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015. [PMID: 26215184 DOI: 10.1007/s00122-015-2584-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A combination of BSA and RNA-seq was performed to identify candidates for the restorer-of-fertility gene in onion. The AcPMS1 involved in DNA mismatch repair was identified as the best candidate. To identify candidate genes of the restorer-of-fertility gene (Ms) responsible for fertility restoration of onion cytoplasmic male-sterility, a combined approach of bulked segregant analysis and RNA-seq was employed. From 32,674 de novo assembled contigs, 430 perfectly homozygous SNPs between male-fertile (MF) and male-sterile (MS) bulks were identified in 141 contigs. After verifying the homozygosity of the SNPs by PCR amplification and sequencing, the SNPs on 139 of the contigs were genotypes for the two recombinants which contained crossover events between the Ms locus and two tightly linked molecular markers. As a result, 30 contigs showing perfect linkage with the Ms locus in the large-sized segregating population were identified. Among them, 14 showed perfect linkage disequilibrium (LD) with the Ms locus, as determined by genotyping 251 domestic breeding lines. Furthermore, molecular markers tagging the 14 contigs also showed almost perfect LD with each other in 124 exotic accessions introduced from 21 countries, except for one accession which contained a crossover event by which the 14 markers were divided into two groups. After sequencing of the full-length cDNA of the 14 contigs showing perfect LD, the deduced amino acids sequences of the MF and MS alleles were compared. Four genes were shown to harbor putative critical amino acid changes in the known domains. Among them, the gene encoding PMS1, involved in the DNA mismatch repair pathway, was assumed to be the best candidate gene responsible for fertility restoration of male-sterility in onion.
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Affiliation(s)
- Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Kwangju, 500-757, Korea.
| | - Cheol-Woo Kim
- National Institute of Horticultural & Herbal Science, RDA, Muan, 534-833, Korea
| | - Minkyu Park
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Doil Choi
- Department of Plant Science, Seoul National University, Seoul, Korea
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28
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Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, Lee HJ, Park JY, Perumal S, Jayakodi M, Lee YS, Kim B, Copetti D, Kim S, Kim S, Lim KB, Kim YD, Lee J, Cho KS, Park BS, Wing RA, Yang TJ. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Sci Rep 2015; 5:15655. [PMID: 26506948 PMCID: PMC4623524 DOI: 10.1038/srep15655] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/30/2015] [Indexed: 12/15/2022] Open
Abstract
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
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Affiliation(s)
- Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.,Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Kiwoung Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hong-Il Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jonghoon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun Oh Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyeon Ju Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Backki Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Hallym University, Chuncheon, Kangwon-do, 200-702, Republic of Korea
| | - Jungho Lee
- Green Plant Institute, #2-202 Biovalley, 89 Seoho-ro, Kwonseon-gu, Suwon, Republic of Korea
| | - Kwang-Su Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang-gun, Kangwon-do, 232-955, Republic of Korea
| | - Beom-Seok Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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29
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Lee YP, Cho Y, Kim S. A high-resolution linkage map of the Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility in radish (Raphanus sativus L.) produced by a combination of bulked segregant analysis and RNA-Seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2243-52. [PMID: 25119873 DOI: 10.1007/s00122-014-2376-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/02/2014] [Indexed: 05/13/2023]
Abstract
We utilized a combination of BSA and RNA-Seq to identify SNPs linked to the Rfd1 locus, a restorer-of-fertility gene in radish. A high-density linkage map was constructed using this approach. Male fertility of cytoplasmic male sterility conditioned by the Dongbu cytoplasmic and genic male-sterility cytoplasm can be restored by a restorer-of-fertility locus, Rfd1, in radish. To construct a high-density linkage map and to identify a candidate gene for the Rfd1 locus, bulked segregant analysis and RNA-seq approaches were combined. A total of 26 and 28 million reads produced from male-fertile and male-sterile bulked RNA were mapped to the radish reference unigenes. After stringent screening of SNPs, 327 reliable SNPs of 109 unigenes were selected. Arabidopsis homologs for 101 of the 109 genes were clustered around the 4,000 kb region of Arabidopsis chromosome 3, which was syntenic to the Rfd1 flanking region. Since the reference unigene set was incomplete, the contigs were de novo assembled to identify 134 contigs harboring SNPs. Most of SNP-containing contigs were also clustered on the same syntenic region in Arabidopsis chromosome. A total of 21 molecular markers positioned within a 2.1 cM interval including the Rfd1 locus were developed, based on the selected unigenes and contigs. A segregating population consisting of 10,459 individuals was analyzed to identify recombinants containing crossovers within this interval. A total of 284 identified recombinants were then used to construct a high-density map, which delimited the Rfd1 locus into an 83-kb syntenic interval of Arabidopsis chromosome 3. Since no candidate gene, such as a pentatricopeptide repeat (PPR)-coding gene, was found in this interval, 231 unigenes and 491 contigs containing putative PPR motifs were analyzed further, but no PPR gene in linkage disequilibrium with the Rfd1 locus could be found.
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Affiliation(s)
- Young-Pyo Lee
- Biotech Research Center, Dongbu Advanced Research Institute, Dongbu Hannong Co., Ltd., Daejeon, 305-708, Korea
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30
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Hao W, Fan S, Hua W, Wang H. Effective extraction and assembly methods for simultaneously obtaining plastid and mitochondrial genomes. PLoS One 2014; 9:e108291. [PMID: 25251391 PMCID: PMC4177114 DOI: 10.1371/journal.pone.0108291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/15/2014] [Indexed: 11/25/2022] Open
Abstract
Background In conventional approaches to plastid and mitochondrial genome sequencing, the sequencing steps are performed separately; thus, plastid DNA (ptDNA) and mitochondrial DNA (mtDNA) should be prepared independently. However, it is difficult to extract pure ptDNA and mtDNA from plant tissue. Following the development of high-throughput sequencing technology, many researchers have attempted to obtain plastid genomes or mitochondrial genomes using high-throughput sequencing data from total DNA. Unfortunately, the huge datasets generated consume massive computing and storage resources and cost a great deal, and even more importantly, excessive pollution reads affect the accuracy of the assembly. Therefore, it is necessary to develop an effective method that can generate base sequences from plant tissue and that is suitable for all plant species. Here, we describe a highly effective, low-cost method for obtaining plastid and mitochondrial genomes simultaneously. Results First, we obtained high-quality DNA employing Partial Concentration Extraction. Second, we evaluated the purity of the DNA sample and determined the sequencing dataset size employing Vector Control Quantitative Analysis. Third, paired-end reads were obtained using a high-throughput sequencing platform. Fourth, we obtained scaffolds employing Two-step Assembly. Finally, we filled in gaps using specific methods and obtained complete plastid and mitochondrial genomes. To ensure the accuracy of plastid and mitochondrial genomes, we validated the assembly using PCR and Sanger sequencing. Using this method,we obtained complete plastid and mitochondrial genomes with lengths of 153,533 nt and 223,412 nt separately. Conclusion A simple method for extracting, evaluating, sequencing and assembling plastid and mitochondrial genomes was developed. This method has many advantages: it is timesaving, inexpensive and reproducible and produces high-quality sequence. Furthermore, this method can produce plastid and mitochondrial genomes simultaneously and be used for other plant species. Due to its simplicity and extensive applicability, this method will support research on plant cytoplasmic genomes.
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Affiliation(s)
- Wanjun Hao
- Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Shihang Fan
- Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan, China
- College of Life Sciences, Hubei University, Wuhan, China
| | - Wei Hua
- Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan, China
- * E-mail:
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Wang Y, Chu P, Yang Q, Chang S, Chen J, Hu M, Guan R. Complete mitochondrial genome of Eruca sativa Mill. (Garden rocket). PLoS One 2014; 9:e105748. [PMID: 25157569 PMCID: PMC4144905 DOI: 10.1371/journal.pone.0105748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/26/2014] [Indexed: 11/18/2022] Open
Abstract
Eruca sativa (Cruciferae family) is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247 696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic structure of the Eruca sativa mtDNA compared with other cruciferous mitotypes. Comparison with the Brassica napus MtDNA revealed that most of the genes with known function are conserved between these two mitotypes except for the ccmFN2 and rrn18 genes, and 27 point mutations were scattered in the 14 protein-coding genes. Evolutionary relationships analysis suggested that Eruca sativa is more closely related to the Brassica species and to Raphanus sativus than to Arabidopsis thaliana.
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Affiliation(s)
- Yankun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qing Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shengxin Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jianmei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Maolong Hu
- Institute of Economic Crop, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Nanjing Agricultural University, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
- * E-mail:
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Jo YD, Choi Y, Kim DH, Kim BD, Kang BC. Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing. BMC Genomics 2014; 15:561. [PMID: 24996600 PMCID: PMC4108787 DOI: 10.1186/1471-2164-15-561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/20/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. RESULTS We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. CONCLUSIONS Although large portion of sequence context was shared by mitochondrial genomes of CMS and male-fertile pepper lines, extensive genome rearrangements were detected. CMS candidate genes located on the edges of highly-rearranged CMS-specific DNA regions and near to repeat sequences. These characteristics were detected among CMS-associated genes in other species, implying a common mechanism might be involved in the evolution of CMS-associated genes.
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Affiliation(s)
- Yeong Deuk Jo
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
- />Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185 South Korea
| | - Yoomi Choi
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
| | - Dong-Hwan Kim
- />Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Byung-Dong Kim
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
| | - Byoung-Cheorl Kang
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
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Jeong YM, Chung WH, Choi AY, Mun JH, Kim N, Yu HJ. The complete mitochondrial genome of cultivated radish WK10039 (Raphanus sativus L.). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:941-2. [PMID: 24937570 DOI: 10.3109/19401736.2014.926496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined the complete nucleotide sequence of the mitochondrial genome of radish cultivar WK10039 (Raphanus sativus L.). The total length of the mtDNA sequence is 244,054 bp, with GC content of 45.3%. The radish mtDNA contains 82 protein-coding genes, 17 tRNA genes, and 3 rRNA genes. Among the protein-coding genes, 34 encode proteins with known functions. There are two 5529 bp repeats in the radish mitochondrial genome that may contribute to DNA recombination resulting in at least three different forms of mtDNA in radish.
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Affiliation(s)
- Young-Min Jeong
- a Department of Life Science , The Catholic University of Korea , Bucheon , Korea
| | - Won-Hyung Chung
- b Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology , Daejeon , Korea
| | - Ah Young Choi
- c National Instrumentation Center for Environmental Management, Seoul National University , Seoul , Korea , and
| | - Jeong-Hwan Mun
- d Department of Bioscience and Bioinformatics , Myongji University , Yongin , Korea
| | - Namshin Kim
- b Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology , Daejeon , Korea
| | - Hee-Ju Yu
- a Department of Life Science , The Catholic University of Korea , Bucheon , Korea
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Yan J, Tian H, Wang S, Shao J, Zheng Y, Zhang H, Guo L, Ding Y. Pollen developmental defects in ZD-CMS rice line explored by cytological, molecular and proteomic approaches. J Proteomics 2014; 108:110-23. [PMID: 24878425 DOI: 10.1016/j.jprot.2014.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Cytoplasmic male sterility (CMS) is a widely observed phenomenon, which is especially useful in hybrid seed production. Meixiang A (MxA) is a new rice CMS line derived from a pollen-free sterile line named Yunnan ZidaoA (ZD-CMS). In this study, a homologous WA352 gene with variation in two nucleotides was identified in MxA. Cytological analysis revealed that MxA was aborted in the early uninucleate stage. The protein expression profiles of MxA and its maintainer line MeixiangB (MxB) were systematically compared using iTRAQ-based quantitative proteomics technology using young florets at the early uninucleate stage. A total of 688 proteins were quantified in both rice lines, and 45 of these proteins were found to be differentially expressed. Bioinformatics analysis indicated a large number of the proteins involved in carbohydrate metabolism or the stress response were downregulated in MxA, suggesting that these metabolic processes had been hindered during pollen development in MxA. The ROS (reactive oxygen species) level was increased in the mitochondrion of MxA, and further ultrastructural analysis showed the mitochondria with disrupted cristae in the rice CMS line MxA. These findings substantially contribute to our knowledge of pollen developmental defects in ZD-CMS rice line. BIOLOGICAL SIGNIFICANCE MeixiangA (MxA) is a new type of rice CMS line, which is derived from pollen-free sterile line Yunnan ZidaoA. In this study, the cytological, molecular and proteomic approaches were used to study the characteristics of this new CMS line. Cytological study indicates the CMS line is aborted at the early uninucleate stage. A potential sterile gene ZD352 is identified in MxA, the protein product of which is mainly accumulated at the MMC/Meiotic stage. iTRAQ based proteomic analysis is performed to study the relevant proteins involved in the CMS occurance, 45 proteins are found to be significant differentially expressed and these proteins are involved in many cellular processes such as carbohydrate metabolism, stress response, protein synthesis. To our knowledge, this is the first report using the iTRAQ-labeled quantitative proteomic to study the protein expression variation during the abortion processes between a CMS line and its maintainer line. These results provide new insights on the CMS mechanisms of ZD-CMS rice line.
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Affiliation(s)
- Junjie Yan
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Han Tian
- State Key Laboratory of Virology, Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Shuzhen Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Jinzhen Shao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yinzhen Zheng
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Lin Guo
- State Key Laboratory of Virology, Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China.
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Yamagishi H, Bhat SR. Cytoplasmic male sterility in Brassicaceae crops. BREEDING SCIENCE 2014; 64:38-47. [PMID: 24987289 PMCID: PMC4031109 DOI: 10.1270/jsbbs.64.38] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/05/2013] [Indexed: 05/20/2023]
Abstract
Brassicaceae crops display strong hybrid vigor, and have long been subject to F1 hybrid breeding. Because the most reliable system of F1 seed production is based on cytoplasmic male sterility (CMS), various types of CMS have been developed and adopted in practice to breed Brassicaceae oil seed and vegetable crops. CMS is a maternally inherited trait encoded in the mitochondrial genome, and the male sterile phenotype arises as a result of interaction of a mitochondrial CMS gene and a nuclear fertility restoring (Rf) gene. Therefore, CMS has been intensively investigated for gaining basic insights into molecular aspects of nuclear-mitochondrial genome interactions and for practical applications in plant breeding. Several CMS genes have been identified by molecular genetic studies, including Ogura CMS from Japanese radish, which is the most extensively studied and most widely used. In this review, we discuss Ogura CMS, and other CMS systems, and the causal mitochondrial genes for CMS. Studies on nuclear Rf genes and the cytoplasmic effects of alien cytoplasm on general crop performance are also reviewed. Finally, some of the unresolved questions about CMS are highlighted.
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Affiliation(s)
- Hiroshi Yamagishi
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo, Kita, Kyoto 603-8555,
Japan
- Corresponding author (e-mail: )
| | - Shripad R. Bhat
- National Research Centre of Plant Biotechnology,
New Delhi 10012,
India
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Heng S, Wei C, Jing B, Wan Z, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288. BMC Genomics 2014; 15:322. [PMID: 24884490 PMCID: PMC4035054 DOI: 10.1186/1471-2164-15-322] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 04/23/2014] [Indexed: 11/10/2022] Open
Abstract
Background Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288. Results Through next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line “J163-4” are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity. Conclusion The hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the mechanism of natural CMS in B. juncea, performing comparative analysis on sequenced mitochondrial genomes in Brassicas, and uncovering the origin of the hau CMS mitotype and structural and evolutionary differences between different mitotypes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-322) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P,R, China.
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Mitochondrion role in molecular basis of cytoplasmic male sterility. Mitochondrion 2014; 19 Pt B:198-205. [PMID: 24732436 DOI: 10.1016/j.mito.2014.04.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 11/24/2022]
Abstract
Cytoplasmic male sterility and its fertility restoration via nuclear genes offer the possibility to understand the role of mitochondria during microsporogenesis. In most cases rearrangements in the mitochondrial DNA involving known mitochondrial genes as well as unknown sequences result in the creation of new chimeric open reading frames, which encode proteins containing transmembrane domains. So far, most of the CMS systems have been characterized via restriction fragment polymorphisms followed by transcript analysis. However, whole mitochondrial genome sequence analyses comparing male sterile and fertile cytoplasm open options for deeper insights into mitochondrial genome rearrangements. We more and more start to unravel how mitochondria are involved in triggering death of the male reproductive organs. Reduced levels of ATP accompanied by increased concentrations of reactive oxygen species, which are produced more under conditions of mitochondrial dysfunction, seem to play a major role in the fate of pollen production. Nuclear genes, so called restorer-of-fertility are able to restore the male fertility. Fertility restoration can occur via pentatricopeptide repeat (PPR) proteins or via different mechanisms involving non-PPR proteins.
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Abstract
In plants, male sterility can be caused either by mitochondrial genes with coupled nuclear genes or by nuclear genes alone; the resulting conditions are known as cytoplasmic male sterility (CMS) and genic male sterility (GMS), respectively. CMS and GMS facilitate hybrid seed production for many crops and thus allow breeders to harness yield gains associated with hybrid vigor (heterosis). In CMS, layers of interaction between mitochondrial and nuclear genes control its male specificity, occurrence, and restoration of fertility. Environment-sensitive GMS (EGMS) mutants may involve epigenetic control by noncoding RNAs and can revert to fertility under different growth conditions, making them useful breeding materials in the hybrid seed industry. Here, we review recent research on CMS and EGMS systems in crops, summarize general models of male sterility and fertility restoration, and discuss the evolutionary significance of these reproductive systems.
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Affiliation(s)
- Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
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