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Lin Y, Yang H, Liu H, Lu X, Cao H, Li B, Chang Y, Guo Z, Ding D, Hu Y, Xue Y, Liu Z, Tang J. A P-type pentatricopeptide repeat protein ZmRF5 promotes 5' region partial cleavages of atp6c transcripts to restore the fertility of CMS-C maize by recruiting a splicing factor. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1269-1281. [PMID: 38073308 PMCID: PMC11022799 DOI: 10.1111/pbi.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/31/2023] [Accepted: 11/26/2023] [Indexed: 04/18/2024]
Abstract
A fast evolution within mitochondria genome(s) often generates discords between nuclear and mitochondria, which is manifested as cytoplasmic male sterility (CMS) and fertility restoration (Rf) system. The maize CMS-C trait is regulated by the chimeric mitochondrial gene, atp6c, and can be recovered by the restorer gene ZmRf5. Through positional cloning in this study, we identified the nuclear restorer gene, ZmRf5, which encodes a P-type pentatricopeptide repeat (PPR) family protein. The over-expression of ZmRf5 brought back the fertility to CMS-C plants, whereas its genomic editing by CRISPR/Cas9 induced abortive pollens in the restorer line. ZmRF5 is sorted to mitochondria, and recruited RS31A, a splicing factor, through MORF8 to form a cleaving/restoring complex, which promoted the cleaving of the CMS-associated transcripts atp6c by shifting the major cleavage site from 480th nt to 344 th nt for fast degradation, and preserved just right amount of atp6c RNA for protein translation, providing adequate ATP6C to assembly complex V, thus restoring male fertility. Interestingly, ATP6C in the sterile line CMo17A, with similar cytology and physiology changes to YU87-1A, was accumulated much less than it in NMo17B, exhibiting a contrary trend in the YU87-1 nuclear genome previously reported, and was restored to normal level in the presence of ZmRF5. Collectively these findings unveil a new molecular mechanism underlying fertility restoration by which ZmRF5 cooperates with MORF8 and RS31A to restore CMS-C fertility in maize, complemented and perfected the sterility mechanism, and enrich the perspectives on communications between nucleus and mitochondria.
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Affiliation(s)
- Yanan Lin
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Huili Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Hongmei Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiuyuan Lu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Haofei Cao
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Bing Li
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yongyuan Chang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhanyong Guo
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Dong Ding
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yanmin Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yadong Xue
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zonghua Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
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Liu Y, Xu Z, Du Y, Huang B, Li M, Zhang L, Zhao X, Liu Q, Tang S, Zhang H. Mapping of Rf20(t), a minor fertility restorer gene for rice wild abortive cytoplasmic male sterility in the maintainer line 'Zhenshan97B'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:248. [PMID: 37978996 DOI: 10.1007/s00122-023-04486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023]
Abstract
Three-line hybrid rice has primarily been developed on wild abortive (WA)-type cytoplasmic male sterility (CMS) and has helped increase the yield of rice globally. The development of WA-type CMS lines and hybrids was expedited through the identification and mapping of the fertility restorer gene (Rf) in maintainers. This study observed fertile plants in WA-TianfengA/Zhenshan97B//TianfengB population, indicating that the maintainer line 'Zhenshan97B' should carry Rfs for WA-type CMS. Several advanced backcross populations were generated with the genetic background of the 'WA-TianfengA,' and the pollen fertility levels of the backcrossed individuals in BC3F1, BC4F1 and BC4F2 populations are governed by a new gene, Rf20(t), from 'Zhenshan97B.' Employing bulk segregant analysis of fertile and sterile pools from the BC4F1 population, Rf20(t) was genetically mapped to a candidate region on chromosome 10. Subsequently, Rf20(t) was located between RM24883 and RM24919 through recombination analysis of molecular markers using the BC4F2 population. Implementing a substitution mapping strategy, Rf20(t) was ultimately mapped to a 245-kb region between the molecular markers STS10-122 and STS10-126 and obtained the most likely candidate gene LOC_Os10g02650, which is predicted to encode pentatricopeptide repeat-containing (PPR) protein. These results enhance our understanding of the fertility restoration of WA-type CMS lines, facilitating the development of high-quality pairs of WA-type CMS and maintainer lines.
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Affiliation(s)
- Yang Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Yuanyue Du
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Benxi Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Meng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Lijia Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiangqiang Zhao
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Honggen Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
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Zhang P, Zhao Z, Zheng M, Liu Y, Niu Q, Liu X, Shi Z, Yi H, Yu T, Rong T, Cao M. Fine mapping and candidate gene analysis of a novel fertility restorer gene for C-type cytoplasmic male sterility in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:234. [PMID: 37878085 DOI: 10.1007/s00122-023-04480-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE A novel strong fertility restorer gene Rf12 for C-type cytoplasmic male sterility of maize was finely mapped on chromosome 2. Its best candidate gene Zm00001d007531 is predicted to encode a p-type PPR protein. The lack of strong restorer gene of maize CMS-C greatly limits its application in hybrid seed production. Therefore, the cloning of maize CMS-C novel strong restorer genes is necessary. In this study, a strong restorer line ZH91 for maize CMS-C was found, and the novel restorer gene named Rf12 in ZH91 had been mapped in a 146 kb physical interval on maize chromosome 2. Using the third-generation high-throughput sequencing (ONT), the whole genome sequence of ZH91 was got, and with integrating the annotation information of the reference genome B73_RefGen_v4 and B73_RefGen_v5, four candidate genes were predicted in ZH91 within the mapping region. Then using gene cloning, stranded specific RNA sequencing, qRT-PCR analysis and subcellular localization, Zm00001d007531 was identified as the most likely candidate gene of Rf12. Zm00001d007531 encodes a p-type PPR protein with 19 PPR motifs and targets mitochondria and chloroplast. Stranded specific RNA sequencing and qRT-PCR results both show that the expression of Zm00001d007531 between anthers of near-isogenic lines C478Rf12Rf12 and C478rf12rf12 was significantly difference in pollen mother cell stage. And the result of sequence alignment for Zm00001d007531 gene in 60 materials showed that there are twelve SNPs in CDS region of Zm00001d007531 were tightly linked to the fertility. The finding of a novel strong restorer germplasm resource ZH91 for maize CMS-C can greatly promote the application of maize CMS-C line in maize hybrid seeds production, and the identification of candidate gene Zm00001d007531 can accelerate the backcrossing process of maize CMS-C strong restorer gene Rf12 to some extent.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Zhuofan Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Mingmin Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
- Chengdu Normal University, Chengdu, 611130, Wenjiang, China
| | - Yongming Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
- Laboratory of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213, China
| | - Qunkai Niu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
- Chengdu Agricultural College, Chengdu, 611130, Wenjiang, China
| | - Xiaowei Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Ziwen Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Hongyang Yi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Tao Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Tingzhao Rong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China
| | - Moju Cao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, Wenjiang, China.
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Cai W, Li W, Duan L, Chen Y, Zhang F, Hu B, Xie J. Genetic Analysis of Novel Fertility Restoration Genes ( qRf3 and qRf6) in Dongxiang Wild Rice Using GradedPool-Seq Mapping and QTL-Seq Correlation Analysis. Int J Mol Sci 2023; 24:14832. [PMID: 37834281 PMCID: PMC10573815 DOI: 10.3390/ijms241914832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The improvement of grain yield, quality, and resistance can be achieved through the utilization of heterosis. The combination of cytoplasmic male sterility (CMS) and fertility restoration (Rf) gene(s) greatly facilitates the commercial development of three-line hybrid rice based on heterosis. The basis for investigating the relationship between CMS and Rf genes lies in the rapid localization of wild rice fertility restoration genes. A set of the BC4F5 population derived from interspecific crosses between Xieqingzao B (XB) and the BC1F9 XB//Dongxiang wild rice (DWR)/XB line L5339 was used to detect quantitative trait loci (QTL) for fertility restoration. The population was then crossed with two male sterile lines, Zhong9A (Z9A) and DongB11A (DB11A), in order to generate a testcrossing population for investigating spikelet fertility. Based on the linkage mapping, seven QTLs were detected on chromosomes 1, 3, 5, 6, 8, and 10, explaining 2.76 to 12.46% of the phenotypic variation. Of them, two novel fertility restoration QTLs, qRf3 and qRf6, can restore fertility of the CMS-DWR line DB11A by 16.56% and 15.12%, respectively. By employing joint QTL-seq and GradedPool-Seq methods, two novel Rf QTLs for DB11A, qRf3 and qRf6, were identified at the physical locations of 10,900,001-11,700,000 bp and 28,016,785-31,247,556 bp, respectively. These findings are useful for exploring the natural variations of Rf genes in rice. Therefore, rice's new genetic resources for the selection and breeding of rice restorer lines provide promising candidates for QTL fine localization and clarification.
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Affiliation(s)
- Wenshan Cai
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Wanlin Li
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Liuying Duan
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Yaling Chen
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Fantao Zhang
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
| | - Biaolin Hu
- Rice Research Institute, National Engineering Laboratory for Rice (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jiankun Xie
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang 330200, China; (W.C.); (W.L.); (L.D.); (Y.C.); (F.Z.)
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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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Farinati S, Draga S, Betto A, Palumbo F, Vannozzi A, Lucchin M, Barcaccia G. Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1223861. [PMID: 37521915 PMCID: PMC10382145 DOI: 10.3389/fpls.2023.1223861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.
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Xu Y, Yu D, Chen J, Duan M. A review of rice male sterility types and their sterility mechanisms. Heliyon 2023; 9:e18204. [PMID: 37519640 PMCID: PMC10372310 DOI: 10.1016/j.heliyon.2023.e18204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Male sterility plays an important role in the utilization of heterosis in rice. The establishment of male sterile lines in rice is one of the key technologies in hybrid rice production systems. The currently widely used male sterile line breeding systems mainly include: three-line hybrid rice based on cytoplasmic male sterility, two-line hybrid rice based on environmental sensitive gene male sterility, and third-generation hybrid rice based on nuclear gene male sterility Seed production system. This study reviewed the types and mechanisms of male sterility in rice, and looked forward to the development direction of hybrid rice.
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Affiliation(s)
- Yusheng Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Dong Yu
- Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Jin Chen
- Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Meijuan Duan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
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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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Cheng C, Nie H, Li H, Adjibolosoo D, Li B, Jiang K, Cui Y, Zhu M, Zhou B, Guo A, Hua J. Identification of fertility restoration candidate genes from a restorer line R186 for Gossypium harknessii cytoplasmic male sterile cotton. BMC PLANT BIOLOGY 2023; 23:175. [PMID: 37016285 PMCID: PMC10071737 DOI: 10.1186/s12870-023-04185-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The utilization of heterosis based on three-line system is an effective strategy in crop breeding. However, cloning and mechanism elucidation of restorer genes for cytoplasmic male sterility (CMS) in upland cotton have yet been realized. RESULTS This research is based on CMS line 2074A with the cytoplasm from Gossypium harknessii (D2-2) and restorer line R186. The offspring of 2074A × R186 were used to conduct genetic analysis. The fertility mechanism of 2074A can be speculated to be governed by multiple genes, since neither the single gene model nor the double genes model could be used. The bulked segregant analysis (BSA) for (2074A × R186) F2 determined the genetic interval of restorer genes on a region of 4.30 Mb on chromosome D05 that contains 77 annotated genes. Four genes were identified as candidates for fertility restoration using the RNA-seq data of 2074A, 2074B, and R186. There are a number of large effect variants in the four genes between 2074A and R186 that could cause amino acid changes. Evolutionary analysis and identity analysis revealed that GH_D05G3183, GH_D05G3384, and GH_D05G3490 have high identity with their homologs in D2-2, respectively. Tissue differential expression analysis revealed that the genes GH_D05G3183, GH_D05G3384, and GH_D05G3490 were highly expressed in the buds of the line R186. The predicted results demonstrated that GH_D05G3183, GH_D05G3384 and GH_D05G3490 might interact with GH_A02G1295 to regulate orf610a in mitochondria. CONCLUSION Our study uncovered candidate genes for fertility restoration in the restorer line R186 and predicted the possible mechanism for restoring the male fertility in 2074A. This research provided valuable insight into the nucleoplasmic interactions.
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Affiliation(s)
- Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Daniel Adjibolosoo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Bin Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Kaiyun Jiang
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yanan Cui
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Meng Zhu
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Baixue Zhou
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China.
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10
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Identification and bioinformatic analysis of the CaCesA/Csls family members and the expression of the CaCslD1 in the flower buds of CMS/Rf system in pepper. Funct Integr Genomics 2022; 22:1411-1431. [PMID: 36138269 DOI: 10.1007/s10142-022-00896-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/04/2022]
Abstract
The cellulose synthase gene superfamily contains cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, which synthesize cellulose and hemicellulose in plant cell walls and play a crucial role in plant growth and development. However, the CesA/Csl gene family has not been reported in pepper. Therefore, the genome-wide research of the CaCesA/CaCsl gene family was conducted in pepper. In this study, a total of 39 CaCesA/CaCsls genes (10 CesAs genes and 29 Csls genes) were identified in pepper and unevenly distributed on 11 chromosomes. These CaCesA/Csls were divided into seven subfamilies (CesAs, CslAs, CslBs, CslCs, CslDs, CslEs, CslGs), and most of CaCesA/Csls genes are closely related to AtCesA/Csls genes. The cis-acting elements in the promoters of CaCesA/Csls genes are mainly related to hormone response and stress response. There are ten collinear gene pairs between the CesA/Csls gene family of pepper and Arabidopsis, and four fragment duplication gene pairs of the CaCesA/Csls genes were discovered. RNA-seq analysis shows that the majority of CaCesA/Csls are expressed in a variety of plant tissues, indicating that most CaCesA/Csls gene expression patterns are not organ-specific, and CaCslD1/D4 have the highest expression in anthers, followed by petal, ovary, and F9. RNA-seq analysis shows that most CaCesA/Csls are responsive to five hormones (IAA, GA3, ABA, SA, and MeJA). The tissue-specific expression analysis of the CaCslD1 gene shows that the CaCslD1 gene is expressed specifically in flowers. In the flower buds IV of cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system, CaCslD1 reach the highest expression respectively. However, the relative expression level of CaCslD1 in the fertile accessions is extremely significantly higher than in the sterile accessions. This study shows an overall understanding of the CaCesA/Csls gene family and provides a new insight for understanding the function of CaCslD1 in pollen development and exploring the fertility restoration of CMS in pepper.
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Fujian cytoplasmic male sterility and the fertility restorer gene OsRf19 provide a promising breeding system for hybrid rice. Proc Natl Acad Sci U S A 2022; 119:e2208759119. [PMID: 35969741 PMCID: PMC9407659 DOI: 10.1073/pnas.2208759119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Although hybrid rice has been widely utilized for nearly half a century, tremendously improving rice productivity worldwide, the breeding of hybrids has been difficult because of genetic complications in male sterility and fertility-restoring systems currently available in rice. Here, we characterized Fujian Abortive cytoplasmic male sterility (CMS-FA) rice, which has shown stable male sterility controlled by the mitochondrial gene FA182; a single nuclear gene, OsRf19, completely restores fertility. This single-gene inheritance has greatly eased the breeding process. By converting CMS-WA hybrids with the CMS-FA system, we developed six hybrids that showed equivalent or better performance relative to their CMS-WA counterparts. CMS-FA/OsRf19 provides a promising system for future hybrid rice breeding. Cytoplasmic male sterility (CMS) determined by mitochondrial genes and restorer of fertility (Rf) controlled by nuclear-encoded genes provide the breeding systems of many hybrid crops for the utilization of heterosis. Although several CMS/Rf systems have been widely exploited in rice, hybrid breeding using these systems has encountered difficulties due to either fertility instability or complications of two-locus inheritance or both. In this work, we characterized a type of CMS, Fujian Abortive cytoplasmic male sterility (CMS-FA), with stable sporophytic male sterility and a nuclear restorer gene that completely restores hybrid fertility. CMS is caused by the chimeric open reading frame FA182 that specifically occurs in the mitochondrial genome of CMS-FA rice. The restorer gene OsRf19 encodes a pentatricopeptide repeat (PPR) protein targeted to mitochondria, where it mediates the cleavage of FA182 transcripts, thus restoring male fertility. Comparative sequence analysis revealed that OsRf19 originated through a recent duplication in wild rice relatives, sharing a common ancestor with OsRf1a/OsRf5, a fertility restorer gene for Boro II and Hong-Lian CMS. We developed six restorer lines by introgressing OsRf19 into parental lines of elite CMS-WA hybrids; hybrids produced from these lines showed equivalent or better agronomic performance relative to their counterparts based on the CMS-WA system. These results demonstrate that CMS-FA/OsRf19 provides a highly promising system for future hybrid rice breeding.
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12
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Histological characterization of anther structure in Tetep-cytoplasmic male sterility and fine mapping of restorer-of-fertility gene in rice. PLoS One 2022; 17:e0268174. [PMID: 35980881 PMCID: PMC9387866 DOI: 10.1371/journal.pone.0268174] [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: 01/25/2022] [Accepted: 04/25/2022] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait that inhibits plants from producing or releasing viable pollen. CMS is caused by mitochondrial–nuclear interaction, and can be rescued by introducing functional nuclear restorer-of-fertility (Rf) gene. The Tetep-CMS/Rf lines were developed through successive inter-subspecific backcrosses between indica and japonica rice accessions. Phenotypic characterization of Tetep-CMS lines revealed abnormal anther dehiscence and the inability to release, while possessing functional pollen. Transverse sections of developing anthers collected from CMS plants showed connective tissue deformities and aberrant dehydration of endothecium and epidermis. Fine mapping of Rf-Tetep using a series of segregating populations, delimited the candidate region to an approximately 109 kb genomic interval between M2099 and FM07 flanking markers. Nanopore long-read sequencing and genome assembly, proceeded by gene prediction and annotation revealed 11 open reading frames (ORFs) within the candidate region, and suggest ORF6 annotated as pentatricopeptide repeat motif containing gene 1 (PPR1), as a possible candidate gene responsible for fertility restoration. This study suggests that tissue-specific abnormalities in anthers are responsible for indehiscence-based sterility, and propose that the functional Rf gene is derived from allelic variation between inter-subspecies in rice.
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Zhang H, Li X, Xu Z, Wan Z, Wang R, Zhao X, Tu G, Liang G, Gu M, Tang S. Precise genetic mapping of Rf18(t), a new fertility restorer gene from 'Nipponbare' for wild abortive cytoplasmic male sterility in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2687-2698. [PMID: 35701585 DOI: 10.1007/s00122-022-04142-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
We mapped Rf18(t), a Restorer-of-fertility gene for wild abortive cytoplasmic male sterility from the japonica maintainer 'Nipponbare', to chromosome 1. The best candidate gene, LOC_Os01g71320, is predicted to encode hexokinase. Three-line hybrid rice obtained through cytoplasmic male sterility (CMS) has helped increase the yield of rice globally, and the wild abortive (WA)-type cytoplasm from wild rice (Oryza rufipogon Griff.) is used widely in three-line indica hybrids. The identification and mapping of the Restorer-of-fertility (Rf) genes in maintainer lines aided in uncovering the genetic basis of fertility restoration of WA-type CMS and the development of WA-type hybrids. In this study, we identified a new Rf gene, Rf18(t), for WA-type CMS from the japonica maintainer line 'Nipponbare' using a chromosome segment substitution line population derived from a cross between the indica line 9311 and 'Nipponbare.' Using a substitution mapping strategy, Rf18(t) was delimited to a 48-kb chromosomal region flanked by molecular marker loci ID01M28791 and ID01M28845 on chromosome 1. By comparative sequence analyses, we propose that LOC_Os01g71320 is the most likely candidate gene for Rf18(t), and it is predicted to encode hexokinase. Furthermore, Rf18(t) was found to function in fertility restoration probably by a posttranscriptional mechanism and its function is dependent on the genetic background of 9311. These results broaden our knowledge on the mechanism of fertility restoration of WA-type CMS lines and will facilitate the development of WA-type rice hybrids.
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Affiliation(s)
- Honggen Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Xixu Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zihao Wan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Ruixuan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | | | - Geliang Tu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Zhang Z, An D, Yu H, Sun L, Cao Y, Zhang B, Wang L. Fine mapping of Rf2, a minor Restorer-of-fertility (Rf) gene for cytoplasmic male sterility in chili pepper G164 (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2699-2709. [PMID: 35710637 DOI: 10.1007/s00122-022-04143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Genome re-sequencing and recombination analyses identified Capana06g000193 as a strong candidate for the minor male fertility restoration locus Rf2 in chili pepper G164 harboring two dominant male fertility restoration genes. Male fertility restoration genes of chili pepper restorer line G164 (Capsicum annuum L.) were studied using molecular marker genotypes of an F2 population (7G) of G164 crossed with the cytoplasmic male sterility line 77013A. The ratio of sterile to fertile single plants in the F2 population was 1:15. This result indicates that chili pepper G164 has two dominant restoration genes, which we designated as Rf1 and Rf2. An individual plant recessive for Rf1 and heterozygous for Rf2, 7G-112 (rf1rf1Rf2rf2), was identified by molecular marker selection and genetic analysis, and a single Rf2 gene-segregating population with a 3:1 ratio of fertile to sterile plants was developed from the self-pollination of male fertile individuals of 77013A and 7G-112 hybrid progeny. Bulk segregant analysis of fertile and sterile pools from the segregating populations was used to genetically map Rf2 to a 3.1-Mb region on chromosome 6. Rf2 was further narrowed to a 179.3-kb interval through recombination analysis of molecular markers and obtained the most likely candidate gene, Capana06g000193.
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Affiliation(s)
- Zhenghai Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Dongliang An
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Hailong Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Liuqing Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Yacong Cao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Baoxi Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Lihao Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China.
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15
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Conjunctive Analyses of BSA-Seq and BSR-Seq Unveil the Msβ-GAL and MsJMT as Key Candidate Genes for Cytoplasmic Male Sterility in Alfalfa (Medicago sativa L.). Int J Mol Sci 2022; 23:ijms23137172. [PMID: 35806189 PMCID: PMC9266382 DOI: 10.3390/ijms23137172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/21/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Knowing the molecular mechanism of male sterility in alfalfa is important to utilize the heterosis more effectively. However, the molecular mechanisms of male sterility in alfalfa are still unclear. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-seq (BSR) were performed with F2 separation progeny to study the molecular mechanism of male sterility in alfalfa. The BSA-seq analysis was located in a candidate region on chromosome 5 containing 626 candidate genes which were associated with male sterility in alfalfa, while the BSR-seq analysis filtered seven candidate DEGs related to male sterility, and these candidate genes including EF-Tu, β-GAL, CESA, PHGDH, and JMT. The conjunctive analyses of BSR and BSA methods revealed that the genes of Msβ-GAL and MsJMT are the common detected candidate genes involved in male sterility in alfalfa. Our research provides a theory basis for further study of the molecular mechanism of male sterility in alfalfa and significant information for the genetic breeding of Medicago sativa.
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Kang MC, Kang HJ, Jung SY, Lee HY, Kang MY, Jo YD, Kang BC. The Unstable Restorer-of-fertility locus in pepper (Capsicum annuum. L) is delimited to a genomic region containing PPR genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1923-1937. [PMID: 35357525 DOI: 10.1007/s00122-022-04084-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Unstable Restorer-of-fertility (Rfu), conferring unstable fertility restoration in the pepper CGMS system, was delimited to a genomic region near Rf and is syntenic to the PPR-like gene-rich region in tomato. The use of cytoplasmic-genic male sterility (CGMS) systems greatly increases the efficiency of hybrid seed production. Although marker development and candidate gene isolation have been performed for the Restorer-of-fertility (Rf) gene in pepper (Capsicum annuum L.), the broad use of CGMS systems has been hampered by the instability of fertility restoration among pepper accessions, especially sweet peppers, due to the widespread presence of the Unstable Restorer-of-fertility (Rfu) locus. Therefore, to investigate the genetic factors controlling unstable fertility restoration in sweet peppers, we developed a segregation population (BC4F5) from crosses using a male-sterile line and an Rfu-containing line. Segregation did not significantly deviate from a 3:1 ratio for unstable fertility restoration to sterility, indicating single dominant locus control for unstable fertility restoration in this population. Genetic mapping delimited the Rfu locus to a 398 kb genomic region on chromosome 6, which is close to but different from the previously identified Rf-containing region. The Rfu-containing region harbors a pentatricopeptide repeat (PPR) gene, along with 10 other candidate genes. In addition, this region is syntenic to the genomic region containing the largest number of Rf-like PPR genes in tomato. Therefore, the dynamic evolution of PPR genes might be responsible for both the restoration and instability of fertility in pepper. During genetic mapping, we developed various molecular markers, including one that co-segregated with Rfu. These markers showed higher accuracy for genotyping than previously developed markers, pointing to their possible use in marker-assisted breeding of sweet peppers.
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Affiliation(s)
- Moo Chan Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hwa-Jeong Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - So-Young Jung
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hae-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min-Young Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, 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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Sun Y, Zhang Y, Jia S, Lin C, Zhang J, Yan H, Peng B, Zhao L, Zhang W, Zhang C. Identification of a Candidate restorer-of-fertility Gene Rf3 Encoding a Pentatricopeptide Repeat Protein for the Cytoplasmic Male Sterility in Soybean. Int J Mol Sci 2022; 23:5388. [PMID: 35628200 PMCID: PMC9140608 DOI: 10.3390/ijms23105388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
The cytoplasmic male sterility/restorer-of-fertility (CMS/Rf) system plays a vital role in high-efficiency hybrid seed production in crops, including soybean (Glycine max (L.) Merr.). The markers linked to fertility restoration and the restorer-of-fertility (Rf) genes are essential because they can facilitate the breeding of new CMS lines and production of commercial hybrid soybean seeds. To date, several soybean Rf genes have been mapped to various genetic loci in diverse genetic populations. However, the mapping range of restorer genes remains narrow, with relatively limited practical applicability. Therefore, in the present study, F2 and F3 segregating populations derived from the CMS line JLCMS5A crossed with the restorer line JLR2 were developed and used for Rf3 gene fine mapping. Genetic investigation indicated that the restorer line JLR2 was controlled by a single dominant gene, Rf3. By integrating bulk-segregant analysis and next-generation sequencing, a 4 Mb region on chromosome 9 was identified, which was most likely the target region harboring the candidate gene responsible for fertility restoration. This region was further narrowed down to 86.44 Kb via fine mapping in F2 and F3 populations using SSR, InDel, and dCAPS markers. This region contained 10 putative genes (Glyma.09G171100-Glyma.09G172000). Finally, Glyma.09G171200, which encodes a mitochondria-targeted pentatricopeptide repeat protein, was proposed as the potential candidate for Rf3 using sequence alignment and expression analysis in restorer and CMS lines. Based on single-nucleotide polymorphisms in Glyma.09G171200, a CAPS marker co-segregated with Rf3 named CAPS1712 was developed. Our results will be fundamental in the assisted selection and creation of potent lines for the production and rapid selection of novel restorer lines.
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Affiliation(s)
- Yanyan Sun
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Yan Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Shungeng Jia
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Chunjing Lin
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Jingyong Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Hao Yan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Bao Peng
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Limei Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Wei Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Chunbao Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
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18
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Li J, Yang H, Xu G, Deng K, Yu J, Xiang S, Zhou K, Zhang Q, Li R, Li M, Ling Y, Yang Z, He G, Zhao F. QTL Analysis of Z414, a Chromosome Segment Substitution Line with Short, Wide Grains, and Substitution Mapping of qGL11 in Rice. RICE (NEW YORK, N.Y.) 2022; 15:25. [PMID: 35532865 PMCID: PMC9085999 DOI: 10.1186/s12284-022-00571-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/27/2022] [Indexed: 05/17/2023]
Abstract
Most agronomic traits of rice (Oryza sativa), such as grain length, are complex traits controlled by multiple genes. Chromosome segment substitution lines (CSSLs) are ideal materials for dissecting these complex traits. We developed the novel rice CSSL 'Z414', which has short, wide grains, from progeny of the recipient parent 'Xihui 18' (an indica restorer line) and the donor parent 'Huhan 3' (a japonica cultivar). Z414 contains four substitution segments with an average length of 3.04 Mb. Z414 displays seven traits that significantly differ from those of Xihui 18, including differences in grain length, width, and weight; degree of chalkiness; and brown rice rate. We identified seven quantitative trait loci (QTL) that are responsible for these differences in an F2 population from a cross between Xihui 18 and Z414. Among these, six QTL (qPL3, qGW5, qGL11, qRLW5, qRLW11, and qGWT5) were detected in newly developed single-segment substitution lines (SSSLs) S1-S6. In addition, four QTL (qGL3, qGL5, qCD3, and qCD5) were detected in S1 and S5. Analysis of these SSSLs attributed the short, wide grain trait of Z414 to qGL11, qGL3, qGL5, and qGW5. Substitution mapping delimited qGL11 within an 810-kb interval on chromosome 11. Sequencing, real time quantitative PCR, and cell morphology analysis revealed that qGL11 might be a novel QTL encoding the cyclin CycT1;3. Finally, pyramiding qGL3 (a = 0.43) and qGL11 (a = - 0.37) led to shorter grains in the dual-segment substitution line D2 and revealed that qGL11 is epistatic to qGL3. In addition, S1 and D2 exhibited different grain sizes and less chalkiness than Z414. In conclusion, the short grain phenotype of the CSSL Z414 is controlled by qGL11, qGL3, and qGL5. qGL11 might be a novel QTL encoding CycT1;3, whose specific role in regulating grain length was previously unknown, and qGL11 is epistatic to qGL3. S1 and D2 could potentially be used in hybrid rice breeding.
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Affiliation(s)
- Juan Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hongxia Yang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guangyi Xu
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Keli Deng
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jinjin Yu
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Qiuli Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhenglin Yang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Sun S, Wang Z, Xiang S, Lv M, Zhou K, Li J, Liang P, Li M, Li R, Ling Y, He G, Zhao F. Identification, pyramid, and candidate gene of QTL for yield-related traits based on rice CSSLs in indica Xihui18 background. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:19. [PMID: 37309460 PMCID: PMC10248596 DOI: 10.1007/s11032-022-01284-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Chromosome segment substitution line (CSSL) is important for functional analysis and design breeding of target genes. Here, a novel rice CSSL-Z431 was identified from indica restorer line Xihui18 as recipient and japonica Huhan3 as donor. Z431 contained six segments from Huhan3, with average substitution length of 2.12 Mb. Compared with Xihui18, Z431 increased panicle number per plant (PN) and displayed short-wide grains. The short-wide grain of Z431 was caused by decreased length and increased width of glume cell. Then, thirteen QTLs were identified in secondary F2 population from Xihui18/Z431. Again, eleven QTLs (qPL3, qPN3, qGPP12, qSPP12, qGL3, qGW5, qRLW2, qRLW3, qRLW5, qGWT3, qGWT5-2) were validated by six single-segment substitution lines (SSSLs, S1-S6) developed in F3. In addition, fifteen QTLs (qPN5, qGL1, qGL2, qGL5, qGW1, qGW5-1, qRLW1, qRLW5-2, qGWT1, qGWT2, qYD1, qYD2, qYD3, qYD5, qYD12) were detected by these SSSLs, while not be identified in the F2 population. Multiple panicles of Z431 were controlled by qPN3 and qPN5. OsIAGLU should be the candidate gene for qPN3. The short-wide grain of Z431 was controlled by qGL3, qGW5, etc. By DNA sequencing and qRT-PCR analysis, two best candidate genes for qGL3 and qGW5 were identified, respectively. In addition, pyramid of different QTLs in D1-D3 and T1-T2 showed independent inheritance or various epistatic effects. So, it is necessary to understand all genetic effects of target QTLs for designing breeding. Furthermore, these secondary substitution lines improved the deficiencies of Xihui18 to some extent, especially increasing yield per plant in S1, S3, S5, D1-D3, T1, and T2. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01284-x.
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Affiliation(s)
- Shuangfei Sun
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Zongbing Wang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Meng Lv
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Juan Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Peixuan Liang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
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Development of New Restorer Lines Carrying Some Restoring Fertility Genes with Flowering, Yield and Grains Quality Characteristics in Rice (Oryza saliva L.). Genes (Basel) 2022; 13:genes13030458. [PMID: 35328012 PMCID: PMC8952259 DOI: 10.3390/genes13030458] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/04/2022] Open
Abstract
This study was carried out using 22 promising restorer lines of rice and their parental lines to study genetic variability and genetic advance for yield and yield-associated grain quality traits and floral traits. These genotypes are evaluated in a replicated trial using Randomized Complete Block Design (RCBD) with three replications at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the seasons from 2012 to 2020. Analysis of variance revealed that highly significant variations were observed among the genotypes for all the studied characters. Both GCV% and PCV% were high for the number of spikelets per panicle, the number of filled grains per panicle, and panicle weight. The genetic advance in the percentage of mean was high for days to plant height, panicle length, number of spikelets per panicle, number of filled grains per panicle, panicle weight, grain yield per plant, anther length, anther breadth, duration of floret opening, and head rice percentage. Mean performance of the rice genotypes indicated that the genotypes NRL 59, NRL 55, NRL 62, NRL 63, NRL 66, and NRL 54-2 were promising for grain yield and associated desirable traits. Thus, some of these promising lines can be promoted as a new rice variety and could be used as a source for developing new hybrid combinations in hybrid rice breeding programs. The percentage of advantage over better parent and Giza 178 as the commercial variety was significant and there were highly significant desirable values among the genotypes for all the studied traits in the two years, indicating that the selection is effective in the genetic improvements for these traits.
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Comparative Transcriptome Analysis of the Anthers from the Cytoplasmic Male-Sterile Pepper Line HZ1A and Its Maintainer Line HZ1B. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cytoplasmic male-sterility (CMS) is important for the utilization of crop heterosis and study of the molecular mechanisms involved in CMS could improve breeding programs. In the present study, anthers of the pepper CMS line HZ1A and its maintainer line HZ1B were collected from stages S1, S2, and S3 for transcriptome sequencing. A total of 47.95 million clean reads were obtained, and the reads were assembled into 31,603 unigenes. We obtained 42 (27 up-regulated and 15 down-regulated), 691 (346 up-regulated and 345 down-regulated), and 709 (281 up-regulated and 428 down-regulated) differentially expressed genes (DEGs) in stages S1, S2, and S3, respectively. Through Gene Ontology (GO) analysis, the DEGs were found to be composed of 46 functional groups. Two GO terms involved in photosynthesis, photosynthesis (GO:0015986) and photosystem I (GO:0009522), may be related to CMS. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, oxidative phosphorylation (ko00190) and phenylpropanoid biosynthesis (ko00940) were significantly enriched in the S1 and S2 stages, respectively. Through the analysis of 104 lipid metabolism-related DEGs, four significantly enriched KEGG pathways may help to regulate male sterility during anther development. The mitochondrial genes orf470 and atp6 were identified as candidate genes of male sterility for the CMS line HZ1A. Overall, the results will provide insights into the molecular mechanisms of pepper CMS.
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Zhang Z, An D, Cao Y, Yu H, Zhu Y, Mei Y, Zhang B, Wang L. Development and application of KASP markers associated with Restorer-of-fertility gene in Capsicum annuum L. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2757-2765. [PMID: 35035134 PMCID: PMC8720122 DOI: 10.1007/s12298-021-01109-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 11/25/2021] [Indexed: 05/09/2023]
Abstract
Fertility restoration of cytoplasmic male sterility (CMS) in Capsicum annuum is controlled by multiple alleles of Restorer-of-fertility (Rf) genes. The isolation of additional Rf genes should therefore enrich the knowledge of CMS/Rf systems and accelerate their exploitation in hybrid seed production. In this study, the fertility restorer gene CaRfm of '0601 M', a non-pungent bell pepper, was genetically mapped to a 1.2-cM region flanked by KASP markers S761 and S183. CaRfm was then physically mapped to a 128.96-Kb interval predicted from 24 recombinants with two co-segregated markers, S423 and S424. CaPPR6 encoding a pentatricopeptide repeat (PPR) protein was suggested as the most likely candidate gene for the CaRfm locus on the basis of sequence alignment as well as genotyping of tightly linked markers. In addition, molecular markers S1597 and S1609, which are immediately adjacent to CaRfm at 15.7 and 57.8-Kb respectively, were developed and applied to marker-assisted selection. The results provided friendly markers for breeding pepper restorer lines and laid the foundation for elucidating the male fertility restoration mechanism. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01109-9.
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Affiliation(s)
- Zhenghai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Dongliang An
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yacong Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Hailong Yu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yanshu Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yajie Mei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Baoxi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Lihao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
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23
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Zhang H, Wang R, Xu Z, Zhao X, Gao H, Liu Q, Tang S. The effects of Rf5 and Rf6 on fertility restoration in Honglian-type cytoplasmic male sterile (CMS) lines of japonica rice ( Oryza sativa L. ssp. japonica). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:64. [PMID: 37309312 PMCID: PMC10236119 DOI: 10.1007/s11032-021-01256-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 06/14/2023]
Abstract
Honglian (HL)-type cytoplasmic male sterility (CMS) has only been used in the development of three-line indica rice hybrids, and the fertility of HL-type indica CMS lines can be restored by two non-allelic fertility-restorer (Rf) genes, Rf5 and Rf6. For the development of HL-type japonica hybrid combinations, it is therefore necessary to determine whether Rf5 and Rf6 can restore the fertility of HL-type japonica CMS lines. Here, we genetically characterized HL-type japonica CMS lines and the ability of Rf5 and Rf6 to restore fertility for breeding HL-type japonica hybrids. I2-KI pollen staining revealed that HL-type japonica CMS lines and their derived testcross F1 hybrids had stained abortive pollen grains, unlike HL-type indica CMS lines. Crossing experiments showed that Rf5 and Rf6 partially restored the fertility of HL-type japonica CMS lines, and Rf6 showed higher restorability than Rf5. Furthermore, we found that there were additive and dosage effects of Rf5 and Rf6 with respect to fertility restoration in HL-type japonica CMS lines. These results give critical insight into the breeding of HL-type japonica CMS lines and restorers, which will be helpful for the development of commercial HL-type japonica hybrids. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01256-7.
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Affiliation(s)
- Honggen Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Ruixuan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | | | - Hailin Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
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Toriyama K. Molecular basis of cytoplasmic male sterility and fertility restoration in rice. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:285-295. [PMID: 34782814 PMCID: PMC8562580 DOI: 10.5511/plantbiotechnology.21.0607a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait that causes dysfunctions in pollen and anther development. CMS is caused by the interaction between nuclear and mitochondrial genomes. A product of a CMS-causing gene encoded by the mitochondrial genome affects mitochondrial function and the regulation of nuclear genes, leading to male sterility. In contrast, the RESTORER OF FERTILITY gene (Rf gene) in the nuclear genome suppresses the expression of the CMS-causing gene and restores male fertility. An alloplasmic CMS line is often bred as a result of nuclear substitution, which causes the removal of functional Rf genes and allows the expression of a CMS-causing gene in mitochondria. The CMS/Rf system is an excellent model for understanding the genetic interactions and cooperative functions of mitochondrial and nuclear genomes in plants, and is also an agronomically important trait for hybrid seed production. In this review article, pollen and anther phenotypes of CMS, CMS-associated mitochondrial genes, Rf genes, and the mechanism that causes pollen abortion and its agronomical application for rice are described.
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Affiliation(s)
- Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
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Vendelbo NM, Mahmood K, Sarup P, Kristensen PS, Orabi J, Jahoor A. Genomic Scan of Male Fertility Restoration Genes in a 'Gülzow' Type Hybrid Breeding System of Rye ( Secale cereale L.). Int J Mol Sci 2021; 22:ijms22179277. [PMID: 34502186 PMCID: PMC8431178 DOI: 10.3390/ijms22179277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/03/2023] Open
Abstract
Efficient and stable restoration of male fertility (Rf) is a prerequisite for large-scale hybrid seed production but remains an inherent issue in the predominant fertility control system of rye (Secale cereale L.). The ‘Gülzow’ (G)-type cytoplasmic male sterility (CMS) system in hybrid rye breeding exhibits a superior Rf. While having received little scientific attention, one major G-type Rf gene has been identified on 4RL (Rfg1) and two minor genes on 3R (Rfg2) and 6R (Rfg3) chromosomes. Here, we report a comprehensive investigation of the genetics underlying restoration of male fertility in a large G-type CMS breeding system using recent advents in rye genomic resources. This includes: (I) genome-wide association studies (GWAS) on G-type germplasm; (II) GWAS on a biparental mapping population; and (III) an RNA sequence study to investigate the expression of genes residing in Rf-associated regions in G-type rye hybrids. Our findings provide compelling evidence of a novel major G-type non-PPR Rf gene on the 3RL chromosome belonging to the mitochondrial transcription termination factor gene family. We provisionally denote the identified novel Rf gene on 3RL RfNOS1. The discovery made in this study is distinct from known P- and C-type systems in rye as well as recognized CMS systems in barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We believe this study constitutes a stepping stone towards understanding the restoration of male fertility in the G-type CMS system and potential resources for addressing the inherent issues of the P-type system.
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Affiliation(s)
- Nikolaj Meisner Vendelbo
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
- Department of Agroecology, Faculty of Technology, Aarhus University, Forsøgsvej 1, Flakkebjerg, 4200 Slagelse, Denmark
- Correspondence:
| | - Khalid Mahmood
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Pernille Sarup
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Peter Skov Kristensen
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Jihad Orabi
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
| | - Ahmed Jahoor
- Nordic Seed A/S, Grindsnabevej 25, 8300 Odder, Denmark; (K.M.); (P.S.); (P.S.K.); (J.O.); (A.J.)
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden
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Tyrka M, Bakera B, Szeliga M, Święcicka M, Krajewski P, Mokrzycka M, Rakoczy-Trojanowska M. Identification of Rf Genes in Hexaploid Wheat ( Triticumaestivum L.) by RNA-Seq and Paralog Analyses. Int J Mol Sci 2021; 22:ijms22179146. [PMID: 34502055 PMCID: PMC8431562 DOI: 10.3390/ijms22179146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study.
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Affiliation(s)
- Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszów University of Technology, Powstańców Warszawy 12, 35-959 Rzeszów, Poland; (M.T.); (M.S.)
| | - Beata Bakera
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland; (B.B.); (M.Ś.)
| | - Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Rzeszów University of Technology, Powstańców Warszawy 12, 35-959 Rzeszów, Poland; (M.T.); (M.S.)
| | - Magdalena Święcicka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland; (B.B.); (M.Ś.)
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (P.K.); (M.M.)
| | - Monika Mokrzycka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (P.K.); (M.M.)
| | - Monika Rakoczy-Trojanowska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland; (B.B.); (M.Ś.)
- Correspondence: ; Tel./Fax: +48-22-59-32152
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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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Cheng Q, Yao P, Li H, Han Y, Xu K, Heng S, Fu T, Wan Z. Genetic mapping reveals BjRf as a candidate gene controlling fertility restoration of the oxa CMS in Brassica juncea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2355-2365. [PMID: 34173856 DOI: 10.1007/s00122-021-03767-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/06/2021] [Indexed: 06/13/2023]
Abstract
A candidate gene for male fertility restoration in Brassica juncea, BjRf, was isolated from a 23-kb interval on chromosome A05 using map-based cloning and BSA methods. The cytoplasmic male sterility/fertility restoration (CMS/Rf) system has been extensively used for heterosis in plants. It also provides valuable resources for studying mitochondrial-nuclear coevolution and interaction. The oxa CMS, which is a new CMS type reported in Brassica juncea (B. juncea), has been broadly used in the exploitation and application of heterosis in this species. However, the oxa CMS fertility restorer gene BjRf has not been reported. In this study, a stable restorer line was successfully constructed via continuous testcross and artificial selection. Besides, a new Rf gene was mapped in a 23-kb region on chromosome A05 in B. juncea with a genetic distance of 0.5 cM by the method incorporating bulk segregant analysis (BSA) and conventional map-based cloning. Finally, BjuA017917, a non-PPR Rf gene encoding a guanosine nucleotide diphosphate dissociation inhibitor (GDI), is proposed to be the candidate gene for fertility restoration of the oxa CMS line in B. juncea. Moreover, a functional marker, CRY3, was developed for marker-assisted selection for Brassica juncea breeding.
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Affiliation(s)
- Qiqi Cheng
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peijie Yao
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hui Li
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiming Han
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kejing Xu
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangping Heng
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science, Xinyang Normal University, Xinyang, 464000, People's Republic of China
| | - Tingdong Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhengjie Wan
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Jin Z, Seo J, Kim B, Lee SY, Koh HJ. Identification of a Candidate Gene for the Novel Cytoplasmic Male Sterility Derived from Inter-Subspecific Crosses in Rice ( Oryza sativa L.). Genes (Basel) 2021; 12:590. [PMID: 33920582 PMCID: PMC8073397 DOI: 10.3390/genes12040590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/09/2023] Open
Abstract
Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies indica and japonica in rice (Oryza sativa L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene orf312, which possesses a transmembrane domain and overlaps with two mitotype-specific sequences (MSSs) that are unique to the Tetep-CMS line. The encoded peptide of orf312 was toxic to Escherichia coli and inhibited cell growth compared to the control under isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The peptide of orf312 contains COX11-interaction domains, which are thought to be a main functional domain for WA352c in the wild abortive (WA-CMS) line of rice. A QTL for Rf-Tetep (restorer-of-fertility gene(s) originating from Tetep) was identified on chromosome 10. In this region, several restorer genes, Rf1a, Rf1b, and Rf4, have previously been reported. Collectively, the interactions of orf312, a candidate gene for Tetep-CMS, and Rf-Tetep, a restorer QTL, confer male sterility and fertility restoration, respectively, which enables a hybrid rice breeding system. Further studies on orf312 and isolation of Rf-Tetep will help to identify the underlying molecular mechanism of mitochondrial ORFs with the COX11-interaction domains.
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Affiliation(s)
- Zhuo Jin
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Jeonghwan Seo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
| | - Backki Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Seung Young Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
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Liang P, Wang H, Zhang Q, Zhou K, Li M, Li R, Xiang S, Zhang T, Ling Y, Yang Z, He G, Zhao F. Identification and Pyramiding of QTLs for Rice Grain Size Based on Short-Wide Grain CSSL-Z563 and Fine-Mapping of qGL3-2. RICE (NEW YORK, N.Y.) 2021; 14:35. [PMID: 33847838 PMCID: PMC8044274 DOI: 10.1186/s12284-021-00477-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/26/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Chromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are thus important for functional analysis and molecular breeding. RESULTS A rice line with short wide grains, CSSL-Z563, was isolated from advanced-generation backcross population (BC3F6) derived from 'Xihui 18' (the recipient parent) and 'Huhan 3' (the donor parent). Z563 carried seven segments from 'Huhan 3', distributed on chromosomes 3, 7, and 8, with average substitution length of 5.52 Mb. Eleven QTLs for grain size were identified using secondary F2 population of 'Xihui 18'/Z563. The QTLs qGL3-1, qGL3-2, and qGL7 control grain length in Z563 and have additive effects to reduce grain length; qGW3-1 and qGW3-2 control grain width in Z563 and have additive effects to increase grain width. Four SSSLs, three double-segment substitution lines (D1-D3), and two triple-segment substitution lines (T1 and T2) were developed containing the target QTLs. The genetic stability of eight QTLs, including qGL3-2, qGL3-1, and qGL7, was verified by the SSSLs. D1 (containing qGL3-2 and qGL3-1), D2 (qGL3-1 and qGL7), and T1 (qGL3-2, qGL3-1, and qGL7) had positive epistatic effects on grain length, and their grain length was shorter than that of the corresponding SSSLs. The QTL qGL3-2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes that differed between 'Xihui 18' and Z563. These results are important for functional research on qGL3-2 and molecular breeding of hybrid rice cultivars. CONCLUSIONS The short and wide grain of Z563 was mainly controlled by qGL3-1, qGL3-2, qGL7, qGW3-1 and qGW3-2. The major QTL qGL3-2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes. Different QTLs pyramiding displayed various phenotypes. In essence, the performance after pyramiding of genes depended on the comparison between the algebraic sum of the additive and epistatic effects of QTLs in the pyramidal line and the additive effect value of the single QTL. The results lay good foundation in the functional analysis of qGL3-2 and molecular design breeding of novel hybrid rice cultivars.
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Affiliation(s)
- Peixuan Liang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hui Wang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Qiuli Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhenglin Yang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Chen Y, Jia Y, Niu F, Wu Y, Ye J, Yang X, Zhang L, Song X. Identification and validation of genetic locus Rfk1 for wheat fertility restoration in the presence of Aegilops kotschyi cytoplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:875-885. [PMID: 33392709 DOI: 10.1007/s00122-020-03738-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Major fertility restorer locus for Aegilops kotschyi cytoplasm in wheat, Rfk1, was mapped to chromosome arm 1BS. Most likely candidate gene is TraesCS1B02G197400LC, which is predicted to encode a pectinesterase/pectinesterase inhibitor. Cytoplasmic male sterility (CMS) is widely used for heterosis and hybrid seed production in wheat. Genes related to male fertility restoration in the presence of Aegilops kotschyi cytoplasm have been reported, but the fertility restoration-associated gene loci have not been investigated systematically. In this study, a BC1F1 population derived from a backcross between KTP116A, its maintainer line TP116B, and its restorer line LK783 was employed to map fertility restoration by bulked segregant RNA-Seq (BSR-Seq). A major fertility allele restorer locus for Ae. kotschyi cytoplasm in wheat, Rfk1, was mapped to chromosome arm 1BS, and it was contributed by LK783. Morphological and cytological studies showed that male fertility restoration occurred mainly after the late uninucleate stage. Based on simple sequence repeat and single-nucleotide polymorphism genotyping, the gene locus was located between Xnwafu_6 and Xbarc137 on chromosome arm 1BS. To further isolate the specific region, six Kompetitive allele-specific polymerase chain reaction markers derived from BSR-Seq were developed to delimit Rfk1 within physical intervals of 26.0 Mb. After searching for differentially expressed genes within the candidate interval in the anthers and sequencing analysis, TraesCS1B02G197400LC was identified as a candidate gene for Rfk1 and it was predicted to encode a pectinesterase/pectinesterase inhibitor. Expression analysis also confirmed that it was specifically expressed in the anthers, and its expression level was higher in fertile lines compared with sterile lines. Thus, TraesCS1B02G197400LC was identified as the most likely candidate gene for Rfk1, thereby providing insights into the fertility restoration mechanism for K-type CMS in wheat.
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Affiliation(s)
- Yanru Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Jia
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuqiang Niu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongfeng Wu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiali Ye
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
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Map and sequence-based chromosome walking towards cloning of the male fertility restoration gene Rf5 linked to R 11 in sunflower. Sci Rep 2021; 11:777. [PMID: 33437028 PMCID: PMC7804242 DOI: 10.1038/s41598-020-80659-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/11/2020] [Indexed: 11/28/2022] Open
Abstract
The nuclear fertility restorer gene Rf5 in HA-R9, originating from the wild sunflower species Helianthus annuus, is able to restore the widely used PET1 cytoplasmic male sterility in sunflowers. Previous mapping placed Rf5 at an interval of 5.8 cM on sunflower chromosome 13, distal to a rust resistance gene R11 at a 1.6 cM genetic distance in an SSR map. In the present study, publicly available SNP markers were further mapped around Rf5 and R11 using 192 F2 individuals, reducing the Rf5 interval from 5.8 to 0.8 cM. Additional SNP markers were developed in the target region of the two genes from the whole-genome resequencing of HA-R9, a donor line carrying Rf5 and R11. Fine mapping using 3517 F3 individuals placed Rf5 at a 0.00071 cM interval and the gene co-segregated with SNP marker S13_216392091. Similarly, fine mapping performed using 8795 F3 individuals mapped R11 at an interval of 0.00210 cM, co-segregating with two SNP markers, S13_225290789 and C13_181790141. Sequence analysis identified Rf5 as a pentatricopeptide repeat-encoding gene. The high-density map and diagnostic SNP markers developed in this study will accelerate the use of Rf5 and R11 in sunflower breeding.
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Niedziela A, Brukwiński W, Bednarek PT. Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa. J Appl Genet 2021; 62:185-198. [PMID: 33409933 PMCID: PMC8032618 DOI: 10.1007/s13353-020-00599-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022]
Abstract
Cytoplasmic male sterility (CMS) is a widely applied plant breeding tool for hybrid seed production. The phenomenon is often caused by chimeric genes with altered open reading frames (ORFs) located in the mitochondrial genomes and expressed as novel genotoxic products that induce pollen abortion. The fertility of CMS plants can be restored by nuclear-encoded genes that inhibit the action of ORFs responsible for pollen sterility. A recombinant inbred line (RIL) mapping population S64/04/01, encompassing 175 individuals, was used for genetic map construction and identification of quantitative trait loci (QTLs) responsible for fertility restoration in rye (Secale cereale L.) with CMS Pampa. The genetic map of all seven rye chromosomes included 15,516 SNP and silicoDArT markers and covered 1070.5 cm. Individual QTLs explaining 60% and 5.5% of the fertility trait’s phenotypic variance were mapped to chromosomes 4R (QRft-4R) and 5R (QRft-5R), respectively. Association mapping identified markers with the highest R2 value of 0.58 (p value = 2.21E-28). Markers showing the highest associations with the trait were also mapped to the 4R chromosome within the QRft-4R region. Based on marker sequence homology, putative genes involved in pollen fertility restoration were suggested. Five silicoDArTs were converted into PCR-based markers for further breeding purposes.
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Affiliation(s)
- Agnieszka Niedziela
- Plant Breeding and Acclimatization Institute, NRI, Radzików, 05-870, Błonie, Poland
| | | | - Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute, NRI, Radzików, 05-870, Błonie, Poland.
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Physical mapping and InDel marker development for the restorer gene Rf 2 in cytoplasmic male sterile CMS-D8 cotton. BMC Genomics 2021; 22:24. [PMID: 33407111 PMCID: PMC7789476 DOI: 10.1186/s12864-020-07342-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07342-y.
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Anisimova IN. Structural and Functional Organization of Genes That Induce and Suppress Cytoplasmic Male Sterility in Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420110022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Molecular Control and Application of Male Fertility for Two-Line Hybrid Rice Breeding. Int J Mol Sci 2020; 21:ijms21217868. [PMID: 33114094 PMCID: PMC7660317 DOI: 10.3390/ijms21217868] [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: 09/18/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 01/24/2023] Open
Abstract
The significance of the climate change may involve enhancement of plant growth as well as utilization of the environmental alterations in male fertility (MF) regulation via male sterility (MS) systems. We described that MS systems provide a fundamental platform for improvement in agriculture production and have been explicated for creating bulk germplasm of the two-line hybrids (EGMS) in rice as compared to the three-line, to gain production sustainability and exploit its immense potential. Environmental alterations such as photoperiod and/or temperature and humidity regulate MS in EGMS lines via genetic and epigenetic changes, regulation of the noncoding RNAs, and RNA-metabolism including the transcriptional factors (TFs) implication. Herein, this article enlightens a deep understanding of the molecular control of MF in EGMS lines and exploring the regulatory driving forces that function efficiently during plant adaption under a changing environment. We highlighted a possible solution in obtaining more stable hybrids through apomixis (single-line system) for seed production.
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Suketomo C, Kazama T, Toriyama K. Fertility restoration of Chinese wild rice-type cytoplasmic male sterility by CRISPR/Cas9-mediated genome editing of nuclear-encoded RETROGRADE-REGULATED MALE STERILITY. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:285-292. [PMID: 33088191 PMCID: PMC7557670 DOI: 10.5511/plantbiotechnology.20.0326b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cytoplasmic male sterility (CMS) is a trait that produces nonfunctional pollen caused by the interaction between mitochondrial and nuclear genes. In Chinese-wild (CW) type CMS, CWA, in rice (Oryza sativa L.), its mitochondria enhance the expression of the nuclear gene RETROGRADE-REGULATED MALE STERILITY (RMS), which causes pollen abortion. Fertility is recovered when its expression decreases in a restorer line, CWR. The expression of RMS is controlled by the single nucleotide polymorphism (SNP) located in the promoter region 2,286 bp upstream of the start codon of RMS. However, another gene, PPR2, which encodes pentatricopeptide repeat-domain containing protein, is predicted in the reverse strand of this region and a premature stop codon is created in CWR by the SNP. To prove RMS is directly involved in restoring fertility of CW-CMS, we introduced mutations into RMS and PPR2 using CRISPR/Cas9. Fertility was recovered in the genome-edited CMS plants with reduced expression of RMS and unaltered expression of PPR2, when the mutation was introduced in the promoter regions of RMS within or outside the coding sequence (CDS) of PPR2. Fertility restoration was not obtained when the mutation was introduced within the CDS of RMS. Our results demonstrated that PPR2 is not responsible for fertility restoration, and fertility was recovered by reduced expression of RMS, providing us with a new artificial fertility restorer line for agronomical use.
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Affiliation(s)
- Chihiro Suketomo
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
- E-mail: Tel: +81-22-757-4231 Fax: +81-22-757-4232
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Zheng W, Ma Z, Zhao M, Xiao M, Zhao J, Wang C, Gao H, Bai Y, Wang H, Sui G. Research and Development Strategies for Hybrid japonica Rice. RICE (NEW YORK, N.Y.) 2020; 13:36. [PMID: 32514748 PMCID: PMC7280405 DOI: 10.1186/s12284-020-00398-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/28/2020] [Indexed: 06/01/2023]
Abstract
The utilization of heterosis has resulted in significant breakthroughs in rice breeding. However, the development of hybrid japonica has been slow in comparison with that of hybrid indica. The present review explores the history and current status of hybrid japonica breeding. With the creation of japonica cytoplasmic male sterility and photo-thermo-sensitive genic male sterile lines, both three-line and two-line systems of hybrid rice have been created, and a series of hybrid japonica rice varieties have been developed and cultivated widely. At the same time, some progress has been made in genetic research of molecular mechanism for heterosis and QTL mapping for traits such as fertility, stigma exposure and flower time. In addition, genomics and transcriptome have been widely used in the research of hybrid rice, which provides a strong support for its development. Although the research on hybrid japonica has made many advances, there are still some restrictive problems. Based on the research and production of hybrid japonica rice, the prospect and development strategies of hybrid japonica rice are analyzed.
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Affiliation(s)
- Wenjing Zheng
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang, 110000, China
| | - Zuobin Ma
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang, 110000, China
| | - Mingzhu Zhao
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang, 110000, China
| | - Minggang Xiao
- Heilongjiang Academy of Agricultural Sciences, Haerbin, 1550086, China
| | - Jiaming Zhao
- Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Changhua Wang
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang, 110000, China
| | - Hong Gao
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang, 110000, China
| | - Yuanjun Bai
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang, 110000, China
| | - Hui Wang
- Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Guomin Sui
- Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China.
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Zhang Z, Zhu Y, Cao Y, Yu H, Bai R, Zhao H, Zhang B, Wang L. Fine mapping of the male fertility restoration gene CaRf032 in Capsicum annuum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1177-1187. [PMID: 31925462 DOI: 10.1007/s00122-020-03540-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/07/2020] [Indexed: 05/24/2023]
Abstract
A novel strong candidate gene CA00g82510 for the male fertility restoration locus CaRf032 in Capsicum annuum was identified by genome re-sequencing and recombination analysis. A single dominant locus (CaRf032) for fertility restoration of cytoplasmic male sterility was identified in the strong restorer inbred line IVF2014032 of chili pepper (Capsicum annuum L.). CaRf032 was localized within an 8.81-Mb candidate intervals on chromosome 6 using bulked segregant analysis based on high-throughput sequencing data. Subsequently, the candidate interval was genetically mapped and defined to a 249.41-kb region using an F2 population of 441 individuals generated by crossing the male-sterile line 77013A and the restorer line IVF2014032. To fine map CaRf032, eight newly developed KASP markers were used to genotype 23 recombinants screened from a larger F2 population of 2877 individuals. The CaRf032 locus was localized to a 148.05-kb region between the KASP markers S1402 and S1354, which was predicted to contain 22 open reading frames (ORFs). One ORF with an incomplete sequence was predicted to contain a PPR motif, and its physical position overlapped with the Rf candidate gene CaPPR6_46. The PPR ORF sequence before the gap showed 100% identity with the CA00g82510 locus of the CM334 reference genome. CA00g82510 encodes a protein of 583 amino acids, containing 14 PPR motifs, and shows significantly differential expression between the flower buds of the maintainer line 77013 and the restorer line IVF2014032. These results indicated that CA00g82510 is a strong candidate gene for CaRf032. Five KASP markers, which detected single-nucleotide polymorphisms in CA00g82510 of 77013 and IVF2014032, co-segregated with CaRf032 and showed 64.4% successful genotyping of 38 maintainer and 63 restorer lines.
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Affiliation(s)
- Zhenghai Zhang
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Yanshu Zhu
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Yacong Cao
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Hailong Yu
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Ruiqin Bai
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Hong Zhao
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Baoxi Zhang
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Lihao Wang
- Key Laboratory of Vegetable Genetics and Physiology of Ministry of the Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China.
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What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply? PLANTS 2020; 9:plants9030361. [PMID: 32182978 PMCID: PMC7154926 DOI: 10.3390/plants9030361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022]
Abstract
Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity.
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Espinas NA, Tu LN, Furci L, Shimajiri Y, Harukawa Y, Miura S, Takuno S, Saze H. Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome. PLoS Genet 2020; 16:e1008637. [PMID: 32187179 PMCID: PMC7145194 DOI: 10.1371/journal.pgen.1008637] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 04/09/2020] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
Intronic regions of eukaryotic genomes accumulate many Transposable Elements (TEs). Intronic TEs often trigger the formation of transcriptionally repressive heterochromatin, even within transcription-permissive chromatin environments. Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of rice genes contain intronic heterochromatin, most of which are associated with TEs and repetitive sequences. These heterochromatic introns are longer and highly enriched in promoter-proximal positions. On the other hand, introns also accumulate hypomethylated short TEs. Genes with heterochromatic introns are implicated in various biological functions. Transcription of genes bearing intronic heterochromatin is regulated by an epigenetic mechanism involving the conserved factor OsIBM2, mutation of which results in severe developmental and reproductive defects. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study demonstrates that heterochromatin is a common epigenetic feature associated with actively transcribed genes in the rice genome.
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Affiliation(s)
- Nino A. Espinas
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama city, Kanagawa, Japan
| | - Le Ngoc Tu
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Yasuka Shimajiri
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- EditForce, Fukuoka, Japan
| | - Yoshiko Harukawa
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Saori Miura
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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Cheng J, Chen Y, Hu Y, Zhou Z, Hu F, Dong J, Chen W, Cui J, Wu Z, Hu K. Fine mapping of restorer-of-fertility gene based on high-density genetic mapping and collinearity analysis in pepper (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:889-902. [PMID: 31863157 DOI: 10.1007/s00122-019-03513-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/13/2019] [Indexed: 05/24/2023]
Abstract
The pepper restorer-of-fertility (CaRf) gene was fine mapped based on conjoint analysis of recombinants and collinearity between the two pepper reference genomes. Capana06g003028, encoding an Rf-like PPR protein, was proposed as the strongest candidate for pepper CaRf based on sequence comparison and expression analysis. The cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system not only provides an excellent model to dissect genetic interactions between the mitochondria and nucleus but also plays a vital role in high-efficiency hybrid seed production in crops including pepper (Capsicum spp.). Although two important CMS candidate genes, orf507 and Ψatp6-2, have previously been suggested, the pepper Rf gene (CaRf) has not yet been isolated. In this study, a high-density genetic map comprising 7566 SNP markers in 1944 bins was first constructed with the array genotyping results from 317 F2 individuals. Based on this map, the CaRf gene was preliminarily mapped to a region of 1.15 Mb in length at the end of chromosome P6. Then, by means of a conjoint analysis of recombinants and collinearity between the two pepper reference genomes, an important candidate interval with 270.10 kb in length was delimited for CaRf. Finally, Capana06g003028, which encodes an Rf-like PPR protein, was proposed as the strongest candidate for CaRf based on sequence analysis and expression characteristics in sterile and fertile plants. The high-density genetic map and fine mapping results provided here lay a foundation for the application of molecular breeding, as well as cloning and functional analysis of CaRf, in pepper.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Yijian Chen
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Yafei Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Ziyan Zhou
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Jichi Dong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Weili Chen
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Junjie Cui
- Department of Horticulture, College of Food Science and Engineering, Foshan University, Foshan, 528200, Guangdong, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China.
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Li P, Zhou H, Yang H, Xia D, Liu R, Sun P, Wang Q, Gao G, Zhang Q, Wang G, He Y. Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2020; 13:11. [PMID: 32040640 PMCID: PMC7010892 DOI: 10.1186/s12284-020-0372-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations. RESULTS In this study, two F1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6. CONCLUSIONS Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.
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Affiliation(s)
- Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quanxiu Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China.
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Jaqueth JS, Hou Z, Zheng P, Ren R, Nagel BA, Cutter G, Niu X, Vollbrecht E, Greene TW, Kumpatla SP. Fertility restoration of maize CMS-C altered by a single amino acid substitution within the Rf4 bHLH transcription factor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:101-111. [PMID: 31487408 DOI: 10.1111/tpj.14521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 05/24/2023]
Abstract
Type C cytoplasmic male sterility (CMS-C) is the most commonly used form of CMS in maize hybrid seed production. Restorer of fertility 4 (Rf4), the major fertility restorer gene of CMS-C, is located on chromosome 8S. To positionally clone Rf4, a large F3 population derived from a cross between a non-restorer and restorer (n = 5104) was screened for recombinants and then phenotyped for tassel fertility, resulting in a final map-based cloning interval of 12 kb. Within this 12-kb interval, the only likely candidate for Rf4 was GRMZM2G021276, a basic helix-loop-helix (bHLH) transcription factor with tassel-specific expression. The Rf4 gene product contains a nuclear localization signal and is likely to not interact directly with the mitochondria. Sequence analysis of Rf4 revealed four encoded amino acid substitutions between restoring and non-restoring inbreds, however only one substitution, F187Y, was within the highly conserved bHLH domain. The hypothesis that Rf4 restoration is altered by a single amino acid was tested by using clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated protein 9 (Cas9) homology directed repair (HDR) to create isogenic lines that varied for the F187Y substitution. In a population of these CRISPR-Cas9 edited plants (n = 780) that was phenotyped for tassel fertility, plants containing F187 were completely fertile, indicating fertility restoration, and plants containing Y187 were sterile, indicating lack of fertility restoration. Structural modeling shows that this amino acid residue 187 is located within the four helix bundle core, a critical region for stabilizing dimer conformation and affecting interaction partner selection.
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Affiliation(s)
| | - Zhenglin Hou
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Peizhong Zheng
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Ruihua Ren
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Bruce A Nagel
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Gary Cutter
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Xiaomu Niu
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Thomas W Greene
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Siva P Kumpatla
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
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Wei B, Wang L, Bosland PW, Zhang G, Zhang R. Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restoration. BMC Genomics 2019; 20:837. [PMID: 31711411 PMCID: PMC6849218 DOI: 10.1186/s12864-019-6210-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/22/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system is an important mechanism to produce F1 hybrid seeds. Understanding the interaction that controls restoration at a molecular level will benefit plant breeders. The CMS is caused by the interaction between mitochondrial and nuclear genes, with the CMS phenotype failing to produce functional anthers, pollen, or male gametes. Thus, understanding the complex processes of anther and pollen development is a prerequisite for understanding the CMS system. Currently it is accepted that the Rf gene in the nucleus restores the fertility of CMS, however the Rf gene has not been cloned. In this study, CMS line 8A and the Rf line R1, as well as a sterile pool (SP) of accessions and a restorer pool (RP) of accessions analyzed the differentially expressed genes (DEGs) between CMS and its fertility restorer using the conjunction of RNA sequencing and bulk segregation analysis. RESULTS A total of 2274 genes were up-regulated in R1 as compared to 8A, and 1490 genes were up-regulated in RP as compared to SP. There were 891 genes up-regulated in both restorer accessions, R1 and RP, as compared to both sterile accessions, 8A and SP. Through annotation and expression analysis of co-up-regulated expressed genes, eight genes related to fertility restoration were selected. These genes encode putative fructokinase, phosphatidylinositol 4-phosphate 5-kinase, pectate lyase, exopolygalacturonase, pectinesterase, cellulose synthase, fasciclin-like arabinogalactan protein and phosphoinositide phospholipase C. In addition, a phosphatidylinositol signaling system and an inositol phosphate metabolism related to the fertility restorer of CMS were ranked as the most likely pathway for affecting the restoration of fertility in pepper. CONCLUSIONS Our study revealed that eight genes were related to the restoration of fertility, which provides new insight into understanding the molecular mechanism of fertility restoration of CMS in Capsicum.
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Affiliation(s)
- Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Lanlan Wang
- Vegetable Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Paul W Bosland
- College of Agriculture, Consumer, and Environmental Sciences, New Mexico State University, Las Cruces, 88001, USA
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ru Zhang
- Vegetable Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
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Lloyd Evans D, Hlongwane TT, Joshi SV, Riaño Pachón DM. The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PeerJ 2019; 7:e7558. [PMID: 31579570 PMCID: PMC6764373 DOI: 10.7717/peerj.7558] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species. METHODS Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer. RESULTS The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed. CONCLUSION Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.
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Affiliation(s)
- Dyfed Lloyd Evans
- Plant Breeding, South African Sugarcane Research Institute, Durban, KwaZulu-Natal, South Africa
- Cambridge Sequence Services (CSS), Waterbeach, Cambridgeshire, UK
- Department of Computer Sciences, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | | | - Shailesh V. Joshi
- Plant Breeding, South African Sugarcane Research Institute, Durban, KwaZulu-Natal, South Africa
- School of Life Sciences, College of Agriculture Engineering and Science, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Diego M. Riaño Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Li H, Guo J, Zhang C, Zheng W, Song Y, Wang Y. Identification of Differentially Expressed miRNAs between a Wheat K-type Cytoplasmic Male Sterility Line and Its Near-Isogenic Restorer Line. PLANT & CELL PHYSIOLOGY 2019; 60:1604-1618. [PMID: 31076750 DOI: 10.1093/pcp/pcz065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
K-type cytoplasmic male sterility (KCMS) lines were ideal material for three-line hybrid wheat system due to the major role in hybrid wheat production. In this study, the morphology of developing microspore and mature pollen was compared between a KCMS line and its near-isogenic restorer line (KCMS-NIL). The most striking difference is that the microspore was unable to develop into tricellular pollen in the KCMS line. MicroRNA plays vital roles in flowering and gametophyte development. Small RNA sequencing identified a total of 274 known and 401 novel miRNAs differentially expressed between two lines or two developmental stages. Most of miRNAs with high abundance were differentially expressed at the uninucleate stage, and their expression level recovered or remained at the binucleate stage. Further degradome sequencing identified target genes which were mainly enriched in transcription regulation, phytohormone signaling and RNA degradation pathways. Combining with the transcriptome data, a correlation was found between the abnormal anther development, such as postmeiotic mitosis cessation, deformative pollen wall and the chromosome condensation of the vegetative cell, and the alterations in the related miRNA and their targets expression profiles. According to the correlation and pathway analysis, we propose a hypothetic miRNA-mediated network for the control of KCMS restoration.
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Affiliation(s)
- Hongxia Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jinglei Guo
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chengyang Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Weijun Zheng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yulong Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yu Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
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Bernhard T, Koch M, Snowdon RJ, Friedt W, Wittkop B. Undesired fertility restoration in msm1 barley associates with two mTERF genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1335-1350. [PMID: 30659305 DOI: 10.1007/s00122-019-03281-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/07/2019] [Indexed: 05/02/2023]
Abstract
The novel Rfm3 locus causing undesired fertility restoration in the msm1 cytoplasm of winter barley is located on the short arm of chromosome 6H. Undesired fertility restoration of cytoplasmic male sterile (CMS) mother lines in absence of the functional Rfm1 restorer gene is a significant problem for hybrid breeding in winter barley. Here, we describe that a novel restorer locus on the short arm of chromosome 6H, designated Rfm3, is closely linked to two mitochondrial transcription termination factor family (mTERF) protein coding genes. Genome-wide association studies in a multiparental mapping population revealed that two of the most significantly associated markers are located very close to these genes, with one marker lying directly within one mTERF gene sequence. Sequences of the candidate genes in the parental lines, segregating individuals and an independent set of breeding lines clearly revealed haplotypes discriminating completely sterile, partially fertile and Rfm1-restorer lines. The haplotypes segregate for several single nucleotide polymorphisms, a 6 bp insertion-deletion (InDel) polymorphism and another 2 bp InDel. CMS-unstable genotypes carrying haplotypes associated with undesired fertility restoration showed significantly higher grain setting on bagged spikes when plants were subjected to elevated temperatures during anthesis, indicating a temperature influence on pollen fertility. SNPs associated with desirable Rfm3 haplotypes can be implemented in marker-assisted selection of stable CMS mother lines.
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Affiliation(s)
- Timm Bernhard
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Michael Koch
- Deutsche Saatveredelung AG, Thueler Str. 30, 33154, Salzkotten, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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49
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Horn R, Radanovic A, Fuhrmann L, Sprycha Y, Hamrit S, Jockovic M, Miladinovic D, Jansen C. Development and Validation of Markers for the Fertility Restorer Gene Rf1 in Sunflower. Int J Mol Sci 2019; 20:ijms20061260. [PMID: 30871146 PMCID: PMC6471545 DOI: 10.3390/ijms20061260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 01/14/2023] Open
Abstract
Hybrid breeding in sunflowers based on CMS PET1 requires development of restorer lines carrying, in most cases, the restorer gene Rf1. Markers for marker-assisted selection have been developed, but there is still need for closer, more versatile, and co-dominant markers linked to Rf1. Homology searches against the reference sunflower genome using sequences of cloned markers, as well as Bacterial Artificial Chromosome (BAC)-end sequences of clones hybridizing to them, allowed the identification of two genomic regions of 30 and 3.9 Mb, respectively, as possible physical locations of the restorer gene Rf1 on linkage group 13. Nine potential candidate genes, encoding six pentatricopeptide repeat proteins, one tetratricopeptide-like helical domain, a probable aldehyde dehydrogenase 22A1, and a probable poly(A) polymerase 3 (PAPS3), were identified in these two genomic regions. Amplicon targeted next generation sequencing of these nine candidate genes for Rf1 was performed in an association panel consisting of 27 maintainer and 32 restorer lines and revealed the presence of 210 Single Nucleotide Polymorphisms (SNPs) and 67 Insertions/Deletions (INDELs). Association studies showed significant associations of 10 SNPs with fertility restoration (p-value < 10−4), narrowing Rf1 down to three candidate genes. Three new markers, one co-dominant marker 67N04_P and two dominant markers, PPR621.5R for restorer, and PPR621.5M for maintainer lines were developed and verified in the association panel of 59 sunflower lines. The versatility of the three newly developed markers, as well as of three existing markers for the restorer gene Rf1 (HRG01 and HRG02, Cleaved Amplified Polymorphic Sequence (CAPS)-marker H13), was analyzed in a large association panel consisting of 557 accessions.
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Affiliation(s)
- Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Aleksandra Radanovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Lena Fuhrmann
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Yves Sprycha
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Sonia Hamrit
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany.
| | - Milan Jockovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Dragana Miladinovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Constantin Jansen
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany.
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50
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Nugent JM, Byrne T, McCormack G, Quiwa M, Stafford E. Progressive programmed cell death inwards across the anther wall in male sterile flowers of the gynodioecious plant Plantago lanceolata. PLANTA 2019; 249:913-923. [PMID: 30483868 DOI: 10.1007/s00425-018-3055-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
A cell death signal is perceived and responded to by epidermal cells first before being conveyed inwards across the anther wall in male sterile Plantago lanceolata flowers. In gynodioecious plants, floral phenotype is determined by an interplay between cytoplasmic male sterility (CMS)-promoting factors and fertility-restoring genes segregating in the nuclear background. Plantago lanceolata exhibits at least four different sterilizing cytoplasms. MS1, a "brown-anther" male sterile phenotype, segregates with a CMSI cytoplasm and a non-restoring nuclear background in P. lanceolata populations. The aim of this study was to investigate the cytology of early anther development in segregating hermaphrodite and male sterile flowers sharing the same CMSI cytoplasm, and to determine if the sterility phenotype correlates with any changes to the normal pattern of programmed cell death (PCD) that occurs during anther development. Cytology shows cellular abnormalities in all four anther wall layers (epidermis, endothecium, middle layer and tapetum), the persistence and enlargement of middle layer and tapetal cells, and the failure of microspore mother cells to complete meiosis in male sterile anthers. In these anthers, apoptotic-PCD occurs earlier than in fertile anthers and is detected in all four cell layers of the anther wall before the middle layer and tapetal cells become enlarged. PCD is separated spatially and temporally within the anther wall, occurring first in epidermal cells before extending radially to cells in the inner anther wall layers. This is the first evidence of a cell death signal being perceived and responded to by epidermal cells first before being conveyed inwards across the anther wall in male sterile plants.
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Affiliation(s)
- Jacqueline M Nugent
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland.
| | - Tómas Byrne
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Grace McCormack
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Marc Quiwa
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Elaine Stafford
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
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