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Tan Z, Han X, Dai C, Lu S, He H, Yao X, Chen P, Yang C, Zhao L, Yang QY, Zou J, Wen J, Hong D, Liu C, Ge X, Fan C, Yi B, Zhang C, Ma C, Liu K, Shen J, Tu J, Yang G, Fu T, Guo L, Zhao H. Functional genomics of Brassica napus: Progresses, challenges, and perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:484-509. [PMID: 38456625 DOI: 10.1111/jipb.13635] [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: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024]
Abstract
Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.
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Affiliation(s)
- Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Xu Han
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanzi He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Chao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, 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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Sharbrough J, Conover JL, Gyorfy MF, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms. Mol Biol Evol 2022; 39:6564157. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary “mismatches” between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA.,Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
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K. Srivastava R, Bollam S, Pujarula V, Pusuluri M, Singh RB, Potupureddi G, Gupta R. Exploitation of Heterosis in Pearl Millet: A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:E807. [PMID: 32605134 PMCID: PMC7412370 DOI: 10.3390/plants9070807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
| | | | | | | | | | | | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
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Long W, Hu M, Gao J, Sun L, Zhang J, Pu H. Identification and application of markers closely linked to the restorer gene ( Rfm) in rapeseed ( Brassica napus L.). BREEDING SCIENCE 2019; 69:316-322. [PMID: 31481841 PMCID: PMC6711744 DOI: 10.1270/jsbbs.18105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/03/2019] [Indexed: 06/10/2023]
Abstract
The Mutsu-Isuzu cytoplasmic male sterility (MI CMS) system is one of the three-line hybrid systems used in China. As we know, the hybrid system is tightly associated with the yield variation in F1 heterosis, while the restorer gene for the MI CMS (Rfm) has not been finely mapped for further application in marker-assisted selection (MAS). In this study, the sets of near-isogenic lines (NILs) of Rfm in two different genetic backgrounds were hybridized with the genome-wide 60 K single-nucleotide polymorphism (SNP) chip of Brassica for screening the possible associated genomic region of Rfm. Through screening genotypes with SNP loci and sequencing the candidate loci, one 2.5 Mb physical region (covering three scaffolds) on chrA09 was identified as the candidate for the Rfm region. Then, the SSR markers for the target scaffolds were used to detect the recombination in an F2 population and narrowed the Rfm gene within the genetic distance of 0.52 cM, equivalent to a 350 kb physical segment. Moreover, the markers were tested to improve new elite restoration lines and to assess the percentage of hybrid seeds. Our results could potentially accelerate the map-based cloning of the Rfm gene to benefit rapeseed breeding.
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Arakawa T, Ue S, Sano C, Matsunaga M, Kagami H, Yoshida Y, Kuroda Y, Taguchi K, Kitazaki K, Kubo T. Identification and characterization of a semi-dominant restorer-of-fertility 1 allele in sugar beet (Beta vulgaris). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:227-240. [PMID: 30341492 DOI: 10.1007/s00122-018-3211-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/11/2018] [Indexed: 05/05/2023]
Abstract
The sugar beet Rf1 locus has a number of molecular variants. We found that one of the molecular variants is a weak allele of a previously identified allele. Male sterility (MS) caused by nuclear-mitochondrial interaction is called cytoplasmic male sterility (CMS) in which MS-inducing mitochondria are suppressed by a nuclear gene, restorer-of-fertility. Rf and rf are the suppressing and non-suppressing alleles, respectively. This dichotomic view, however, seems somewhat unsatisfactory to explain the recently discovered molecular diversity of Rf loci. In the present study, we first identified sugar beet line NK-305 as a new source of Rf1. Our crossing experiment revealed that NK-305 Rf1 is likely a semi-dominant allele that restores partial fertility when heterozygous but full fertility when homozygous, whereas Rf1 from another sugar beet line appeared to be a dominant allele. Proper degeneration of anther tapetum is a prerequisite for pollen development; thus, we compared tapetal degeneration in the NK-305 Rf1 heterozygote and the homozygote. Degeneration occurred in both genotypes but to a lesser extent in the heterozygote, suggesting an association between NK-305 Rf1 dose and incompleteness of tapetal degeneration leading to partial fertility. Our protein analyses revealed a quantitative correlation between NK-305 Rf1 dose and a reduction in the accumulation of a 250 kDa mitochondrial protein complex consisting of a CMS-specific mitochondrial protein encoded by MS-inducing mitochondria. The abundance of Rf1 transcripts correlated with NK-305 Rf1 dose. The molecular organization of NK-305 Rf1 suggested that this allele evolved through intergenic recombination. We propose that the sugar beet Rf1 locus has a series of multiple alleles that differ in their ability to restore fertility and are reflective of the complexity of Rf evolution.
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Affiliation(s)
- Takumi Arakawa
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Sachiyo Ue
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Chihiro Sano
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Muneyuki Matsunaga
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Hiroyo Kagami
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Yu Yoshida
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Yosuke Kuroda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Minami 9-4, Memuro, 082-0081, Japan
| | - Kazunori Taguchi
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Minami 9-4, Memuro, 082-0081, Japan
| | - Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, 060-8589, Japan.
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Liu Z, Dong F, Wang X, Wang T, Su R, Hong D, Yang G. A pentatricopeptide repeat protein restores nap cytoplasmic male sterility in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4115-4123. [PMID: 28922764 PMCID: PMC5853434 DOI: 10.1093/jxb/erx239] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/19/2017] [Indexed: 05/20/2023]
Abstract
Two forms of male-sterile cytoplasm, designated nap and pol, are found in the oilseed rape species, Brassica napus. The nap cytoplasm is observed in most B. napus varieties, and it confers male sterility on a limited number of cultivars that lack the corresponding restorer gene, Rfn. In the present study, using linkage analysis in combination with 5652 BC1 progeny derived from a cross between a nap cytoplasmic male sterility (CMS) line 181A and a restorer line H5, we delimited the Rfn gene to a 10.5 kb region on chromosome A09, which contained three putative ORFs. Complementation by transformation rescue revealed that the introduction of ORF2, which encodes a pentatricopeptide repeat (PPR) protein, resulted in the recovery of fertility of nap CMS plants. Expression analysis suggested that the Rfn was highly expressed in flower buds and it was preferentially expressed in the tapetum and meiocytes during anther development. Further RNA gel blots and immunodetection suggested that the Rfn gene may play a complicated role in restoring the nap CMS. Our work laid the foundation for dissecting the molecular basis of CMS fertility restoration and the nuclear-mitochondrial interactions in CMS/Rf systems.
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Affiliation(s)
- Zhi Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Faming Dong
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Xiang Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Tao Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Rui Su
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Dengfeng Hong
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Guangsheng Yang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
- Correspondence:
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Gaborieau L, Brown GG. Comparative genomic analysis of the compound Brassica napus Rf locus. BMC Genomics 2016; 17:834. [PMID: 27782804 PMCID: PMC5080715 DOI: 10.1186/s12864-016-3117-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 09/23/2016] [Indexed: 11/24/2022] Open
Abstract
Background The plant trait of cytoplasmically-inherited male sterility (CMS) and its suppression by nuclear restorer-of-fertility (Rf) genes can be viewed as a genetic arms race between the mitochondrial and nuclear genomes. Most nuclear Rf genes have been shown to encode P-type pentatricopeptide repeat proteins (PPRs). Phylogenetic analysis of P-class PPRs from sequenced plants genomes has shown that Rf-proteins cluster in a distinct clade of P-class PPRs, RFL-PPRs, that display hallmarks of positive evolutionary selection. Genes encoding RFL-PPRs (RFLs) within a given plant genome tend to be closely related both in sequence and position, but a detailed understanding of how such species-specific expansion occurs is lacking. In the canola, (oilseed rape) species Brassica napus, previous work has indicated the nuclear restorer genes for the two native forms of CMS, Rfn (for nap CMS) and Rfp (pol CMS), represent alternate haplotypes, or alleles, of a single nuclear locus. Results Fine genetic mapping indicates that Rfn does indeed localize to the same genomic region as Rfp. We find this region is enriched in RFL genes, three of which, based on their position and expression, represent potential candidates for Rfn; one of these genes, designated PPR4, is a preferred candidate in that it is not expressed in the nap CMS line. Comparison of the corresponding regions of the genomes of B. rapa, B. oleracea, Arabidopsis thaliana and A. lyrata provides insight into the expansion of this group of RFL genes in different lines of evolutionary descent. Conclusions Unlike other nuclear restorer loci containing multiple RFL genes, the RFL genes in the Rf region of B. napus are not present in tandem arrays but rather are dispersed in genomic location. The genes do not share similar flanking non-coding regions and do not contain introns, indicating that they have duplicated primarily through a retrotransposition-mediated process. In contrast, segmental duplication has been responsible for the distribution of the 10 sequences we annotated as RFL genes in the corresponding region of the A. lyrata genome. Our observations define the Brassica Rf locus and indicate that different mechanisms may be responsible for the proliferation of RFL genes even among closely related genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3117-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lydiane Gaborieau
- Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC, H3A 1B1, Canada
| | - Gregory G Brown
- Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC, H3A 1B1, Canada.
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Bohra A, Jha UC, Adhimoolam P, Bisht D, Singh NP. Cytoplasmic male sterility (CMS) in hybrid breeding in field crops. PLANT CELL REPORTS 2016; 35:967-93. [PMID: 26905724 DOI: 10.1007/s00299-016-1949-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
A comprehensive understanding of CMS/Rf system enabled by modern omics tools and technologies considerably improves our ability to harness hybrid technology for enhancing the productivity of field crops. Harnessing hybrid vigor or heterosis is a promising approach to tackle the current challenge of sustaining enhanced yield gains of field crops. In the context, cytoplasmic male sterility (CMS) owing to its heritable nature to manifest non-functional male gametophyte remains a cost-effective system to promote efficient hybrid seed production. The phenomenon of CMS stems from a complex interplay between maternally-inherited (mitochondrion) and bi-parental (nucleus) genomic elements. In recent years, attempts aimed to comprehend the sterility-inducing factors (orfs) and corresponding fertility determinants (Rf) in plants have greatly increased our access to candidate genomic segments and the cloned genes. To this end, novel insights obtained by applying state-of-the-art omics platforms have substantially enriched our understanding of cytoplasmic-nuclear communication. Concomitantly, molecular tools including DNA markers have been implicated in crop hybrid breeding in order to greatly expedite the progress. Here, we review the status of diverse sterility-inducing cytoplasms and associated Rf factors reported across different field crops along with exploring opportunities for integrating modern omics tools with CMS-based hybrid breeding.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, India.
| | - Uday C Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Deepak Bisht
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, India
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Non-destructive in vitro selection of microspore-derived embryos with the fertility restorer gene for CMS Ogu-INRA in winter oilseed rape (Brassica napus L.). ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2014.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Qin X, Warguchuk R, Arnal N, Gaborieau L, Mireau H, Brown GG. In vivo functional analysis of a nuclear restorer PPR protein. BMC PLANT BIOLOGY 2014; 14:313. [PMID: 25403785 PMCID: PMC4240901 DOI: 10.1186/s12870-014-0313-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/30/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Nuclear restorers of cytoplasmic male fertility (CMS) act to suppress the male sterile phenotype by down-regulating the expression of novel CMS-specifying mitochondrial genes. One such restorer gene is Rfo, which restores fertility to the radish Ogura or ogu CMS. Rfo, like most characterized restorers, encodes a pentatricopeptide repeat (PPR) protein, a family of eukaryotic proteins characterized by tandem repeats of a 35 amino acid motif. While over 400 PPR genes are found in characterized plant genomes and the importance of this gene family in organelle gene expression is widely recognized, few detailed in vivo assessments of primary structure-function relationships in this protein family have been conducted. RESULTS In contrast to earlier studies, which identified 16 or 17 PPR domains in the Rfo protein, we now find, using a more recently developed predictive tool, that Rfo has 18 repeat domains with the additional domain N-terminal to the others. Comparison of transcript sequences from pooled rfo/rfo plants with pooled Rfo/Rfo plants of a mapping population led to the identification of a non-restoring rfo allele with a 12 bp deletion in the fourth domain. Introduction into ogu CMS plants of a genetic construct in which this deletion had been introduced into Rfo led to a partial loss in the capacity to produce viable pollen, as assessed by vital staining, pollen germination and the capacity for seed production following pollination of CMS plants. The degree of viable pollen production among different transgenic plants roughly correlated with the copy number of the introduced gene and with the reduction of the levels of the ORF138 CMS-associated protein. All other constructs tested, including one in which only the C-terminal PPR repeat was deleted and another in which this repeat was replaced by the corresponding domain of the related, non-restoring gene, PPR-A, failed to result in any measure of fertility restoration. CONCLUSIONS The identification of the additional PPR domain in Rfo indicates that the protein, apart from its N-terminal mitochondrial targeting presequence, consists almost entirely of PPR repeats. The newly identified rfo allele carries the same 4 amino acid deletion as that found in the neighboring, related, non-restoring PPR gene, PPR-A. Introduction of this four amino acid deletion into a central domain the Rfo protein, however, only partially reduces its restoration capacity, even though this alteration might be expected to alter the spacing between the adjoining repeats. All other tested alterations, generated by deleting specific PPR repeats or exchanging repeats with corresponding domains of PPR-A, led to a complete loss of restorer function. Overall we demonstrate that introduction of targeted alterations of Rfo into ogu CMS plants provides a sensitive in vivo readout for analysis of the relationship between primary structure and biological function in this important family of plant proteins.
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Affiliation(s)
- Xike Qin
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
- />Current address: Lady Davis Institute for Medical research, 3999 Cote Ste-Catherine Rd., Montreal, QC H3T 1E2 Canada
| | - Richard Warguchuk
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
- />Current address: Deparment of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Montréal, QC H3G 1Y6 Canada
| | - Nadège Arnal
- />INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
- />AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
- />Current address: INRA, Centre National de Ressources Génomiques Végétales, Castanet Tolosan, France
| | - Lydiane Gaborieau
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
| | - Hakim Mireau
- />INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
- />AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Gregory G Brown
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
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Li XQ, Du D. Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals. BMC Evol Biol 2014; 14:162. [PMID: 25052519 PMCID: PMC4360255 DOI: 10.1186/s12862-014-0162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown. Results We analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of “U-rich—A-rich—U-rich—Poly(A) site—U-rich regions”, or U-A-U-A-U for short, with some variation for each kingdom or subkingdom. Conclusion This study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution.
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Affiliation(s)
- Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada.
| | - Donglei Du
- Quantitative Methods Research Group, Faculty of Business Administration, University of New Brunswick, 7 Macaulay Lane, Fredericton, NB, E3B 5A3, Canada.
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Yamagishi H, Bhat SR. Cytoplasmic male sterility in Brassicaceae crops. BREEDING SCIENCE 2014; 64:38-47. [PMID: 24987289 PMCID: PMC4031109 DOI: 10.1270/jsbbs.64.38] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/05/2013] [Indexed: 05/20/2023]
Abstract
Brassicaceae crops display strong hybrid vigor, and have long been subject to F1 hybrid breeding. Because the most reliable system of F1 seed production is based on cytoplasmic male sterility (CMS), various types of CMS have been developed and adopted in practice to breed Brassicaceae oil seed and vegetable crops. CMS is a maternally inherited trait encoded in the mitochondrial genome, and the male sterile phenotype arises as a result of interaction of a mitochondrial CMS gene and a nuclear fertility restoring (Rf) gene. Therefore, CMS has been intensively investigated for gaining basic insights into molecular aspects of nuclear-mitochondrial genome interactions and for practical applications in plant breeding. Several CMS genes have been identified by molecular genetic studies, including Ogura CMS from Japanese radish, which is the most extensively studied and most widely used. In this review, we discuss Ogura CMS, and other CMS systems, and the causal mitochondrial genes for CMS. Studies on nuclear Rf genes and the cytoplasmic effects of alien cytoplasm on general crop performance are also reviewed. Finally, some of the unresolved questions about CMS are highlighted.
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Affiliation(s)
- Hiroshi Yamagishi
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo, Kita, Kyoto 603-8555,
Japan
- Corresponding author (e-mail: )
| | - Shripad R. Bhat
- National Research Centre of Plant Biotechnology,
New Delhi 10012,
India
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Li XQ, Du D. RNA polyadenylation sites on the genomes of microorganisms, animals, and plants. PLoS One 2013; 8:e79511. [PMID: 24260238 PMCID: PMC3832601 DOI: 10.1371/journal.pone.0079511] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/29/2013] [Indexed: 01/15/2023] Open
Abstract
Pre–messenger RNA (mRNA) 3′-end cleavage and subsequent polyadenylation strongly regulate gene expression. In comparison with the upstream or downstream motifs, relatively little is known about the feature differences of polyadenylation [poly(A)] sites among major kingdoms. We suspect that the precise poly(A) sites are very selective, and we therefore mapped mRNA poly(A) sites on complete and nearly complete genomes using mRNA sequences available in the National Center for Biotechnology Information (NCBI) Nucleotide database. In this paper, we describe the mRNA nucleotide [i.e., the poly(A) tail attachment position] that is directly in attachment with the poly(A) tail and the pre-mRNA nucleotide [i.e., the poly(A) tail starting position] that corresponds to the first adenosine of the poly(A) tail in the 29 most-mapped species (2 fungi, 2 protists, 18 animals, and 7 plants). The most representative pre-mRNA dinucleotides covering these two positions were UA, CA, and GA in 17, 10, and 2 of the species, respectively. The pre-mRNA nucleotide at the poly(A) tail starting position was typically an adenosine [i.e., A-type poly(A) sites], sometimes a uridine, and occasionally a cytidine or guanosine. The order was U>C>G at the attachment position but A>>U>C≥G at the starting position. However, in comparison with the mRNA nucleotide composition (base composition), the poly(A) tail attachment position selected C over U in plants and both C and G over U in animals, in both A-type and non-A-type poly(A) sites. Animals, dicot plants, and monocot plants had clear differences in C/G ratios at the poly(A) tail attachment position of the non-A-type poly(A) sites. This study of poly(A) site evolution indicated that the two positions within poly(A) sites had distinct nucleotide compositions and were different among kingdoms.
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Affiliation(s)
- Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
- * E-mail:
| | - Donglei Du
- Quantitative Methods Research Group, Faculty of Business Administration, University of New Brunswick, Fredericton, New Brunswick, Canada
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15
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Dahan J, Mireau H. The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes. RNA Biol 2013; 10:1469-76. [PMID: 23872480 DOI: 10.4161/rna.25568] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In the last years, a number of nuclear genes restoring cytoplasmic male sterility (CMS) have been cloned in various crop species. The majority of these genes have been shown to encode pentatricopeptide repeat proteins (PPR) that act by specifically suppressing the expression of sterility-causing mitochondrial transcripts. Functional analysis of these proteins has indicated that the inhibitory effects of restoring PPR (Rf-PPR) proteins involve various mechanisms, including RNA cleavage, RNA destabilization, or translation inhibition. Cross-species sequence comparison of PPR protein complements revealed that most plant genomes encode 10-30 Rf-like (RFL) proteins sharing high-sequence similarity with the identified Rf-PPRs from crops. Evolutionary analyses further showed that they constitute a monophyletic group apart in the PPR family, with peculiar evolution dynamic and constraints. Here we review recent data on RF-PPRs and present the latest discoveries on the RFL family, with prospects on the functionality and evolution of this peculiar subclass of PPR.
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Affiliation(s)
- Jennifer Dahan
- INRA; UMR1318; Institut Jean-Pierre Bourgin; RD10; Versailles, France; AgroParisTech; Institut Jean-Pierre Bourgin; RD10; Versailles, France
| | - Hakim Mireau
- INRA; UMR1318; Institut Jean-Pierre Bourgin; RD10; Versailles, France; AgroParisTech; Institut Jean-Pierre Bourgin; RD10; Versailles, France
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16
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Jing B, Heng S, Tong D, Wan Z, Fu T, Tu J, Ma C, Yi B, Wen J, Shen J. A male sterility-associated cytotoxic protein ORF288 in Brassica juncea causes aborted pollen development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1285-95. [PMID: 22090439 PMCID: PMC3276091 DOI: 10.1093/jxb/err355] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/02/2011] [Accepted: 10/11/2011] [Indexed: 05/20/2023]
Abstract
Cytoplasmic male sterility (CMS) is a widespread phenomenon in higher plants, and several studies have established that this maternally inherited defect is often associated with a mitochondrial mutant. Approximately 10 chimeric genes have been identified as being associated with corresponding CMS systems in the family Brassicaceae, but there is little direct evidence that these genes cause male sterility. In this study, a novel chimeric gene (named orf288) was found to be located downstream of the atp6 gene and co-transcribed with this gene in the hau CMS sterile line. Western blotting analysis showed that this predicted open reading frame (ORF) was translated in the mitochondria of male-sterile plants. Furthermore, the growth of Escherichia coli was significantly repressed in the presence of ORF288, which indicated that this protein is toxic to the E. coli host cells. To confirm further the function of orf288 in male sterility, the gene was fused to a mitochondrial-targeting pre-sequence under the control of the Arabidopsis APETALA3 promoter and introduced into Arabidopsis thaliana. Almost 80% of transgenic plants with orf288 failed to develop anthers. It was also found that the independent expression of orf288 caused male sterility in transgenic plants, even without the transit pre-sequence. Furthermore, transient expression of orf288 and green fluorescent protein (GFP) as a fused protein in A. thaliana protoplasts showed that ORF288 was able to anchor to mitochondria even without the external mitochondrial-targeting peptide. These observations provide important evidence that orf288 is responsible for the male sterility of hau CMS in Brassica juncea.
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18
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Kohls S, Stamp P, Knaak C, Messmer R. QTL involved in the partial restoration of male fertility of C-type cytoplasmic male sterility in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:327-38. [PMID: 21479555 DOI: 10.1007/s00122-011-1586-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/24/2011] [Indexed: 05/08/2023]
Abstract
Partial restoration of male fertility limits the use of C-type cytoplasmic male sterility (C-CMS) for the production of hybrid seeds in maize. Nevertheless, the genetic basis of the trait is still unknown. Therefore, the aim to this study was to identify genomic regions that govern partial restoration by means of a QTL analysis carried out in an F(2) population (n = 180). This population was derived from the Corn Belt inbred lines B37C and K55. F(2)BC(1) progenies were phenotyped at three locations in Switzerland. Male fertility was rated according to the quality and number of anthers as well as the anthesis-silking interval. A weak effect of environment on the expression of partial restoration was reflected by high heritabilities of all fertility-related traits. Partial restoration was inherited like an oligogenic trait. Three major QTL regions were found consistently across environments in the chromosomal bins 2.09, 3.06 and 7.03. Therefore, a marker-assisted counter-selection of partial restoration is promising. Minor QTL regions were found on chromosomes 3, 4, 5, 6 and 8. A combination of partial restorer alleles at different QTL can lead to full restoration of fertility. The maternal parent was clearly involved in the partial restoration, because the restorer alleles at QTL in bins 2.09, 6.04 and 7.03 originated from B37. The three major QTL regions collocated with other restorer genes of maize, a phenomenon, which seems to be typical for restorer genes. Therefore, a study of the clusters of restorer genes in maize could lead to a better understanding of their evolution and function. In this respect, the long arm of chromosome 2 is particularly interesting, because it harbors restorer genes for the three major CMS systems (C, T and S) of maize.
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Affiliation(s)
- Susanne Kohls
- Institute of Agricultural Sciences, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland.
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19
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Li XQ, Zhang T, Donnelly D. Selective loss of cysteine residues and disulphide bonds in a potato proteinase inhibitor II family. PLoS One 2011; 6:e18615. [PMID: 21494600 PMCID: PMC3073943 DOI: 10.1371/journal.pone.0018615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 03/14/2011] [Indexed: 11/26/2022] Open
Abstract
Disulphide bonds between cysteine residues in proteins play a key role in protein folding, stability, and function. Loss of a disulphide bond is often associated with functional differentiation of the protein. The evolution of disulphide bonds is still actively debated; analysis of naturally occurring variants can promote understanding of the protein evolutionary process. One of the disulphide bond-containing protein families is the potato proteinase inhibitor II (PI-II, or Pin2, for short) superfamily, which is found in most solanaceous plants and participates in plant development, stress response, and defence. Each PI-II domain contains eight cysteine residues (8C), and two similar PI-II domains form a functional protein that has eight disulphide bonds and two non-identical reaction centres. It is still unclear which patterns and processes affect cysteine residue loss in PI-II. Through cDNA sequencing and data mining, we found six natural variants missing cysteine residues involved in one or two disulphide bonds at the first reaction centre. We named these variants Pi7C and Pi6C for the proteins missing one or two pairs of cysteine residues, respectively. This PI-II-7C/6C family was found exclusively in potato. The missing cysteine residues were in bonding pairs but distant from one another at the nucleotide/protein sequence level. The non-synonymous/synonymous substitution (Ka/Ks) ratio analysis suggested a positive evolutionary gene selection for Pi6C and various Pi7C. The selective deletion of the first reaction centre cysteine residues that are structure-level-paired but sequence-level-distant in PI-II illustrates the flexibility of PI-II domains and suggests the functionality of their transient gene versions during evolution.
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Affiliation(s)
- Xiu-Qing Li
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, Canada.
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20
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Engelke T, Hirsche J, Roitsch T. Metabolically engineered male sterility in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:163-174. [PMID: 20821307 DOI: 10.1007/s00122-010-1432-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 08/09/2010] [Indexed: 05/29/2023]
Abstract
Male sterility is of special interest as a mechanism allowing hybrid breeding, especially in important crops such as rapeseed (Brassica napus). Male sterile plants are also suggested to be used as a biological safety method to prevent the spread of transgenes, a risk that is high in the case of rapeseed due to the mode of pollination, out-crossing by wind or insects, and the presence of related, cross-pollinating species in the surrounding ecosystem in Europe. Different natural occurring male sterilities and alloplasmic forms have been tried to be used in rapeseed with more or less success. Due to the difficulties and limitations with these systems, we present a biotechnological alternative: a metabolically engineered male sterility caused by interference with anther-specific cell wall-bound invertase. This is an essential enzyme for carbohydrate supply of the symplastically isolated pollen. The activity of this enzyme is reduced either by antisense interference or by expressing an invertase inhibitor under control of the anther-specific promoter of the invertase with the consequence of a strong decrease of pollen germination ability.
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Affiliation(s)
- Thomas Engelke
- Lehrstuhl für Pharmazeutische Biologie, Julius von Sachs Institut, Universität Würzburg, Julius von Sachs Platz 2, 97082, Würzburg, Germany.
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21
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Formanová N, Stollar R, Geddy R, Mahé L, Laforest M, Landry BS, Brown GG. High-resolution mapping of the Brassica napus Rfp restorer locus using Arabidopsis-derived molecular markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:843-851. [PMID: 19921138 DOI: 10.1007/s00122-009-1215-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 10/30/2009] [Indexed: 05/28/2023]
Abstract
The two forms of cytoplasmic male sterility (CMS) native to the oilseed rape or canola species Brassica napus, nap and pol, have novel features that may provide insight into the molecular mechanisms through which CMS/nuclear restorer systems evolve. One such feature is the finding that the distinct nuclear restorer genes for the two systems represent different alleles or haplotypes of the same nuclear locus. Improved understanding of how these systems have evolved will require molecular cloning and characterization of this novel locus. We have employed an approach that exploits the regional co-linearity between the Arabidopsis and Brassica genomes to construct a high-resolution genetic map of the nuclear restorer for the pol system, Rfp. Specifically, Arabidopsis-derived sequences have been used as a set of ordered RFLP probes to localize Rfp to a region of the B. napus genome equivalent to a 115 kb interval on Arabidopsis chromosome 1. Based on the known relationship of physical distances between orthologous segments of Arabidopsis and Brassica chromosomes, it is anticipated that the B. napus restorer locus is now mapped to sufficient resolution to permit its isolation and characterization.
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Abstract
The occurrence of gynodioecy among angiosperms appears to be associated with self-compatibility. We use individual-based simulations to investigate the conditions for breakdown of a gametophytic self-incompatibility system in gynodioecious populations and make a comparison with hermaphroditic populations where the conditions are well known. We study three types of mutations causing self-compatibility. We track the fate of these mutations in both gynodioecious and hermaphroditic populations, where we vary the number of S-alleles, inbreeding depression and selfing rate. We find that the conditions for breakdown are less stringent if the population is gynodioecious and that the breakdown of self-incompatibility tends to promote stability of gynodioecious populations since it results in a higher frequency of females. We also find that fecundity selection has a large effect on the probability of breakdown of self-incompatibility, in particular if caused by a mutation destroying the female function of the S-locus.
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Carlsson J, Leino M, Sohlberg J, Sundström JF, Glimelius K. Mitochondrial regulation of flower development. Mitochondrion 2008; 8:74-86. [PMID: 18054525 DOI: 10.1016/j.mito.2007.09.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 08/27/2007] [Accepted: 09/02/2007] [Indexed: 11/19/2022]
Abstract
Flower development in plants depends not only on a set of nuclear genes but also on the coordinate action of the mitochondrion. Certain mitochondrial genomes in combination with certain nuclear genomes lead to the expression of cytoplasmic male-sterility (CMS). Both mitochondrial genes that determine male-sterility and nuclear Restorer-of-fertility genes that suppress the male-sterile phenotype have been cloned. Lately, the interactions between mitochondrial and nuclear genes through retrograde signalling in CMS-systems have been dissected. Of special interest are the altered expression patterns of floral homeotic genes in certain CMS-systems. Here, we review the mitochondrial influence on flower development and give examples from CMS-systems developed in Brassica, Daucus carota, Nicotiana tabacum and Triticum aestivum.
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Affiliation(s)
- Jenny Carlsson
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Ivanov MK, Dymshits GM. Cytoplasmic male sterility and restoration of pollen fertility in higher plants. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407040023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Formanová N, Li XQ, Ferrie AMR, Depauw M, Keller WA, Landry B, Brown GG. Towards positional cloning in Brassica napus: generation and analysis of doubled haploid B. rapa possessing the B. napus pol CMS and Rfp nuclear restorer gene. PLANT MOLECULAR BIOLOGY 2006; 61:269-81. [PMID: 16786306 DOI: 10.1007/s11103-006-0008-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 01/06/2006] [Indexed: 05/10/2023]
Abstract
The Polima (pol) system of cytoplasmic male sterility (CMS) and its fertility restorer gene Rfp are used in hybrid rapeseed production in Brassica napus. To facilitate map-based cloning of the Rfp gene, we have successfully transferred the pol cytoplasm and Rfp from the amphidiploid B. napus to the diploid species B. rapa and generated a doubled haploid pol cytoplasm B. rapa population that segregates for the Rfp gene. This was achieved through interspecific crosses, in vitro rescue of hybrid embryos, backcrosses, and microspore culture. Male fertility conditioned by Rfp was shown to co-segregate in this population with Rfp-specific mitochondrial transcript modifications and with DNA markers previously shown to be linked to Rfp in B. napus. The selfed-progeny of one doubled haploid plant were confirmed to be characteristic B. rapa diploids by cytogenetic analysis. Clones recovered from a genomic library derived from this plant line using the RFLP probe cRF1 fell into several distinct physical contigs, one of which contained Rfp-linked polymorphic restriction fragments detected by this probe. This indicates that chromosomal DNA segments anchored in the Rfp region can be recovered from this library and that the library may therefore prove to be a useful resource for the eventual isolation of the Rfp gene.
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Affiliation(s)
- Natasa Formanová
- Department of Biology, McGill University, Montreal, Quebec, Canada
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Wade MJ, McCauley DE. Paternal leakage sustains the cytoplasmic polymorphism underlying gynodioecy but remains invasible by nuclear restorers. Am Nat 2005; 166:592-602. [PMID: 16224724 DOI: 10.1086/491660] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Accepted: 06/20/2005] [Indexed: 11/03/2022]
Abstract
Cytoplasmic male sterility (CMS) in plants often results in gynodioecious populations, composed of hermaphrodites and male-sterile females. All models of gynodioecy assume maternal inheritance of the cytoplasmic alleles and postulate a variety of negatively frequency-dependent mechanisms to maintain the cytoplasmic polymorphisms observed in many natural populations. However, in some plant species, mitochondria are transmitted at least occasionally by pollen, a process called paternal leakage. We show that even a small amount of paternal leakage is sufficient to sustain a permanent, stable cytoplasmic polymorphism. Because only hermaphrodites provide pollen in gynodioecious species, the effects of paternal leakage are biased and occur more often from the non-CMS male-fertile haplotype to the CMS male-sterile haplotype. We also show that a nuclear restorer disrupts the polymorphic cytoplasmic equilibrium, leading to fixation of both the CMS allele and the restorer. Although a dominant nuclear restorer fixes, it fixes much more slowly than in the standard CMS models. Although a stable cytonuclear polymorphism is possible with "matching alleles" nuclear restoration, oscillations to low frequencies present a risk of loss by drift. Paternal leakage enhances the stability of joint cytonuclear polymorphism by reducing the chance that a CMS allele is lost by drift.
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Affiliation(s)
- Michael J Wade
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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Leino M, Landgren M, Glimelius K. Alloplasmic effects on mitochondrial transcriptional activity and RNA turnover result in accumulated transcripts of Arabidopsis orfs in cytoplasmic male-sterile Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:469-80. [PMID: 15860006 DOI: 10.1111/j.1365-313x.2005.02389.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mitochondrial transcription was investigated in a cytoplasmic male-sterile (CMS) Brassica napus line with rearranged mitochondrial (mt) DNA mostly inherited from Arabidopsis thaliana. The transcript patterns were compared with the corresponding male-fertile progenitors, B. napus and A. thaliana, and a fertility-restored line. Transcriptional activities, gene stoichiometry and transcript steady-state levels were analysed for all protein and rRNA coding genes and for several orfs present in the A. thaliana mitochondrial genome. The transcriptional activities were highly variable when comparing the parental species, while the CMS and restored lines displayed similar activities. For several ribosomal protein genes transcriptional activity was reduced while it was increased for orf139 in comparison with the parental species. The differences in transcriptional activity observed could be related to differences in relative promoter strength, as gene stoichiometry between lines was very limited. Transcript steady-state levels were more homogenous than the transcriptional activities demonstrating RNA turnover as a compensating mechanism. In the CMS line higher transcript abundance and novel transcript patterns in comparison with the parental lines were found for several genes. Of those, the transcripts for orf139, orf240a and orf294 were less abundant in the fertility-restored line. These putative CMS-associated transcripts were mapped by cRT-PCR. In conclusion we show that (mt) DNA from A. thaliana was non-correctly transcribed and processed/degraded in the B. napus nuclear background. Furthermore, the introgressed nuclear A. thaliana DNA in the fertility-restored line contributes to a more rapid degradation of transcripts accumulated from A. thaliana derived orfs in the CMS line.
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Affiliation(s)
- Matti Leino
- Department of Plant Biology and Forest Genetics, Box 7080, Swedish University for Agricultural Sciences, S-750 07 Uppsala, Sweden.
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Geddy R, Mahé L, Brown GG. Cell-specific regulation of a Brassica napus CMS-associated gene by a nuclear restorer with related effects on a floral homeotic gene promoter. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 41:333-345. [PMID: 15659093 DOI: 10.1111/j.1365-313x.2004.02305.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited defect in pollen production specified by novel mitochondrial genes. It can be suppressed by nuclear restorer (Rf) genes which normally downregulate expression of a CMS-associated novel mitochondrial gene. Two forms of Brassica napus CMS, nap and pol, are associated with related chimeric genes, orf222 and orf224, respectively. We show that in pol and nap CMS, anther locule development is asynchronous and asymmetric, that one or more locules within each anther may fail to develop entirely and that CMS anthers display polarity in locule development. We show, by in situ hybridization, that orf222 transcripts accumulate in sterile anthers prior to development of morphological differences between CMS and restored stamens, and remain preferentially localized to microsporangia. In fertility-restored anthers, however, orf222 transcript levels remain low throughout development. Some sporogenous and meiotic cells differentiate within CMS anthers and form functional pollen despite retaining high orf222 transcript levels, suggesting that the effect of orf222 expression in blocking pollen development is limited to an early and specific stage. Transcripts of other mitochondrial genes, exemplified by atp6 and cob, and of the nuclear-encoded ATP synthase gamma subunit, accumulate preferentially in the microsporangia of both sterile and fertile anthers. Thus nuclear fertility restoration reduces orf222 transcript levels in a gene and tissue-specific manner. We observe differences between CMS and fertile plants in the timing and patterning of APETALA3 promoter activity that suggest a possible basis for the developmental abnormalities of CMS flowers.
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Affiliation(s)
- Rachel Geddy
- Department of Biology, McGill University, Montreal, Quebec, Canada
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Touzet P, Budar F. Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility? TRENDS IN PLANT SCIENCE 2004; 9:568-70. [PMID: 15564120 DOI: 10.1016/j.tplants.2004.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cytoplasmic male sterility can be thought of as the product of a genetic conflict between two genomes that have different modes of inheritance. Male sterilizing factors, generally encoded by chimeric mitochondrial genes, can be down-regulated by specific nuclear restorer genes. The recent cloning of a restorer gene in rice and its comparison with restorer genes cloned in petunia and radish could be regarded as the beginning of a general molecular scenario in this peculiar arms race.
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Affiliation(s)
- Pascal Touzet
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR-CNRS 8016, FR CNRS 1818, Université de Lille I, F-59655 Villeneuve d'Ascq cedex, France.
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Gabay-Laughnan S, Chase CD, Ortega VM, Zhao L. Molecular-genetic characterization of CMS-S restorer-of-fertility alleles identified in Mexican maize and teosinte. Genetics 2004; 166:959-70. [PMID: 15020480 PMCID: PMC1470741 DOI: 10.1534/genetics.166.2.959] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Restorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm.
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Touzet P, Hueber N, Bürkholz A, Barnes S, Cuguen J. Genetic analysis of male fertility restoration in wild cytoplasmic male sterility G of beet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:240-247. [PMID: 15085261 DOI: 10.1007/s00122-004-1627-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Accepted: 02/09/2004] [Indexed: 05/24/2023]
Abstract
Cytoplasmic male sterility (CMS) has been used in the breeding of sugar beet for decades but is also more generally an important feature of the reproductive system in its wild relative, Beta vulgaris ssp. maritima. Among the several CMSs found in wild populations, the G CMS is a mitochondrial variant of the respiratory chain. The segregants derived from a cross between a restored plant and a female (male-sterile) plant on G cytoplasm exhibited three sexual phenotypic classes: female, hermaphrodite and intermediate. The pattern of segregation suggests a genetic inheritance with two loci in epistatic interaction. Nevertheless, it was possible to apply a bulk segregant analysis approach to search for AFLP and microsatellite markers linked to the restorer locus ( RfG(1)) which controls the capacity to produce pollen [female versus non female (i.e. intermediates and hermaphrodites)] in the segregating population. A linkage group was constructed with four AFLP markers and nine microsatellites, and a total size of 40 cM (Kosambi). The closest marker, a microsatellite, was totally linked to RfG1, which was also flanked by two AFLP markers delimiting a 5 cM window. This linkage group was identified as being chromosome VIII where neither of the restorer loci of the Owen CMS are located.
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Affiliation(s)
- Pascal Touzet
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR-CNRS 8016, FR CNRS 1818, Université de Lille I, 59655 Villeneuve d'Ascq Cedex, France.
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32
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Akagi H, Nakamura A, Yokozeki-Misono Y, Inagaki A, Takahashi H, Mori K, Fujimura T. Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1449-57. [PMID: 14968308 DOI: 10.1007/s00122-004-1591-2] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2003] [Accepted: 01/05/2004] [Indexed: 05/18/2023]
Abstract
The combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene ( Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames ( Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome.
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Affiliation(s)
- H Akagi
- Laboratory of Plant Breeding and Genetics, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Kaidoubata-Nishi 241-7, Shimoshinjyo-Nakano, 010-0195 Akita, Japan.
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Gabay-Laughnan S, Chase CD, Ortega VM, Zhao L. Molecular-Genetic Characterization of CMS-S Restorer-of-Fertility Alleles Identified in Mexican Maize and Teosinte. Genetics 2004. [DOI: 10.1093/genetics/166.2.959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Restorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm.
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Affiliation(s)
| | - Christine D Chase
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Victor M Ortega
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Liming Zhao
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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Hanson MR, Bentolila S. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. THE PLANT CELL 2004; 16 Suppl:S154-69. [PMID: 15131248 PMCID: PMC2643387 DOI: 10.1105/tpc.015966] [Citation(s) in RCA: 451] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-0001, USA.
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Brown GG, Formanová N, Jin H, Wargachuk R, Dendy C, Patil P, Laforest M, Zhang J, Cheung WY, Landry BS. The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 35:262-72. [PMID: 12848830 DOI: 10.1046/j.1365-313x.2003.01799.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A single radish nuclear gene, Rfo, restores Ogura (ogu) cytoplasmic male sterility (CMS) in Brassica napus. A map-based cloning approach relying on synteny between radish and Arabidopsis was used to clone Rfo. A radish gene encoding a 687-amino-acid protein with a predicted mitochondrial targeting pre-sequence was found to confer male fertility upon transformation into ogu CMS B. napus. This gene, like the recently described Petunia Rf gene, codes for a pentatricopeptide repeat (PPR)-containing protein with multiple, in this case 16, PPR domains. Two similar genes that do not appear to function as Rfo flank this gene. Comparison of the Rfo region with the syntenic Arabidopsis region indicates that a PPR gene is not present at the Rfo-equivalent site in Arabidopsis, although a smaller and related PPR gene is found about 40 kb from this site. The implications of these findings for the evolution of restorer genes and other PPR encoding genes are discussed.
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Affiliation(s)
- Gregory G Brown
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1.
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Imai R, Koizuka N, Fujimoto H, Hayakawa T, Sakai T, Imamura J. Delimitation of the fertility restorer locus Rfk1 to a 43-kb contig in Kosena radish (Raphanus sativus L.). Mol Genet Genomics 2003; 269:388-94. [PMID: 12712328 DOI: 10.1007/s00438-003-0847-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2002] [Accepted: 03/12/2003] [Indexed: 10/26/2022]
Abstract
We are pursuing a positional cloning strategy to isolate the fertility restoration gene Rfk1 from radish. Random polymorphic DNA-sequence-tagged site (RAPD-STS) markers tightly linked to the gene in radish were isolated, and a RAPD map surrounding the Rfk1 locus was constructed. We surveyed 948 F2 plants with adjacent RAPD-STS markers to isolate recombinants for bulk segregant analysis. This analysis was effective in isolating tightly linked amplification fragment length polymorphism (AFLP) markers surrounding the gene of interest. Ten tightly linked AFLP markers were obtained and used to construct a high-resolution map of the region. The closest AFLP-STS markers flanking Rfk1 were 0.1 cM and 0.2 cM away. Using the four adjacent AFLP markers, we screened lambda and cosmid libraries. The lambda and cosmid clones were aligned by examination of end sequences and restriction fragment length polymorphism (RFLP) patterns for each clone, and by hybridization to the DNA isolated from recombinants. Finally, we constructed a 198-kb contig encompassing the Rfk1 gene and comprising 20 lambda and two cosmid clones. By analysis of the breakpoints in recombinants with the rfk1/rfk1 or Rfk1/- genotype, the Rfk1 locus could be assigned to a 43-kb region comprising four lambda clones and one cosmid clone. This pinpoint localization in the radish genome has made it possible for us to identify the gene by sequence analysis and genetic transformation of cytoplasmic male-sterile Brassica napus plants.
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Affiliation(s)
- R Imai
- Plantech Research Institute, 1000 Kamoshida Aoba-ku, 227-0033 Yokohama, Japan
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40
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Bailey MF, Delph LF, Lively CM. Modeling gynodioecy: novel scenarios for maintaining polymorphism. Am Nat 2003; 161:762-76. [PMID: 12858283 DOI: 10.1086/374803] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2001] [Accepted: 10/29/2002] [Indexed: 11/04/2022]
Abstract
Nuclear-cytoplasmic gynodioecy is a breeding system of plants in which females and hermaphrodites co-occur in populations, and gender is jointly determined by cytoplasmic male sterility (CMS) genes and nuclear restorers of male fertility. Persistent polymorphism at both CMS and nuclear-restorer loci is necessary to maintain this breeding system. Theoretical models have explained how nuclear-cytoplasmic gynodioecy can be stable for certain assumptions. However, recent advances in our understanding of the genetics, population biology, and molecular mechanisms of sex determination in nuclear-cytoplasmic gynodioecious species suggest the utility of new models with different underlying assumptions. In this article, we examine different negative pleiotropic fitness effects of nuclear restorers (costs of restoration) using genetic and population assumptions based on recent literature. Specifically, we model populations with two CMS types and separate nuclear restorer loci for each CMS type. Under these assumptions, both overdominance for fitness and frequency-dependent selection at nuclear-restorer loci can support nuclear-cytoplasmic gynodioecy. Costs of restoration can be either dependent or independent of the cytoplasmic background. Seed fitness costs are more vulnerable to fixation of CMS types than pollen costs. Survivorship costs are effective at maintaining polymorphism even when total reproductive effects are low. Overall, our models display differences in the stability of nuclear-cytoplasmic gynodioecy and predicted population sex ratios that should be informative to researchers studying gynodioecy in the wild.
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Affiliation(s)
- Maia F Bailey
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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Bentolila S, Alfonso AA, Hanson MR. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci U S A 2002; 99:10887-92. [PMID: 12136123 PMCID: PMC125068 DOI: 10.1073/pnas.102301599] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2002] [Accepted: 05/17/2002] [Indexed: 11/18/2022] Open
Abstract
Known in over 150 species, cytoplasmic male sterility is encoded by aberrant mitochondrial genes that prevent pollen development. The RNA- or protein-level expression of most of the mitochondrial genes encoding cytoplasmic male sterility is altered in the presence of one or more nuclear genes called restorers of fertility that suppress the male-sterile phenotype. Cytoplasmic male sterility/restorer systems have been proven to be an invaluable tool in the production of hybrid seeds. Despite their importance for both the production of major crops such as rice and sunflower and the study of organelle/nuclear interactions in plants, none of the nuclear fertility-restorer genes that reduce the expression of aberrant mitochondrial proteins have previously been cloned. Here we report the isolation of a gene directly involved in the control of the expression of a cytoplasmic male sterility-encoding gene. The Petunia restorer of fertility gene product is a mitochondrially targeted protein that is almost entirely composed of 14 repeats of the 35-aa pentatricopeptide repeat motif. In a nonrestoring genotype we identified a homologous gene that exhibits a deletion in the promoter region and is expressed in roots but not in floral buds.
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Affiliation(s)
- Stephane Bentolila
- Department of Molecular Biology and Genetics, 323 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
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Bellaoui M, Grelon M, Pelletier G, Budar F. The restorer Rfo gene acts post-translationally on the stability of the ORF138 Ogura CMS-associated protein in reproductive tissues of rapeseed cybrids. PLANT MOLECULAR BIOLOGY 1999; 40:893-902. [PMID: 10487223 DOI: 10.1023/a:1006223908044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This paper describes the analysis of the effect of the restorer gene Rfo on the expression of the ORF138 protein associated with Ogura cytoplasmic male sterility (CMS) which has been engineered in rapeseed by protoplast fusion. We show that the presence of the Rfo gene in the genome of the plants decreases the amount of ORF138 protein in floral buds, this effect being the most dramatic in anthers at the stage of development when the sterile phenotype is normally expressed. However, the amount of orf138 transcripts is not affected by the Rfo gene in the same organs at the same stages. Total polysome analyses of buds and anthers show that the orf138 transcripts are translated with the same efficiency in sterile and restored plants. From these results we infer that the Rfo gene product acts on the post-translational stability of the ORF138 protein, leading to a decrease in the accumulation of the protein and a restoration of fertility.
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Affiliation(s)
- M Bellaoui
- Station de Génétique et d'Amélioration des Plantes, INRA, Versailles, France
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