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Zeng T, Ni Y, Li J, Chen H, Lu Q, Jiang M, Xu L, Liu C, Xiao P. Comprehensive analysis of the mitochondrial genome of Rehmannia glutinosa: insights into repeat-mediated recombinations and RNA editing-induced stop codon acquisition. FRONTIERS IN PLANT SCIENCE 2024; 15:1326387. [PMID: 38807783 PMCID: PMC11130359 DOI: 10.3389/fpls.2024.1326387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Rehmannia glutinosa is an economically significant medicinal plant. Yet, the structure and sequence of its mitochondrial genome has not been published, which plays a crucial role in evolutionary analysis and regulating respiratory-related macromolecule synthesis. In this study, the R. glutinosa mitogenome was sequenced employing a combination of Illumina short reads and Nanopore long reads, with subsequent assembly using a hybrid strategy. We found that the predominant configuration of the R. glutinosa mitogenome comprises two circular chromosomes. The primary structure of the mitogenome encompasses two mitochondrial chromosomes corresponding to the two major configurations, Mac1-1 and Mac1-2. The R. glutinosa mitogenome encoded an angiosperm-typical set of 24 core genes, nine variable genes, three rRNA genes, and 15 tRNA genes. A phylogenetic analysis using the 16 shared protein-coding genes (PCG) yielded a tree consistent with the phylogeny of Lamiales species and two outgroup taxa. Mapping RNA-seq data to the coding sequences (CDS) of the PCGs revealed 507 C-to-U RNA editing sites across 31 PCGs of the R. glutinosa mitogenome. Furthermore, one start codon (nad4L) and two stop codons (rpl10 and atp6) were identified as products of RNA editing events in the R. glutinosa mitogenome.
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Affiliation(s)
- Tiexin Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingling Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qianqi Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lijia Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Liu J, Ni Y, Liu C. Polymeric structure of the Cannabis sativa L. mitochondrial genome identified with an assembly graph model. Gene 2023; 853:147081. [PMID: 36470482 DOI: 10.1016/j.gene.2022.147081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Cannabis sativa L. belongs to the family Cannabaceae in Rosales. It has been widely used as medicines, building materials, and textiles. Elucidating its genome is critical for molecular breeding and synthetic biology study. Many studies have shown that the mitochondrial genomes (mitogenomes) and even chloroplast genomes (plastomes) had complex polymeric structures. Using the Nanopore sequencing platform, we sequenced, assembled, and analyzed its mitogenome and plastome. The resulting unitig graph suggested that the mitogenome had a complex polymeric structure. However, a gap-free, circular sequence was further assembled from the unitig graph. In contrast, a circular sequence representing the plastome was obtained. The mitogenome major conformation was 415,837 bp long, and the plastome was 153,927 bp long. To test if the repeat sequences promote recombination, which corresponds to the branch points in the structure, we tested the sequences around repeats by long-read mapping. Among 208 pairs of predicted repeats, the mapping results supported the presence of cross-over around 25 pairs of repeats. Subsequent PCR amplification confirmed the presence of cross-over around 15 of the 25 repeats. By comparing the mitogenome and plastome sequences, we identified 19 mitochondria plastid DNAs, including seven complete genes (trnW-CCA, trnP-UGG, psbJ, trnN-GUU, trnD-GUC, trnH-GUG, trnM-CAU) and nine gene fragments. Furthermore, the selective pressure analysis results showed that five genes (atp1, ccmB, ccmC, cox1, nad7) had 19 positively selected sites. Lastly, we predicted 28 RNA editing sites. A total of 8 RNA editing sites located in the coding regions were successfully validated by PCR amplification and Sanger sequencing, of which four were synonymous, and four were nonsynonymous. In particular, the RNA editing events appeared to be tissue-specific in C. sativa mitogenome. In summary, we have confirmed the major confirmation of C. sativa mitogenome and characterized its structural features in detail. These results provide critical information for future variety breeding and resource development for C. sativa.
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Affiliation(s)
- Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.
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Fujian cytoplasmic male sterility and the fertility restorer gene OsRf19 provide a promising breeding system for hybrid rice. Proc Natl Acad Sci U S A 2022; 119:e2208759119. [PMID: 35969741 PMCID: PMC9407659 DOI: 10.1073/pnas.2208759119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Although hybrid rice has been widely utilized for nearly half a century, tremendously improving rice productivity worldwide, the breeding of hybrids has been difficult because of genetic complications in male sterility and fertility-restoring systems currently available in rice. Here, we characterized Fujian Abortive cytoplasmic male sterility (CMS-FA) rice, which has shown stable male sterility controlled by the mitochondrial gene FA182; a single nuclear gene, OsRf19, completely restores fertility. This single-gene inheritance has greatly eased the breeding process. By converting CMS-WA hybrids with the CMS-FA system, we developed six hybrids that showed equivalent or better performance relative to their CMS-WA counterparts. CMS-FA/OsRf19 provides a promising system for future hybrid rice breeding. Cytoplasmic male sterility (CMS) determined by mitochondrial genes and restorer of fertility (Rf) controlled by nuclear-encoded genes provide the breeding systems of many hybrid crops for the utilization of heterosis. Although several CMS/Rf systems have been widely exploited in rice, hybrid breeding using these systems has encountered difficulties due to either fertility instability or complications of two-locus inheritance or both. In this work, we characterized a type of CMS, Fujian Abortive cytoplasmic male sterility (CMS-FA), with stable sporophytic male sterility and a nuclear restorer gene that completely restores hybrid fertility. CMS is caused by the chimeric open reading frame FA182 that specifically occurs in the mitochondrial genome of CMS-FA rice. The restorer gene OsRf19 encodes a pentatricopeptide repeat (PPR) protein targeted to mitochondria, where it mediates the cleavage of FA182 transcripts, thus restoring male fertility. Comparative sequence analysis revealed that OsRf19 originated through a recent duplication in wild rice relatives, sharing a common ancestor with OsRf1a/OsRf5, a fertility restorer gene for Boro II and Hong-Lian CMS. We developed six restorer lines by introgressing OsRf19 into parental lines of elite CMS-WA hybrids; hybrids produced from these lines showed equivalent or better agronomic performance relative to their counterparts based on the CMS-WA system. These results demonstrate that CMS-FA/OsRf19 provides a highly promising system for future hybrid rice breeding.
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Histological characterization of anther structure in Tetep-cytoplasmic male sterility and fine mapping of restorer-of-fertility gene in rice. PLoS One 2022; 17:e0268174. [PMID: 35980881 PMCID: PMC9387866 DOI: 10.1371/journal.pone.0268174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/25/2022] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait that inhibits plants from producing or releasing viable pollen. CMS is caused by mitochondrial–nuclear interaction, and can be rescued by introducing functional nuclear restorer-of-fertility (Rf) gene. The Tetep-CMS/Rf lines were developed through successive inter-subspecific backcrosses between indica and japonica rice accessions. Phenotypic characterization of Tetep-CMS lines revealed abnormal anther dehiscence and the inability to release, while possessing functional pollen. Transverse sections of developing anthers collected from CMS plants showed connective tissue deformities and aberrant dehydration of endothecium and epidermis. Fine mapping of Rf-Tetep using a series of segregating populations, delimited the candidate region to an approximately 109 kb genomic interval between M2099 and FM07 flanking markers. Nanopore long-read sequencing and genome assembly, proceeded by gene prediction and annotation revealed 11 open reading frames (ORFs) within the candidate region, and suggest ORF6 annotated as pentatricopeptide repeat motif containing gene 1 (PPR1), as a possible candidate gene responsible for fertility restoration. This study suggests that tissue-specific abnormalities in anthers are responsible for indehiscence-based sterility, and propose that the functional Rf gene is derived from allelic variation between inter-subspecies in rice.
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Yang H, Xue Y, Li B, Lin Y, Li H, Guo Z, Li W, Fu Z, Ding D, Tang J. The chimeric gene atp6c confers cytoplasmic male sterility in maize by impairing the assembly of the mitochondrial ATP synthase complex. MOLECULAR PLANT 2022; 15:872-886. [PMID: 35272047 DOI: 10.1016/j.molp.2022.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/30/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Cytoplasmic male sterility (CMS) is a powerful tool for the exploitation of hybrid heterosis and the study of signaling and interactions between the nucleus and the cytoplasm. C-type CMS (CMS-C) in maize has long been used in hybrid seed production, but the underlying sterility factor and its mechanism of action remain unclear. In this study, we demonstrate that the mitochondrial gene atp6c confers male sterility in CMS-C maize. The ATP6C protein shows stronger interactions with ATP8 and ATP9 than ATP6 during the assembly of F1Fo-ATP synthase (F-type ATP synthase, ATPase), thereby reducing the quantity and activity of assembled F1Fo-ATP synthase. By contrast, the quantity and activity of the F1' component are increased in CMS-C lines. Reduced F1Fo-ATP synthase activity causes accumulation of excess protons in the inner membrane space of the mitochondria, triggering a burst of reactive oxygen species (ROS), premature programmed cell death of the tapetal cells, and pollen abortion. Collectively, our study identifies a chimeric mitochondrial gene (ATP6C) that causes CMS in maize and documents the contribution of ATP6C to F1Fo-ATP synthase assembly, thereby providing novel insights into the molecular mechanisms of male sterility in plants.
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Affiliation(s)
- Huili Yang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yadong Xue
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China.
| | - Bing Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yanan Lin
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haochuan Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Weihua Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China; The Shennong Laboratory, Zhengzhou, China.
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Chen L, Ren W, Zhang B, Chen W, Fang Z, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Zhang Y. Organelle Comparative Genome Analysis Reveals Novel Alloplasmic Male Sterility with orf112 in Brassica oleracea L. Int J Mol Sci 2021; 22:ijms222413230. [PMID: 34948024 PMCID: PMC8703919 DOI: 10.3390/ijms222413230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
B. oleracea Ogura CMS is an alloplasmic male-sterile line introduced from radish by interspecific hybridization and protoplast fusion. The introduction of alien cytoplasm resulted in many undesirable traits, which affected the yield of hybrids. Therefore, it is necessary to identify the composition and reduce the content of alien cytoplasm in B. oleracea Ogura CMS. In the present study, we sequenced, assembled, and compared the organelle genomes of Ogura CMS cabbage and its maintainer line. The chloroplast genome of Ogura-type cabbage was completely derived from normal-type cabbage, whereas the mitochondrial genome was recombined from normal-type cabbage and Ogura-type radish. Nine unique regions derived from radish were identified in the mitochondrial genome of Ogura-type cabbage, and the total length of these nine regions was 35,618 bp, accounting for 13.84% of the mitochondrial genome. Using 32 alloplasmic markers designed according to the sequences of these nine regions, one novel sterile source with less alien cytoplasm was discovered among 305 materials and named Bel CMS. The size of the alien cytoplasm in Bel CMS was 21,587 bp, accounting for 8.93% of its mtDNA, which was much less than that in Ogura CMS. Most importantly, the sterility gene orf138 was replaced by orf112, which had a 78-bp deletion, in Bel CMS. Interestingly, Bel CMS cabbage also maintained 100% sterility, although orf112 had 26 fewer amino acids than orf138. Field phenotypic observation showed that Bel CMS was an excellent sterile source with stable 100% sterility and no withered buds at the early flowering stage, which could replace Ogura CMS in cabbage heterosis utilization.
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Affiliation(s)
- Li Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ren
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wendi Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- Correspondence:
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Kuwabara K, Harada I, Matsuzawa Y, Ariizumi T, Shirasawa K. Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato. HORTICULTURE RESEARCH 2021; 8:250. [PMID: 34848681 PMCID: PMC8632925 DOI: 10.1038/s41438-021-00676-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
To identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA-sequencing analysis indicated that these three genes transcriptionally expressed in anther, and identified different RNA editing levels in one gene, orf265, that was partially similar to ATP synthase subunit 8, between fertile and sterile lines. The orf265 was a highly potential candidate for CMS-associated gene. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.
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Affiliation(s)
- Kosuke Kuwabara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Issei Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | | | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
- Tsukuba Plant Innovation Research Center, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan.
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Toriyama K. Molecular basis of cytoplasmic male sterility and fertility restoration in rice. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:285-295. [PMID: 34782814 PMCID: PMC8562580 DOI: 10.5511/plantbiotechnology.21.0607a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait that causes dysfunctions in pollen and anther development. CMS is caused by the interaction between nuclear and mitochondrial genomes. A product of a CMS-causing gene encoded by the mitochondrial genome affects mitochondrial function and the regulation of nuclear genes, leading to male sterility. In contrast, the RESTORER OF FERTILITY gene (Rf gene) in the nuclear genome suppresses the expression of the CMS-causing gene and restores male fertility. An alloplasmic CMS line is often bred as a result of nuclear substitution, which causes the removal of functional Rf genes and allows the expression of a CMS-causing gene in mitochondria. The CMS/Rf system is an excellent model for understanding the genetic interactions and cooperative functions of mitochondrial and nuclear genomes in plants, and is also an agronomically important trait for hybrid seed production. In this review article, pollen and anther phenotypes of CMS, CMS-associated mitochondrial genes, Rf genes, and the mechanism that causes pollen abortion and its agronomical application for rice are described.
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Affiliation(s)
- Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
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Takatsuka A, Kazama T, Toriyama K. Cytoplasmic Male Sterility-Associated Mitochondrial Gene orf312 Derived from Rice (Oryza sativa L.) Cultivar Tadukan. RICE (NEW YORK, N.Y.) 2021; 14:46. [PMID: 34021837 PMCID: PMC8141088 DOI: 10.1186/s12284-021-00488-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is a trait associated with non-functional pollen or anthers, caused by the interaction between mitochondrial and nuclear genes. FINDINGS A Tadukan-type CMS line (TAA) and a restorer line (TAR) were obtained by successive backcrossing between the Oryza sativa cultivars Tadukan (a cytoplasmic donor) and Taichung 65 (a recurrent pollen parent). Using Illumina HiSeq, we determined whole-genome sequences of the mitochondria of TAA and screened the mitochondrial genome for the presence of open reading frame (orf) genes specific to this genome. One of these orf genes, orf312, showed differential expression patterns in TAA and TAR anthers at the meiotic and mature stages, with transcript amounts in TAR being less than those in TAA. The orf312 gene is similar to the previously described orf288, a part of which is among the components comprising WA352, a chimeric CMS-associated gene of wild-abortive-type CMS. CONCLUSIONS The orf312 gene is a promising candidate for CMS-associated gene in TAA.
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Affiliation(s)
- Ayumu Takatsuka
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572 Japan
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572 Japan
- Present address: Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0385 Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572 Japan
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Transcriptome and MiRNAomics Analyses Identify Genes Associated with Cytoplasmic Male Sterility in Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2021; 22:ijms22094684. [PMID: 33925234 PMCID: PMC8124215 DOI: 10.3390/ijms22094684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is important for large-scale hybrid seed production. Rearrangements in the mitochondrial DNA (mtDNA) for the cotton (Gossypium hirsutum L.) CMS line J4A were responsible for pollen abortion. However, the expression patterns of nuclear genes associated with pollen abortion and the molecular basis of CMS for J4A are unknown, and were the objectives of this study by comparing J4A with the J4B maintainer line. Cytological evaluation of J4A anthers showed that microspore abortion occurs during meiosis preventing pollen development. Changes in enzyme activity of mitochondrial respiratory chain complex IV and mitochondrial respiratory chain complex V and the content of ribosomal protein and ATP during anther abortion were observed for J4A suggesting insufficient synthesis of ATP hindered pollen production. Additionally, levels of sucrose, starch, soluble sugar, and fructose were significantly altered in J4A during the meiosis stage, suggesting reduced sugar metabolism contributed to sterility. Transcriptome and miRNAomics analyses identified 4461 differentially expressed mRNAs (DEGs) and 26 differentially expressed microRNAs (DEMIs). Pathway enrichment analysis indicated that the DEMIs were associated with starch and sugar metabolism. Six deduced target gene regulatory pairs that may participate in CMS were identified, ghi-MIR7484-10/mitogen-activated protein kinase kinase 6 (MAPKK6), ghi-undef-156/agamous-like MADS-box protein AGL19 (AGL19), ghi-MIR171-1-22/SNF1-related protein kinase regulatory subunit gamma-1 and protein trichome birefringence-like 38, and ghi-MIR156-(8/36)/WRKY transcription factor 28 (WRKY28). Overall, a putative CMS mechanism involving mitochondrial dysfunction, the ghi-MIR7484-10/MAPKK6 network, and reduced glucose metabolism was suggested, and ghi-MIR7484-10/MAPKK6 may be related to abnormal microspore meiosis and induction of excessive sucrose accumulation in anthers.
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Jin Z, Seo J, Kim B, Lee SY, Koh HJ. Identification of a Candidate Gene for the Novel Cytoplasmic Male Sterility Derived from Inter-Subspecific Crosses in Rice ( Oryza sativa L.). Genes (Basel) 2021; 12:590. [PMID: 33920582 PMCID: PMC8073397 DOI: 10.3390/genes12040590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/09/2023] Open
Abstract
Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies indica and japonica in rice (Oryza sativa L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene orf312, which possesses a transmembrane domain and overlaps with two mitotype-specific sequences (MSSs) that are unique to the Tetep-CMS line. The encoded peptide of orf312 was toxic to Escherichia coli and inhibited cell growth compared to the control under isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The peptide of orf312 contains COX11-interaction domains, which are thought to be a main functional domain for WA352c in the wild abortive (WA-CMS) line of rice. A QTL for Rf-Tetep (restorer-of-fertility gene(s) originating from Tetep) was identified on chromosome 10. In this region, several restorer genes, Rf1a, Rf1b, and Rf4, have previously been reported. Collectively, the interactions of orf312, a candidate gene for Tetep-CMS, and Rf-Tetep, a restorer QTL, confer male sterility and fertility restoration, respectively, which enables a hybrid rice breeding system. Further studies on orf312 and isolation of Rf-Tetep will help to identify the underlying molecular mechanism of mitochondrial ORFs with the COX11-interaction domains.
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Affiliation(s)
- Zhuo Jin
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Jeonghwan Seo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
| | - Backki Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Seung Young Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Z.J.); (J.S.); (B.K.); (S.Y.L.)
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Tang D, Wei F, Khan A, Munsif F, Zhou R. Degradation of mitochondrial structure and deficiency of complex I were associated with the transgenic CMS of rice. Biol Res 2021; 54:6. [PMID: 33612118 PMCID: PMC7898427 DOI: 10.1186/s40659-020-00326-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria play a significant role in plant cytoplasmic male sterility (CMS). In our previous study, mitochondrial complex I genes, nad4, nad5, and nad7 showed polymorphisms between the transgenic CMS line M2BS and its wild type M2B. The sterility mechanism of the M2BS at cytological, physiological, biochemical, and molecular level is not clear. RESULTS Cytological observation showed that the anthers were light yellow, fissured, invalid in KI-I2, and full of irregularly typical abortion pollen grains in M2BS. Transmission electron microscopic (TEM) observation revealed no nucleus and degraded mitochondria with obscure cristae in anther cells of M2BS. The results of staining for H2O2 presented a large number of electron dense precipitates (edp) in intercellular space of anther cells of M2BS at anthesis. Moreover, the anther respiration rate and complex I activity of M2BS were significantly lower than those of wild type M2B during pollen development. Furthermore, RNA editing results showed only nad7 presented partially edited at 534th nucleotides. The expression of nad5 and nad7 revealed significant differences between M2B and M2BS. CONCLUSIONS Our data demonstrated that mitochondrial structural degradation and complex I deficiency might be associated with transgenic CMS of rice.
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Affiliation(s)
- Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plant, Nanning, 530023 China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023 China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plant, Nanning, 530023 China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023 China
| | - Aziz Khan
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Fazal Munsif
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Ruiyang Zhou
- College of Agriculture, Guangxi University, Nanning, 530004 China
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Sang SF, Mei DS, Liu J, Zaman QU, Zhang HY, Hao MY, Fu L, Wang H, Cheng HT, Hu Q. Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus. BMC Genomics 2019; 20:813. [PMID: 31694534 PMCID: PMC6836354 DOI: 10.1186/s12864-019-6187-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022] Open
Abstract
Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.
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Affiliation(s)
- Shi-Fei Sang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - De-Sheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Qamar U Zaman
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hai-Yan Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Meng-Yu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China
| | - Hong-Tao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences / Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
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Lloyd Evans D, Hlongwane TT, Joshi SV, Riaño Pachón DM. The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PeerJ 2019; 7:e7558. [PMID: 31579570 PMCID: PMC6764373 DOI: 10.7717/peerj.7558] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species. METHODS Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer. RESULTS The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed. CONCLUSION Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.
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Affiliation(s)
- Dyfed Lloyd Evans
- Plant Breeding, South African Sugarcane Research Institute, Durban, KwaZulu-Natal, South Africa
- Cambridge Sequence Services (CSS), Waterbeach, Cambridgeshire, UK
- Department of Computer Sciences, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | | | - Shailesh V. Joshi
- Plant Breeding, South African Sugarcane Research Institute, Durban, KwaZulu-Natal, South Africa
- School of Life Sciences, College of Agriculture Engineering and Science, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Diego M. Riaño Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Wu Z, Hu K, Yan M, Song L, Wen J, Ma C, Shen J, Fu T, Yi B, Tu J. Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea. BMC Genomics 2019; 20:348. [PMID: 31068124 PMCID: PMC6507029 DOI: 10.1186/s12864-019-5721-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/22/2019] [Indexed: 01/15/2023] Open
Abstract
Background Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea. Results The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes. Conclusions On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengxiang Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjiao Yan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liping Song
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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Xie H, Peng X, Qian M, Cai Y, Ding X, Chen Q, Cai Q, Zhu Y, Yan L, Cai Y. The chimeric mitochondrial gene orf182 causes non-pollen-type abortion in Dongxiang cytoplasmic male-sterile rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:715-726. [PMID: 29876974 DOI: 10.1111/tpj.13982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/04/2018] [Accepted: 05/18/2018] [Indexed: 05/25/2023]
Abstract
D1-cytoplasmic male sterility (CMS) rice is a sporophytic cytoplasmic male-sterile rice developed from Dongxiang wild rice that exhibits a no-pollen-grain phenotype. A mitochondrial chimeric gene (orf182) was detected by mitochondrial genome sequencing and a comparative analysis. Orf182 is composed of three recombinant fragments, the largest of which is homologous to Sorghum bicolor mitochondrial sequences. In addition, orf182 was found only in wild rice species collected from China. Northern blot analysis showed that orf182 transcripts were affected by Rf genes in the isocytoplasmic restorer line DR7. Western blot analysis showed that the ORF182 product was localized in the mitochondria of the CMS line. An expression cassette containing orf182 fused to a mitochondrial transit peptide induced the maintainer line of male sterility, which lacked pollen grains in the anthers. Furthermore, the in vivo expression of orf182 also inhibited the growth of Escherichia coli, with lower respiration rate, excess accumulation of reactive oxygen species and decreased ATP levels. We conclude that the mitochondrial chimeric gene orf182 possesses a unique structure and origin differing from other identified mitochondrial CMS genes, and this gene is connected to non-pollen type of sporophytic male sterility in D1-CMS rice.
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Affiliation(s)
- Hongwei Xie
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Xiaojue Peng
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China
| | - Mingjuan Qian
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yicong Cai
- China National Rice Research Institute, Hangzhou, China
| | - Xia Ding
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China
| | - Qiusheng Chen
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China
| | - Qiying Cai
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China
| | - Youlin Zhu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, China
| | - Longan Yan
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
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Bhatnagar-Mathur P, Gupta R, Reddy PS, Reddy BP, Reddy DS, Sameerkumar CV, Saxena RK, Sharma KK. A novel mitochondrial orf147 causes cytoplasmic male sterility in pigeonpea by modulating aberrant anther dehiscence. PLANT MOLECULAR BIOLOGY 2018; 97:131-147. [PMID: 29667000 DOI: 10.1007/s11103-018-0728-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE A novel open reading frame (ORF) identified and cloned from the A4 cytoplasm of Cajanus cajanifolius induced partial to complete male sterility when introduced into Arabidopsis and tobacco. Pigeonpea (Cajanus cajan L. Millsp.) is the only legume known to have commercial hybrid seed technology based on cytoplasmic male sterility (CMS). We identified a novel ORF (orf147) from the A4 cytoplasm of C. cajanifolius that was created via rearrangements in the CMS line and co-transcribes with the known and unknown sequences. The bi/poly-cistronic transcripts cause gain-of-function variants in the mitochondrial genome of CMS pigeonpea lines having distinct processing mechanisms and transcription start sites. In presence of orf147, significant repression of Escherichia coli growth indicated its toxicity to the host cells and induced partial to complete male sterility in transgenic progenies of Arabidopsis thaliana and Nicotiana tabacum where phenotype co-segregated with the transgene. The male sterile plants showed aberrant floral development and reduced lignin content in the anthers. Gene expression studies in male sterile pigeonpea, Arabidopsis and tobacco plants confirmed down-regulation of several anther biogenesis genes and key genes involved in monolignol biosynthesis, indicative of regulation of retrograde signaling. Besides providing evidence for the involvement of orf147 in pigeonpea CMS, this study provides valuable insights into its function. Cytotoxicity and aberrant programmed cell death induced by orf147 could be important for mechanism underlying male sterility that offers opportunities for possible translation for these findings for exploiting hybrid vigor in other recalcitrant crops as well.
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Affiliation(s)
- Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
| | - Ranadheer Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Bommineni Pradeep Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Dumbala Srinivas Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - C V Sameerkumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Rachit Kumar Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Kiran K Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
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Reddemann A, Horn R. Recombination Events Involving the atp9 Gene Are Associated with Male Sterility of CMS PET2 in Sunflower. Int J Mol Sci 2018; 19:E806. [PMID: 29534485 PMCID: PMC5877667 DOI: 10.3390/ijms19030806] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
Cytoplasmic male sterility (CMS) systems represent ideal mutants to study the role of mitochondria in pollen development. In sunflower, CMS PET2 also has the potential to become an alternative CMS source for commercial sunflower hybrid breeding. CMS PET2 originates from an interspecific cross of H. petiolaris and H. annuus as CMS PET1, but results in a different CMS mechanism. Southern analyses revealed differences for atp6, atp9 and cob between CMS PET2, CMS PET1 and the male-fertile line HA89. A second identical copy of atp6 was present on an additional CMS PET2-specific fragment. In addition, the atp9 gene was duplicated. However, this duplication was followed by an insertion of 271 bp of unknown origin in the 5' coding region of the atp9 gene in CMS PET2, which led to the creation of two unique open reading frames orf288 and orf231. The first 53 bp of orf288 are identical to the 5' end of atp9. Orf231 consists apart from the first 3 bp, being part of the 271-bp-insertion, of the last 228 bp of atp9. These CMS PET2-specific orfs are co-transcribed. All 11 editing sites of the atp9 gene present in orf231 are fully edited. The anther-specific reduction of the co-transcript in fertility-restored hybrids supports the involvement in male-sterility based on CMS PET2.
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Affiliation(s)
- Antje Reddemann
- Institut für Biowissenschaften, Abt. Pflanzengenetik, Universität Rostock, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
| | - Renate Horn
- Institut für Biowissenschaften, Abt. Pflanzengenetik, Universität Rostock, Albert-Einstein-Straße 3, D-18059 Rostock, Germany.
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Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes. Cell Res 2016; 27:130-146. [PMID: 27725674 DOI: 10.1038/cr.2016.115] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/04/2016] [Accepted: 09/01/2016] [Indexed: 01/28/2023] Open
Abstract
New gene origination is a major source of genomic innovations that confer phenotypic changes and biological diversity. Generation of new mitochondrial genes in plants may cause cytoplasmic male sterility (CMS), which can promote outcrossing and increase fitness. However, how mitochondrial genes originate and evolve in structure and function remains unclear. The rice Wild Abortive type of CMS is conferred by the mitochondrial gene WA352c (previously named WA352) and has been widely exploited in hybrid rice breeding. Here, we reconstruct the evolutionary trajectory of WA352c by the identification and analyses of 11 mitochondrial genomic recombinant structures related to WA352c in wild and cultivated rice. We deduce that these structures arose through multiple rearrangements among conserved mitochondrial sequences in the mitochondrial genome of the wild rice Oryza rufipogon, coupled with substoichiometric shifting and sequence variation. We identify two expressed but nonfunctional protogenes among these structures, and show that they could evolve into functional CMS genes via sequence variations that could relieve the self-inhibitory potential of the proteins. These sequence changes would endow the proteins the ability to interact with the nucleus-encoded mitochondrial protein COX11, resulting in premature programmed cell death in the anther tapetum and male sterility. Furthermore, we show that the sequences that encode the COX11-interaction domains in these WA352c-related genes have experienced purifying selection during evolution. We propose a model for the formation and evolution of new CMS genes via a "multi-recombination/protogene formation/functionalization" mechanism involving gradual variations in the structure, sequence, copy number, and function.
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Igarashi K, Kazama T, Toriyama K. A Gene Encoding Pentatricopeptide Repeat Protein Partially Restores Fertility in RT98-Type Cytoplasmic Male-Sterile Rice. PLANT & CELL PHYSIOLOGY 2016; 57:2187-2193. [PMID: 27498808 DOI: 10.1093/pcp/pcw135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/25/2016] [Indexed: 05/03/2023]
Abstract
Cytoplasmic male sterility (CMS) lines in rice, which have the cytoplasm of a wild species and the nuclear genome of cultivated rice, are of value for the study of genetic interactions between the mitochondrial and nuclear genomes. The RT98-type CMS line RT98A and the fertility restorer line RT98C carry the cytoplasm of the wild species Oryza rufipogon and the nuclear genome of the Taichung 65 cultivar (Oryza sativa L.). Based on a classical crossing experiment, fertility is reported to be restored gametophytically by the presence of a tentative single gene, designated Rf98, which is derived from the cytoplasm donor. Fine mapping of Rf98 revealed that at least two genes, which are closely positioned, are required for complete fertility restoration in RT98A. Here, we identified seven pentatricopeptide repeat (PPR) genes that are located within a 170 kb region as candidates for Rf98 Complementation tests revealed that the introduction of one of these PPR genes, PPR762, resulted in the partial recovery of fertility with a seed setting rate up to 9.3%. We conclude that PPR762 is an essential fertility restorer gene for RT98-type CMS. The low rate of seed setting suggested that some other genes near the Rf98 locus are also necessary for the full recovery of seed setting.
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Affiliation(s)
- Keisuke Igarashi
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
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Kazama T, Toriyama K. Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice. PLoS One 2016; 11:e0159379. [PMID: 27414645 PMCID: PMC4944960 DOI: 10.1371/journal.pone.0159379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/03/2016] [Indexed: 11/19/2022] Open
Abstract
Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6. These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orfs, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79-containing RNA but was not detected in other Boro-type mitochondria-specific orfs, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria.
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Affiliation(s)
- Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- * E-mail:
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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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Sinha P, Saxena KB, Saxena RK, Singh VK, Suryanarayana V, Sameer Kumar CV, Katta MAVS, Khan AW, Varshney RK. Association of nad7a Gene with Cytoplasmic Male Sterility in Pigeonpea. THE PLANT GENOME 2015; 8:eplantgenome2014.11.0084. [PMID: 33228303 DOI: 10.3835/plantgenome2014.11.0084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/26/2015] [Indexed: 06/11/2023]
Abstract
Cytoplasmic male sterility (CMS) has been exploited in the commercial pigeonpea [Cajanus cajan (L.) Millsp.] hybrid breeding system; however, the molecular mechanism behind this system is unknown. To understand the underlying molecular mechanism involved in A4 CMS system derived from C. cajanifolius (Haines) Maesen, 34 mitochondrial genes were analyzed for expression profiling and structural variation analysis between CMS line (ICRISAT Pigeonpea A line, ICPA 2039) and its cognate maintainer (ICPB 2039). Expression profiling of 34 mitochondrial genes revealed nine genes with significant fold differential gene expression at P ≤ 0.01, including one gene, nad4L, with 1366-fold higher expression in CMS line as compared with the maintainer. Structural variation analysis of these mitochondrial genes identified length variation between ICPA 2039 and ICPB 2039 for nad7a (subunit of nad7 gene). Sanger sequencing of nad4L and nad7a genes in the CMS and the maintainer lines identified two single nucleotide polymorphisms (SNPs) in upstream region of nad4L and a deletion of 10 bp in nad7a in the CMS line. Protein structure evaluation showed conformational changes in predicted protein structures for nad7a between ICPA 2039 and ICPB 2039 lines. All above analyses indicate association of nad7a gene with the CMS for A4 cytoplasm in pigeonpea. Additionally, one polymerase chain reaction (PCR) based Indel marker (nad7a_del) has been developed and validated for testing genetic purity of A4 derived CMS lines to strengthen the commercial hybrid breeding program in pigeonpea.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - V Suryanarayana
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Mohan A V S Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
- School of Plant Biology and Institute of Agriculture, The Univ. of Western Australia, 35 Stirling Hwy., Crawley, WA, 6009, Australia
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Aya K, Kobayashi M, Tanaka J, Ohyanagi H, Suzuki T, Yano K, Takano T, Yano K, Matsuoka M. De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB. ACTA ACUST UNITED AC 2014; 56:e5. [DOI: 10.1093/pcp/pcu184] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Yan J, Tian H, Wang S, Shao J, Zheng Y, Zhang H, Guo L, Ding Y. Pollen developmental defects in ZD-CMS rice line explored by cytological, molecular and proteomic approaches. J Proteomics 2014; 108:110-23. [PMID: 24878425 DOI: 10.1016/j.jprot.2014.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Cytoplasmic male sterility (CMS) is a widely observed phenomenon, which is especially useful in hybrid seed production. Meixiang A (MxA) is a new rice CMS line derived from a pollen-free sterile line named Yunnan ZidaoA (ZD-CMS). In this study, a homologous WA352 gene with variation in two nucleotides was identified in MxA. Cytological analysis revealed that MxA was aborted in the early uninucleate stage. The protein expression profiles of MxA and its maintainer line MeixiangB (MxB) were systematically compared using iTRAQ-based quantitative proteomics technology using young florets at the early uninucleate stage. A total of 688 proteins were quantified in both rice lines, and 45 of these proteins were found to be differentially expressed. Bioinformatics analysis indicated a large number of the proteins involved in carbohydrate metabolism or the stress response were downregulated in MxA, suggesting that these metabolic processes had been hindered during pollen development in MxA. The ROS (reactive oxygen species) level was increased in the mitochondrion of MxA, and further ultrastructural analysis showed the mitochondria with disrupted cristae in the rice CMS line MxA. These findings substantially contribute to our knowledge of pollen developmental defects in ZD-CMS rice line. BIOLOGICAL SIGNIFICANCE MeixiangA (MxA) is a new type of rice CMS line, which is derived from pollen-free sterile line Yunnan ZidaoA. In this study, the cytological, molecular and proteomic approaches were used to study the characteristics of this new CMS line. Cytological study indicates the CMS line is aborted at the early uninucleate stage. A potential sterile gene ZD352 is identified in MxA, the protein product of which is mainly accumulated at the MMC/Meiotic stage. iTRAQ based proteomic analysis is performed to study the relevant proteins involved in the CMS occurance, 45 proteins are found to be significant differentially expressed and these proteins are involved in many cellular processes such as carbohydrate metabolism, stress response, protein synthesis. To our knowledge, this is the first report using the iTRAQ-labeled quantitative proteomic to study the protein expression variation during the abortion processes between a CMS line and its maintainer line. These results provide new insights on the CMS mechanisms of ZD-CMS rice line.
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Affiliation(s)
- Junjie Yan
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Han Tian
- State Key Laboratory of Virology, Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Shuzhen Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Jinzhen Shao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yinzhen Zheng
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Lin Guo
- State Key Laboratory of Virology, Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China.
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Heng S, Wei C, Jing B, Wan Z, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288. BMC Genomics 2014; 15:322. [PMID: 24884490 PMCID: PMC4035054 DOI: 10.1186/1471-2164-15-322] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 04/23/2014] [Indexed: 11/10/2022] Open
Abstract
Background Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288. Results Through next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line “J163-4” are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity. Conclusion The hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the mechanism of natural CMS in B. juncea, performing comparative analysis on sequenced mitochondrial genomes in Brassicas, and uncovering the origin of the hau CMS mitotype and structural and evolutionary differences between different mitotypes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-322) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P,R, China.
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Mitochondrion role in molecular basis of cytoplasmic male sterility. Mitochondrion 2014; 19 Pt B:198-205. [PMID: 24732436 DOI: 10.1016/j.mito.2014.04.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 11/24/2022]
Abstract
Cytoplasmic male sterility and its fertility restoration via nuclear genes offer the possibility to understand the role of mitochondria during microsporogenesis. In most cases rearrangements in the mitochondrial DNA involving known mitochondrial genes as well as unknown sequences result in the creation of new chimeric open reading frames, which encode proteins containing transmembrane domains. So far, most of the CMS systems have been characterized via restriction fragment polymorphisms followed by transcript analysis. However, whole mitochondrial genome sequence analyses comparing male sterile and fertile cytoplasm open options for deeper insights into mitochondrial genome rearrangements. We more and more start to unravel how mitochondria are involved in triggering death of the male reproductive organs. Reduced levels of ATP accompanied by increased concentrations of reactive oxygen species, which are produced more under conditions of mitochondrial dysfunction, seem to play a major role in the fate of pollen production. Nuclear genes, so called restorer-of-fertility are able to restore the male fertility. Fertility restoration can occur via pentatricopeptide repeat (PPR) proteins or via different mechanisms involving non-PPR proteins.
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Hu J, Huang W, Huang Q, Qin X, Yu C, Wang L, Li S, Zhu R, Zhu Y. Mitochondria and cytoplasmic male sterility in plants. Mitochondrion 2014; 19 Pt B:282-8. [PMID: 24566371 DOI: 10.1016/j.mito.2014.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
Abstract
Mitochondria are essential organelles in cells not only because they supply over 90% of the cell's energy but also because their dysfunction is associated with disease. Owing to the importance of mitochondria, there are many questions about mitochondria that must be answered. Cytoplasmic male sterility (CMS) is a mysterious natural phenomenon, and the mechanism of the origin of CMS is unknown. Despite successful utilization of CMS and restoration of fertility (Rf) in practice, the underlying mechanisms of these processes remain elusive. This review summarizes the genes involved in CMS and Rf, with a special focus on recent studies reporting the mechanisms of the CMS and Rf pathways, and concludes with potential working models.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Qi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Xiaojian Qin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Changchun Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Lili Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China.
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Shearman JR, Sangsrakru D, Ruang-areerate P, Sonthirod C, Uthaipaisanwong P, Yoocha T, Poopear S, Theerawattanasuk K, Tragoonrung S, Tangphatsornruang S. Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript. BMC PLANT BIOLOGY 2014; 14:45. [PMID: 24512148 PMCID: PMC3925788 DOI: 10.1186/1471-2229-14-45] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/07/2014] [Indexed: 05/29/2023]
Abstract
BACKGROUND The rubber tree, Hevea brasiliensis, is an important plant species that is commercially grown to produce latex rubber in many countries. The rubber tree variety BPM 24 exhibits cytoplasmic male sterility, inherited from the variety GT 1. RESULTS We constructed the rubber tree mitochondrial genome of a cytoplasmic male sterile variety, BPM 24, using 454 sequencing, including 8 kb paired-end libraries, plus Illumina paired-end sequencing. We annotated this mitochondrial genome with the aid of Illumina RNA-seq data and performed comparative analysis. We then compared the sequence of BPM 24 to the contigs of the published rubber tree, variety RRIM 600, and identified a rearrangement that is unique to BPM 24 resulting in a novel transcript containing a portion of atp9. CONCLUSIONS The novel transcript is consistent with changes that cause cytoplasmic male sterility through a slight reduction to ATP production efficiency. The exhaustive nature of the search rules out alternative causes and supports previous findings of novel transcripts causing cytoplasmic male sterility.
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Affiliation(s)
- Jeremy R Shearman
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Panthita Ruang-areerate
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Pichahpuk Uthaipaisanwong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Supannee Poopear
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Kanikar Theerawattanasuk
- Rubber Research Institute of Thailand (RRIT), Department of Agriculture, Ministry of Agriculture and Cooperatives, 50 Phaholyothin Road, Chatuchack, Bangkok 10900, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
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Abstract
In plants, male sterility can be caused either by mitochondrial genes with coupled nuclear genes or by nuclear genes alone; the resulting conditions are known as cytoplasmic male sterility (CMS) and genic male sterility (GMS), respectively. CMS and GMS facilitate hybrid seed production for many crops and thus allow breeders to harness yield gains associated with hybrid vigor (heterosis). In CMS, layers of interaction between mitochondrial and nuclear genes control its male specificity, occurrence, and restoration of fertility. Environment-sensitive GMS (EGMS) mutants may involve epigenetic control by noncoding RNAs and can revert to fertility under different growth conditions, making them useful breeding materials in the hybrid seed industry. Here, we review recent research on CMS and EGMS systems in crops, summarize general models of male sterility and fertility restoration, and discuss the evolutionary significance of these reproductive systems.
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Affiliation(s)
- Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
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Okazaki M, Kazama T, Murata H, Motomura K, Toriyama K. Whole mitochondrial genome sequencing and transcriptional analysis to uncover an RT102-type cytoplasmic male sterility-associated candidate Gene Derived from Oryza rufipogon. PLANT & CELL PHYSIOLOGY 2013; 54:1560-8. [PMID: 23852329 DOI: 10.1093/pcp/pct102] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants fail to produce functional pollen and is associated with the expression of a novel open reading frame (orf) gene encoded by the mitochondrial genome. An RT102A CMS line and an RT102C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1125 and O. sativa Taichung 65. Using next-generation pyrosequencing, we determined whole-genome sequences of the mitochondria in RT102-CMS cytoplasm. To identify candidates for the CMS-associated gene in RT102 mitochondria, we screened the mitochondrial genome for the presence of specific orf genes that were chimeric or whose products carried predicted transmembrane domains. One of these orf genes, orf352, which showed different transcript sizes depending on whether the restorer of fertility (Rf) gene was present or not, was identified. The orf352 gene was co-transcribed with the ribosomal protein gene rpl5, and the 2.8 kb rpl5-orf352 transcripts were processed into 2.6 kb transcripts with a cleavage at the inside of the orf352 coding region in the presence of the Rf gene. The orf352 gene is an excellent candidate for the CMS-associated gene for RT102-CMS.
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Affiliation(s)
- Masayuki Okazaki
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, 981-8555 Japan
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Bokszczanin KL, Fragkostefanakis S. Perspectives on deciphering mechanisms underlying plant heat stress response and thermotolerance. FRONTIERS IN PLANT SCIENCE 2013; 4:315. [PMID: 23986766 PMCID: PMC3750488 DOI: 10.3389/fpls.2013.00315] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/27/2013] [Indexed: 05/17/2023]
Abstract
Global warming is a major threat for agriculture and food safety and in many cases the negative effects are already apparent. The current challenge of basic and applied plant science is to decipher the molecular mechanisms of heat stress response (HSR) and thermotolerance in detail and use this information to identify genotypes that will withstand unfavorable environmental conditions. Nowadays X-omics approaches complement the findings of previous targeted studies and highlight the complexity of HSR mechanisms giving information for so far unrecognized genes, proteins and metabolites as potential key players of thermotolerance. Even more, roles of epigenetic mechanisms and the involvement of small RNAs in thermotolerance are currently emerging and thus open new directions of yet unexplored areas of plant HSR. In parallel it is emerging that although the whole plant is vulnerable to heat, specific organs are particularly sensitive to elevated temperatures. This has redirected research from the vegetative to generative tissues. The sexual reproduction phase is considered as the most sensitive to heat and specifically pollen exhibits the highest sensitivity and frequently an elevation of the temperature just a few degrees above the optimum during pollen development can have detrimental effects for crop production. Compared to our knowledge on HSR of vegetative tissues, the information on pollen is still scarce. Nowadays, several techniques for high-throughput X-omics approaches provide major tools to explore the principles of pollen HSR and thermotolerance mechanisms in specific genotypes. The collection of such information will provide an excellent support for improvement of breeding programs to facilitate the development of tolerant cultivars. The review aims at describing the current knowledge of thermotolerance mechanisms and the technical advances which will foster new insights into this process.
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Affiliation(s)
- Kamila L. Bokszczanin
- GenXPro GmbH, Frankfurt am MainGermany
- *Correspondence: Kamila L. Bokszczanin, GenXPro GmbH, Altenhöferallee 3, Frankfurt am Main 60438, Germany e-mail: ; Sotirios Fragkostefanakis, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Street 9, Frankfurt am Main 60438, Germany e-mail:
| | | | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am MainGermany
- *Correspondence: Kamila L. Bokszczanin, GenXPro GmbH, Altenhöferallee 3, Frankfurt am Main 60438, Germany e-mail: ; Sotirios Fragkostefanakis, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Street 9, Frankfurt am Main 60438, Germany e-mail:
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