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Martina M, Zayas A, Portis E, Di Nardo G, Polli MF, Comino C, Gilardi G, Martin E, Acquadro A. The Dark Side of the pollen: BSA-seq identified genomic regions linked to male sterility in globe artichoke. BMC PLANT BIOLOGY 2024; 24:415. [PMID: 38760683 PMCID: PMC11100218 DOI: 10.1186/s12870-024-05119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffusion. Despite globe artichoke's significant agricultural value and the critical role of heterosis in the development of superior varieties, the production of hybrids remains challenging without a reliable system for large-scale industrial seed production. Male sterility (MS) presents a promising avenue for overcoming these challenges by simplifying the hybridization process and enabling cost-effective seed production. However, within the Cynara genus, genic male sterility has been linked to three recessive loci in globe artichoke, with no definitive genetic mechanism elucidated to date. A 250 offsprings F2 population, derived from a cross between a MS globe artichoke and a male fertile (MF) cultivated cardoon (C. cardunculus var. altilis) and fitting a monogenic segregation model (3:1), was analyzed through BSA-seq, aiming at the identification of genomic regions/genes affecting male sterility. Four QTL regions were identified on chromosomes 4, 12, and 14. By analyzing the sequence around the highest pick on chromosome 14, a cytochrome P450 (CYP703A2) was identified, carrying a deleterious substitution (R/Q) fixed in the male sterile parent. A single dCAPS marker was developed around this SNP, allowing the discrimination between MS and MF genotypes within the population, suitable for applications in plant breeding programs. A 3D model of the protein was generated by homology modeling, revealing that the mutated amino acid is part of a highly conserved motif crucial for protein folding.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Aldana Zayas
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Giovanna Di Nardo
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Cinzia Comino
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Gianfranco Gilardi
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Eugenia Martin
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina.
| | - Alberto Acquadro
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy.
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Huynh SD, Melonek J, Colas des Francs-Small C, Bond CS, Small I. A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria. THE NEW PHYTOLOGIST 2023; 240:830-845. [PMID: 37551058 DOI: 10.1111/nph.19166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.
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Affiliation(s)
- Sang Dang Huynh
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Joanna Melonek
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Catherine Colas des Francs-Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
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Cheng C, Nie H, Li H, Adjibolosoo D, Li B, Jiang K, Cui Y, Zhu M, Zhou B, Guo A, Hua J. Identification of fertility restoration candidate genes from a restorer line R186 for Gossypium harknessii cytoplasmic male sterile cotton. BMC PLANT BIOLOGY 2023; 23:175. [PMID: 37016285 PMCID: PMC10071737 DOI: 10.1186/s12870-023-04185-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The utilization of heterosis based on three-line system is an effective strategy in crop breeding. However, cloning and mechanism elucidation of restorer genes for cytoplasmic male sterility (CMS) in upland cotton have yet been realized. RESULTS This research is based on CMS line 2074A with the cytoplasm from Gossypium harknessii (D2-2) and restorer line R186. The offspring of 2074A × R186 were used to conduct genetic analysis. The fertility mechanism of 2074A can be speculated to be governed by multiple genes, since neither the single gene model nor the double genes model could be used. The bulked segregant analysis (BSA) for (2074A × R186) F2 determined the genetic interval of restorer genes on a region of 4.30 Mb on chromosome D05 that contains 77 annotated genes. Four genes were identified as candidates for fertility restoration using the RNA-seq data of 2074A, 2074B, and R186. There are a number of large effect variants in the four genes between 2074A and R186 that could cause amino acid changes. Evolutionary analysis and identity analysis revealed that GH_D05G3183, GH_D05G3384, and GH_D05G3490 have high identity with their homologs in D2-2, respectively. Tissue differential expression analysis revealed that the genes GH_D05G3183, GH_D05G3384, and GH_D05G3490 were highly expressed in the buds of the line R186. The predicted results demonstrated that GH_D05G3183, GH_D05G3384 and GH_D05G3490 might interact with GH_A02G1295 to regulate orf610a in mitochondria. CONCLUSION Our study uncovered candidate genes for fertility restoration in the restorer line R186 and predicted the possible mechanism for restoring the male fertility in 2074A. This research provided valuable insight into the nucleoplasmic interactions.
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Affiliation(s)
- Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Daniel Adjibolosoo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Bin Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Kaiyun Jiang
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yanan Cui
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Meng Zhu
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Baixue Zhou
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China.
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Simon M, Durand S, Ricou A, Vrielynck N, Mayjonade B, Gouzy J, Boyer R, Roux F, Camilleri C, Budar F. APOK3, a pollen killer antidote in Arabidopsis thaliana. Genetics 2022; 221:6603116. [PMID: 35666201 DOI: 10.1093/genetics/iyac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
The principles of heredity state that the two alleles carried by a heterozygote are equally transmitted to the progeny. However, genomic regions that escape this rule have been reported in many organisms. It is notably the case of genetic loci referred to as gamete killers, where one allele enhances its transmission by causing the death of the gametes that do not carry it. Gamete killers are of great interest, particularly to understand mechanisms of evolution and speciation. Although being common in plants, only a few, all in rice, have so far been deciphered to the causal genes. Here, we studied a pollen killer found in hybrids between two accessions of Arabidopsis thaliana. Exploring natural variation, we observed this pollen killer in many crosses within the species. Genetic analyses revealed that three genetically linked elements are necessary for pollen killer activity. Using mutants, we showed that this pollen killer works according to a poison-antidote model, where the poison kills pollen grains not producing the antidote. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. De novo genomic sequencing in twelve natural variants with different behaviors regarding the pollen killer revealed a hyper variable locus, with important structural variations particularly in killer genotypes, where the antidote gene recently underwent duplications. Our results strongly suggest that the gene has newly evolved within A. thaliana. Finally, we identified in the protein sequence polymorphisms related to its antidote activity.
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Affiliation(s)
- Matthieu Simon
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Stéphanie Durand
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Anthony Ricou
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Nathalie Vrielynck
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | | | - Jérôme Gouzy
- LIPME,Université de Toulouse,INRAE,CNRS, 31326 Castanet-Tolosan, France
| | - Roxane Boyer
- INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France(doi : 10.15454/1.5572370921303193E12)
| | - Fabrice Roux
- LIPME,Université de Toulouse,INRAE,CNRS, 31326 Castanet-Tolosan, France
| | - Christine Camilleri
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Françoise Budar
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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Pei H, Xie H, Wang X, Yan X, Wang B, Feng H, Zhao Y, Gao J, Gao J. Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L. PeerJ 2022; 10:e13168. [PMID: 35651745 PMCID: PMC9150696 DOI: 10.7717/peerj.13168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/04/2022] [Indexed: 01/13/2023] Open
Abstract
Background Pepper (Capsicum annuum L.) is a major cash crop throughout the world. Male sterility is an important characteristic in crop species that leads to a failure to produce functional pollen, and it has crucial roles in agricultural breeding and the utilization of heterosis. Objectives In this study, we identified many crucial factors and important components in metabolic pathways in anther and pollen development, and elucidated the molecular mechanism related to pollen abortion in pepper. Methods Pepper pollen was observed at different stages to detect the characteristics associated with male sterility and fertility. The phytohormone and oxidoreductase activities were detected in spectrophotometric and redox reaction assays, respectively. Proteins were extracted from male sterile and fertile pepper lines, and identified by TMT/iTRAQ (tandem mass tags/isobaric tags for relative and absolute quantitation) and LC-MS/MS (liquid chromatograph-mass spectrometer) analysis. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes database according to |fold change)| > 1.3 and P value < 0.05. DAPs were quantified in the meiosis, tetrad, and binucleate stages by parallel reaction monitoring (PRM). Results In this study, we screened and identified one male sterile pepper line with abnormal cytological characteristics in terms of pollen development. The peroxidase and catalase enzyme activities were significantly reduced and increased, respectively, in the male sterile line compared with the male fertile line. Phytohormone analysis demonstrated that the gibberellin, jasmonic acid, and auxin contents changed by different extents in the male sterile pepper line. Proteome analysis screened 1,645 DAPs in six clusters, which were mainly associated with the chloroplast and cytoplasm based on their similar expression levels. According to proteome analysis, 45 DAPs were quantitatively identified in the meiosis, tetrad, and binucleate stages by PRM, which were related to monoterpenoid biosynthesis, and starch and sucrose metabolism pathways. Conclusions We screened 1,645 DAPs by proteomic analysis and 45 DAPs were related to anther and pollen development in a male sterile pepper line. In addition, the activities of peroxidase and catalase as well as the abundances of phytohormones such as gibberellin, jasmonic acid, and auxin were related to male sterility. The results obtained in this study provide insights into the molecular mechanism responsible for male sterility and fertility in pepper.
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Affiliation(s)
- Hongxia Pei
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China,Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Hua Xie
- Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xuemei Wang
- Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xiujuan Yan
- Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiping Feng
- Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yunxia Zhao
- Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Jingxia Gao
- Institute of Horticulture Crops, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Jie Gao
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
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