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Du J, Ge C, Li T, Wang S, Gao Z, Sassa H, Qiao Y. Molecular characteristics of S-RNase alleles as the determinant of self-incompatibility in the style of Fragaria viridis. HORTICULTURE RESEARCH 2021; 8:185. [PMID: 34333550 PMCID: PMC8325692 DOI: 10.1038/s41438-021-00623-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 05/11/2023]
Abstract
Strawberry (Fragaria spp.) is a member of the Rosoideae subfamily in the family Rosaceae. The self-incompatibility (SI) of some diploid species is a key agronomic trait that acts as a basic pollination barrier; however, the genetic mechanism underlying SI control in strawberry remains unclear. Two candidate S-RNases (Sa- and Sb-RNase) identified in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were confirmed to be SI determinants at the S locus following genotype identification and intraspecific hybridization using selfing progenies. Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria; however, none of the compatible species contained S-RNase. Although the results of interspecific hybridization experiments showed that F. viridis (SI) styles could accept pollen from F. mandshurica (self-compatible), the reciprocal cross was incompatible. Sa and Sb-RNase contain large introns, and their noncoding sequences (promotors and introns) can be transcribed into long noncoding RNAs (lncRNAs). Overall, the genus Fragaria exhibits S-RNase-based gametophytic SI, and S-RNase loss occurs at the S locus of compatible germplasms. In addition, a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species. Furthermore, the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.
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Affiliation(s)
- Jianke Du
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Chiba, Japan
| | - Chunfeng Ge
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu, China
| | - Tingting Li
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Sanhong Wang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhihong Gao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hidenori Sassa
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Chiba, Japan
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Vieira J, Pimenta J, Gomes A, Laia J, Rocha S, Heitzler P, Vieira CP. The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems. Sci Rep 2021; 11:3710. [PMID: 33580108 PMCID: PMC7881130 DOI: 10.1038/s41598-021-83243-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
In Rosaceae species, two gametophytic self-incompatibility (GSI) mechanisms are described, the Prunus self-recognition system and the Maleae (Malus/Pyrus/Sorbus) non-self- recognition system. In both systems the pistil component is a S-RNase gene, but from two distinct phylogenetic lineages. The pollen component, always a F-box gene(s), in the case of Prunus is a single gene, and in Maleae there are multiple genes. Previously, the Rosa S-locus was mapped on chromosome 3, and three putative S-RNase genes were identified in the R. chinensis ‘Old Blush’ genome. Here, we show that these genes do not belong to the S-locus region. Using R. chinensis and R. multiflora genomes and a phylogenetic approach, we identified the S-RNase gene, that belongs to the Prunus S-lineage. Expression patterns support this gene as being the S-pistil. This gene is here also identified in R. moschata, R. arvensis, and R. minutifolia low coverage genomes, allowing the identification of positively selected amino acid sites, and thus, further supporting this gene as the S-RNase. Furthermore, genotype–phenotype association experiments also support this gene as the S-RNase. For the S-pollen GSI component we find evidence for multiple F-box genes, that show the expected expression pattern, and evidence for diversifying selection at the F-box genes within an S-haplotype. Thus, Rosa has a non-self-recognition system, like in Maleae species, despite the S-pistil gene belonging to the Prunus S-RNase lineage. These findings are discussed in the context of the Rosaceae GSI evolution. Knowledge on the Rosa S-locus has practical implications since genes controlling floral and other ornamental traits are in linkage disequilibrium with the S-locus.
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Affiliation(s)
- J Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - J Pimenta
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - A Gomes
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - J Laia
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - S Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - P Heitzler
- Institut de Biologie Moléculaire Des Plantes, CNRS, Université de Strasbourg, UPR 2357, 67000, Strasbourg, France
| | - C P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
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3
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Li Y, Duan X, Wu C, Yu J, Liu C, Wang J, Zhang X, Yan G, Jiang F, Li T, Zhang K, Li W. Ubiquitination of S 4-RNase by S-LOCUS F-BOX LIKE2 Contributes to Self-Compatibility of Sweet Cherry 'Lapins'. PLANT PHYSIOLOGY 2020; 184:1702-1716. [PMID: 33037127 PMCID: PMC7723103 DOI: 10.1104/pp.20.01171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 05/15/2023]
Abstract
Recent studies have shown that loss of pollen-S function in S4' pollen from sweet cherry (Prunus avium) is associated with a mutation in an S haplotype-specific F-box4 (SFB4) gene. However, how this mutation leads to self-compatibility is unclear. Here, we examined this mechanism by analyzing several self-compatible sweet cherry varieties. We determined that mutated SFB4 (SFB4') in S4' pollen (pollen harboring the SFB4' gene) is approximately 6 kD shorter than wild-type SFB4 due to a premature termination caused by a four-nucleotide deletion. SFB4' did not interact with S-RNase. However, a protein in S4' pollen ubiquitinated S-RNase, resulting in its degradation via the 26S proteasome pathway, indicating that factors in S4' pollen other than SFB4 participate in S-RNase recognition and degradation. To identify these factors, we used S4-RNase as a bait to screen S4' pollen proteins. Our screen identified the protein encoded by S 4 -SLFL2, a low-polymorphic gene that is closely linked to the S-locus. Further investigations indicate that SLFL2 ubiquitinates S-RNase, leading to its degradation. Subcellular localization analysis showed that SFB4 is primarily localized to the pollen tube tip, whereas SLFL2 is not. When S 4 -SLFL2 expression was suppressed by antisense oligonucleotide treatment in wild-type pollen tubes, pollen still had the capacity to ubiquitinate S-RNase; however, this ubiquitin-labeled S-RNase was not degraded via the 26S proteasome pathway, suggesting that SFB4 does not participate in the degradation of S-RNase. When SFB4 loses its function, S4-SLFL2 might mediate the ubiquitination and degradation of S-RNase, which is consistent with the self-compatibility of S4' pollen.
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Affiliation(s)
- Yang Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, 100097 Beijing, China
| | - Chuanbao Wu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
| | - Jie Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
| | - Chunsheng Liu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, 100097 Beijing, China
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, 100097 Beijing, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, 100097 Beijing, China
| | - Feng Jiang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, 100097 Beijing, China
| | - Wei Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, 100193 Beijing, China
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Vieira J, Rocha S, Vázquez N, López-Fernández H, Fdez-Riverola F, Reboiro-Jato M, Vieira CP. Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model. FRONTIERS IN PLANT SCIENCE 2019; 10:879. [PMID: 31379893 PMCID: PMC6649718 DOI: 10.3389/fpls.2019.00879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
Non-self gametophytic self-incompatibility (GSI) recognition system is characterized by the presence of multiple F-box genes tandemly located in the S-locus, that regulate pollen specificity. This reproductive barrier is present in Solanaceae, Plantaginacea and Maleae (Rosaceae), but only in Petunia functional assays have been performed to get insight on how this recognition mechanism works. In this system, each of the encoded S-pollen proteins (called SLFs in Solanaceae and Plantaginaceae /SFBBs in Maleae) recognizes and interacts with a sub-set of non-self S-pistil proteins, called S-RNases, mediating their ubiquitination and degradation. In Petunia there are 17 SLF genes per S-haplotype, making impossible to determine experimentally each SLF specificity. Moreover, domain -swapping experiments are unlikely to be performed in large scale to determine S-pollen and S-pistil specificities. Phylogenetic analyses of the Petunia SLFs and those from two Solanum genomes, suggest that diversification of SLFs predate the two genera separation. Here we first identify putative SLF genes from nine Solanum and 10 Nicotiana genomes to determine how many gene lineages are present in the three genera, and the rate of origin of new SLF gene lineages. The use of multiple genomes per genera precludes the effect of incompleteness of the genome at the S-locus. The similar number of gene lineages in the three genera implies a comparable effective population size for these species, and number of specificities. The rate of origin of new specificities is one per 10 million years. Moreover, here we determine the amino acids positions under positive selection, those involved in SLF specificity recognition, using 10 Petunia S-haplotypes with more than 11 SLF genes. These 16 amino acid positions account for the differences of self-incompatible (SI) behavior described in the literature. When SLF and S-RNase proteins are divided according to the SI behavior, and the positively selected amino acids classified according to hydrophobicity, charge, polarity and size, we identified fixed differences between SI groups. According to the in silico 3D structure of the two proteins these amino acid positions interact. Therefore, this methodology can be used to infer SLF/S-RNase specificity recognition.
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Affiliation(s)
- Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sara Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Noé Vázquez
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
| | - Hugo López-Fernández
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
- SING Research Group, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Florentino Fdez-Riverola
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
- SING Research Group, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Miguel Reboiro-Jato
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
- SING Research Group, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Cristina P. Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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5
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Claessen H, Keulemans W, Van de Poel B, De Storme N. Finding a Compatible Partner: Self-Incompatibility in European Pear ( Pyrus communis); Molecular Control, Genetic Determination, and Impact on Fertilization and Fruit Set. FRONTIERS IN PLANT SCIENCE 2019; 10:407. [PMID: 31057563 PMCID: PMC6477101 DOI: 10.3389/fpls.2019.00407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/18/2019] [Indexed: 05/25/2023]
Abstract
Pyrus species display a gametophytic self-incompatibility (GSI) system that actively prevents fertilization by self-pollen. The GSI mechanism in Pyrus is genetically controlled by a single locus, i.e., the S-locus, which includes at least two polymorphic and strongly linked S-determinant genes: a pistil-expressed S-RNase gene and a number of pollen-expressed SFBB genes (S-locus F-Box Brothers). Both the molecular basis of the SI mechanism and its functional expression have been widely studied in many Rosaceae fruit tree species with a particular focus on the characterization of the elusive SFBB genes and S-RNase alleles of economically important cultivars. Here, we discuss recent advances in the understanding of GSI in Pyrus and provide new insights into the mechanisms of GSI breakdown leading to self-fertilization and fruit set. Molecular analysis of S-genes in several self-compatible Pyrus cultivars has revealed mutations in both pistil- or pollen-specific parts that cause breakdown of self-incompatibility. This has significantly contributed to our understanding of the molecular and genetic mechanisms that underpin self-incompatibility. Moreover, the existence and development of self-compatible mutants open new perspectives for pear production and breeding. In this framework, possible consequences of self-fertilization on fruit set, development, and quality in pear are also reviewed.
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Affiliation(s)
- Hanne Claessen
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bram Van de Poel
- Laboratory for Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
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Vázquez N, López-Fernández H, Vieira CP, Fdez-Riverola F, Vieira J, Reboiro-Jato M. BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus. Interdiscip Sci 2019; 11:57-67. [PMID: 30712176 DOI: 10.1007/s12539-019-00320-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 11/25/2022]
Abstract
Nowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of many researchers. In this context, high-quality sequence datasets are needed to perform inferences on the evolution of species, genes, and gene families, or to get evidence for adaptive amino acid evolution, among others. Nevertheless, sequence data are very often spread over several databases, many useful genomes and transcriptomes are non-annotated, the available annotation is not for the desired coding sequence isoform, and/or is unlikely to be accurate. Moreover, although the FASTA text-based format is quite simple and usable by most software applications, there are a number of issues that may be critical depending on the software used to analyse such files. Therefore, researchers without training in informatics often use a fraction of all available data. The above issues can be addressed using already available software applications, but there is no easy-to-use single piece of software that allows performing all these tasks within the same graphical interface, such as the one here presented, named BDBM (Blast DataBase Manager). BDBM can be used to efficiently get gene sequences from annotated and non-annotated genomes and transcriptomes. Moreover, it can be used to look for alternatives to existing annotations and to easily create reliable custom databases. Such databases are essential to prepare high-quality datasets. The analyses that we have performed on the Coffea canephora genome using BDBM aimed at the identification of the S-locus region (that harbours the genes involved in gametophytic self-incompatibility) led to the conclusion that there are two likely regions, one on chromosome 2 (around region 6600000-6650000), and another on chromosome 5 (around 15830000-15930000). Such findings are discussed in the context of the Rubiaceae gametophytic self-incompatibility evolution.
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Affiliation(s)
- Noé Vázquez
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
| | - Hugo López-Fernández
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain.
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain.
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Florentino Fdez-Riverola
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Miguel Reboiro-Jato
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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7
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De Franceschi P, Bianco L, Cestaro A, Dondini L, Velasco R. Characterization of 25 full-length S-RNase alleles, including flanking regions, from a pool of resequenced apple cultivars. PLANT MOLECULAR BIOLOGY 2018; 97:279-296. [PMID: 29845556 DOI: 10.1007/s11103-018-0741-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/17/2018] [Indexed: 05/07/2023]
Abstract
Data obtained from Illumina resequencing of 63 apple cultivars were used to obtain full-length S-RNase sequences using a strategy based on both alignment and de novo assembly of reads. The reproductive biology of apple is regulated by the S-RNase-based gametophytic self-incompatibility system, that is genetically controlled by the single, multi-genic and multi-allelic S locus. Resequencing of apple cultivars provided a huge amount of genetic data, that can be aligned to the reference genome in order to characterize variation to a genome-wide level. However, this approach is not immediately adaptable to the S-locus, due to some peculiar features such as the high degree of polymorphism, lack of colinearity between haplotypes and extensive presence of repetitive elements. In this study we describe a dedicated procedure aimed at characterizing S-RNase alleles from resequenced cultivars. The S-genotype of 63 apple accessions is reported; the full length coding sequence was determined for the 25 S-RNase alleles present in the 63 resequenced cultivars; these included 10 previously incomplete sequences (S 5 , S 6a , S 6b , S 8 , S 11 , S 23 , S 39 , S 46 , S 50 and S 58 ). Moreover, sequence divergence clearly suggests that alleles S 6a and S 6b , proposed to be neutral variants of the same alleles, should be instead considered different specificities. The promoter sequences have also been analyzed, highlighting regions of homology conserved among all the alleles.
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Affiliation(s)
- Paolo De Franceschi
- Dipartimento di Scienze e Tecnologie Agroalimentari (DISTAL), Università degli Studi di Bologna, Bologna, Italy.
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Luca Dondini
- Dipartimento di Scienze e Tecnologie Agroalimentari (DISTAL), Università degli Studi di Bologna, Bologna, Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
- Centro di Ricerca in Viticoltura ed Enologia del Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA-VE), Conegliano, Treviso, Italy
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8
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Pratas MI, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP. Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system. Sci Rep 2018; 8:1717. [PMID: 29379047 PMCID: PMC5788982 DOI: 10.1038/s41598-018-19820-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
In Malus × domestica (Rosaceae) the product of each SFBB gene (the pollen component of the gametophytic self-incompatibility (GSI) system) of a S-haplotype (the combination of pistil and pollen genes that are linked) interacts with a sub-set of non-self S-RNases (the pistil component), but not with the self S-RNase. To understand how the Malus GSI system works, we identified 24 SFBB genes expressed in anthers, and determined their gene sequence in nine M. domestica cultivars. Expression of these SFBBs was not detected in the petal, sepal, filament, receptacle, style, stigma, ovary or young leaf. For all SFBBs (except SFBB15), identical sequences were obtained only in cultivars having the same S-RNase. Linkage with a particular S-RNase was further established using the progeny of three crosses. Such data is needed to understand how other genes not involved in GSI are affected by the S-locus region. To classify SFBBs specificity, the amino acids under positive selection obtained when performing intra-haplotypic analyses were used. Using this information and the previously identified S-RNase positively selected amino acid sites, inferences are made on the S-RNase amino acid properties (hydrophobicity, aromatic, aliphatic, polarity, and size), at these positions, that are critical features for GSI specificity determination.
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Affiliation(s)
- Maria I Pratas
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Bruno Aguiar
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Vanessa Nunes
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Vanessa Teixeira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Nuno A Fonseca
- European Bioinformatics Institute (EMBL-EBI,) Welcome Trust Genome Campus, CB10 1SD, Cambridge, United Kingdom
| | - Amy Iezzoni
- Michigan State University, East Lansing, MI, 48824-1325, USA
| | | | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.
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9
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Niu SC, Huang J, Zhang YQ, Li PX, Zhang GQ, Xu Q, Chen LJ, Wang JY, Luo YB, Liu ZJ. Lack of S-RNase-Based Gametophytic Self-Incompatibility in Orchids Suggests That This System Evolved after the Monocot-Eudicot Split. FRONTIERS IN PLANT SCIENCE 2017; 8:1106. [PMID: 28690630 PMCID: PMC5479900 DOI: 10.3389/fpls.2017.01106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/07/2017] [Indexed: 05/25/2023]
Abstract
Self-incompatibility (SI) is found in approximately 40% of flowering plant species and at least 100 families. Although orchids belong to the largest angiosperm family, only 10% of orchid species present SI and have gametophytic SI (GSI). Furthermore, a majority (72%) of Dendrobium species, which constitute one of the largest Orchidaceae genera, show SI and have GSI. However, nothing is known about the molecular mechanism of GSI. The S-determinants of GSI have been well characterized at the molecular level in Solanaceae, Rosaceae, and Plantaginaceae, which use an S-ribonuclease (S-RNase)-based system. Here, we investigate the hypothesis that Orchidaceae uses a similar S-RNase to those described in Rosaceae, Solanaceae, and Plantaginaceae SI species. In this study, two SI species (Dendrobium longicornu and D. chrysanthum) were identified using fluorescence microscopy. Then, the S-RNase- and SLF-interacting SKP1-like1 (SSK1)-like genes present in their transcriptomes and the genomes of Phalaenopsis equestris, D. catenatum, Vanilla shenzhenica, and Apostasia shenzhenica were investigated. Sequence, phylogenetic, and tissue-specific expression analyses revealed that none of the genes identified was an S-determinant, suggesting that Orchidaceae might have a novel SI mechanism. The results also suggested that RNase-based GSI might have evolved after the split of monocotyledons (monocots) and dicotyledons (dicots) but before the split of Asteridae and Rosidae. This is also the first study to investigate S-RNase-based GSI in monocots. However, studies on gene identification, differential expression, and segregation analyses in controlled crosses are needed to further evaluate the genes with high expression levels in GSI tissues.
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Affiliation(s)
- Shan-Ce Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Graduate University of the Chinese Academy of SciencesBeijing, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Jie Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Pei-Xing Li
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
- The Centre for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangzhou, China
- College of Arts, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityFuzhou, China
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10
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Ma Y, Li Q, Hu G, Qin Y. Comparative transcriptional survey between self-incompatibility and self-compatibility in Citrus reticulata Blanco. Gene 2017; 609:52-61. [PMID: 28137595 DOI: 10.1016/j.gene.2017.01.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 11/27/2022]
Abstract
Seedlessness is an excellent economical trait, and self-incompatibility (SI) is one of important factors resulting in seedless fruit in Citrus. However, SI molecular mechanism in Citrus is still unclear. In this study, RNA-Seq technology was used to identify differentially expressed genes related to SI reaction of 'Wuzishatangju' (Citrus reticulata Blanco). A total of 35.67GB raw RNA-Seq data was generated and was de novo assembled into 50,364 unigenes with an average length of 897bp and N50 value of 1549. Twenty-three candidate unigenes related to SI were analyzed using qPCR at different tissues and stages after self- and cross-pollination. Seven pollen S genes (Unigene0050323, Unigene0001060, Unigene0004230, Unigene0004222, Unigene0012037, Unigene0048889 and Unigene0004272), three pistil S genes (Unigene0019191, Unigene0040115, Unigene0036542) and three genes (Unigene0038751, Unigene0031435 and Unigene0029897) associated with the pathway of ubiquitin-mediated proteolysis were identified. Unigene0031435, Unigene0038751 and Unigene0029897 are probably involved in SI reaction of 'Wuzishatangju' based on expression analyses. The present study provides a new insight into the molecular mechanism of SI in Citrus at the transcriptional level.
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Affiliation(s)
- Yuewen Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Qiulei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yonghua Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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11
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Matsumoto D, Tao R. Recognition of a wide-range of S-RNases by S locus F-box like 2, a general-inhibitor candidate in the Prunus-specific S-RNase-based self-incompatibility system. PLANT MOLECULAR BIOLOGY 2016; 91:459-69. [PMID: 27071402 DOI: 10.1007/s11103-016-0479-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/04/2016] [Indexed: 05/27/2023]
Abstract
Many species in the Rosaceae, the Solanaceae, and the Plantaginaceae exhibit S-RNase-based gametophytic self-incompatibility (GSI). This system comprises S-ribonucleases (S-RNases) as the pistil S determinant and a single or multiple F-box proteins as the pollen S determinants. In Prunus, pollen specificity is determined by a single S haplotype-specific F-box protein (SFB). The results of several studies suggested that SFB exerts cognate S-RNase cytotoxicity, and a hypothetical general inhibitor (GI) is assumed to detoxify S-RNases in non-specific manner unless it is affected by SFB. Although the identity of the GI is unknown, phylogenetic and evolutionary analyses have indicated that S locus F-box like 1-3 (or S locus F-box with low allelic sequence polymorphism 1-3; SLFL1-3), which are encoded by a region of the Prunus genome linked to the S locus, are good GI candidates. Here, we examined the biochemical characteristics of SLFL1-3 to determine whether they have appropriate GI characteristics. Pull-down assays and quantitative expression analyses indicated that Prunus avium SLFL1-3 mainly formed a canonical SCF complex with PavSSK1 and PavCul1A. Binding assays with PavS(1,3,4,6)-RNases showed that PavSLFL1, PavSLFL2, and PavSLFL3 bound to PavS(3)-RNase, all PavS-RNases tested, and none of the PavS-RNases tested, respectively. Together, these results suggested that SLFL2 has the appropriate characteristics to be the GI in sweet cherry pollen, while SLFL1 may redundantly work with SLFL2 to detoxify all S-RNases. We discuss the possible roles of SLFL1-3 as the GI in the Prunus-specific S-RNase-based GSI mechanism.
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Affiliation(s)
- Daiki Matsumoto
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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12
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Akagi T, Henry IM, Morimoto T, Tao R. Insights into the Prunus-Specific S-RNase-Based Self-Incompatibility System from a Genome-Wide Analysis of the Evolutionary Radiation of S Locus-Related F-box Genes. PLANT & CELL PHYSIOLOGY 2016; 57:1281-1294. [PMID: 27081098 DOI: 10.1093/pcp/pcw077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
Self-incompatibility (SI) is an important plant reproduction mechanism that facilitates the maintenance of genetic diversity within species. Three plant families, the Solanaceae, Rosaceae and Plantaginaceae, share an S-RNase-based gametophytic SI (GSI) system that involves a single S-RNase as the pistil S determinant and several F-box genes as pollen S determinants that act via non-self-recognition. Previous evidence has suggested a specific self-recognition mechanism in Prunus (Rosaceae), raising questions about the generality of the S-RNase-based GSI system. We investigated the evolution of the pollen S determinant by comparing the sequences of the Prunus S haplotype-specific F-box gene (SFB) with those of its orthologs in other angiosperm genomes. Our results indicate that the Prunus SFB does not cluster with the pollen S of other plants and diverged early after the establishment of the Eudicots. Our results further indicate multiple F-box gene duplication events, specifically in the Rosaceae family, and suggest that the Prunus SFB gene originated in a recent Prunus-specific gene duplication event. Transcriptomic and evolutionary analyses of the Prunus S paralogs are consistent with the establishment of a Prunus-specific SI system, and the possibility of subfunctionalization differentiating the newly generated SFB from the original pollen S determinant.
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Affiliation(s)
- Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Takuya Morimoto
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
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13
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Sassa H. Molecular mechanism of the S-RNase-based gametophytic self-incompatibility in fruit trees of Rosaceae. BREEDING SCIENCE 2016; 66:116-21. [PMID: 27069396 PMCID: PMC4780795 DOI: 10.1270/jsbbs.66.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/11/2015] [Indexed: 05/07/2023]
Abstract
Self-incompatibility (SI) is a major obstacle for stable fruit production in fruit trees of Rosaceae. SI of Rosaceae is controlled by the S locus on which at least two genes, pistil S and pollen S, are located. The product of the pistil S gene is a polymorphic and extracellular ribonuclease, called S-RNase, while that of the pollen S gene is a protein containing the F-box motif, SFB (S haplotype-specific F-box protein)/SFBB (S locus F-box brothers). Recent studies suggested that SI of Rosaceae includes two different systems, i.e., Prunus of tribe Amygdaleae exhibits a self-recognition system in which its SFB recognizes self-S-RNase, while tribe Pyreae (Pyrus and Malus) shows a non-self-recognition system in which many SFBB proteins are involved in SI, each recognizing subset of non-self-S-RNases. Further biochemical and biological characterization of the S locus genes, as well as other genes required for SI not located at the S locus, will help our understanding of the molecular mechanisms, origin, and evolution of SI of Rosaceae, and may provide the basis for breeding of self-compatible fruit tree cultivars.
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14
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Saito T. Advances in Japanese pear breeding in Japan. BREEDING SCIENCE 2016; 66:46-59. [PMID: 27069390 PMCID: PMC4780802 DOI: 10.1270/jsbbs.66.46] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/04/2015] [Indexed: 05/09/2023]
Abstract
The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan's history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars 'Chojuro' and 'Nijisseiki' around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars 'Niitaka' and 'Shinko' were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including 'Kosui', 'Hosui', and 'Akizuki', which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, 'Gold Nijisseiki' has become a leading cultivar. Moreover, 'Nansui' from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress.
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15
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Aguiar B, Vieira J, Cunha AE, Vieira CP. No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes. BMC PLANT BIOLOGY 2015; 15:129. [PMID: 26032621 PMCID: PMC4451870 DOI: 10.1186/s12870-015-0497-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/20/2015] [Indexed: 05/30/2023]
Abstract
BACKGROUND Fabaceae species are important in agronomy and livestock nourishment. They have a long breeding history, and most cultivars have lost self-incompatibility (SI), a genetic barrier to self-fertilization. Nevertheless, to improve legume crop breeding, crosses with wild SI relatives of the cultivated varieties are often performed. Therefore, it is fundamental to characterize Fabaceae SI system(s). We address the hypothesis of Fabaceae gametophytic (G)SI being RNase based, by recruiting the same S-RNase lineage gene of Rosaceae, Solanaceae or Plantaginaceae SI species. RESULTS We first identify SSK1 like genes (described only in species having RNase based GSI), in the Trifolium pratense, Medicago truncatula, Cicer arietinum, Glycine max, and Lupinus angustifolius genomes. Then, we characterize the S-lineage T2-RNase genes in these genomes. In T. pratense, M. truncatula, and C. arietinum we identify S-RNase lineage genes that in phylogenetic analyses cluster with Pyrinae S-RNases. In M. truncatula and C. arietinum genomes, where large scaffolds are available, these sequences are surrounded by F-box genes that in phylogenetic analyses also cluster with S-pollen genes. In T. pratense the S-RNase lineage genes show, however, expression in tissues not involved in GSI. Moreover, levels of diversity are lower than those observed for other S-RNase genes. The M. truncatula and C. arietinum S-RNase and S-pollen like genes phylogenetically related to Pyrinae S-genes, are also expressed in tissues other than those involved in GSI. To address if other T2-RNases could be determining Fabaceae GSI, here we obtained a style with stigma transcriptome of Cytisus striatus, a species that shows significant difference on the percentage of pollen growth in self and cross-pollinations. Expression and polymorphism analyses of the C. striatus S-RNase like genes revealed that none of these genes, is the S-pistil gene. CONCLUSION We find no evidence for Fabaceae GSI being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes. There is no evidence that T2-RNase lineage genes could be determining GSI in C. striatus. Therefore, to characterize the Fabaceae S-pistil gene(s), expression analyses, levels of diversity, and segregation analyses in controlled crosses are needed for those genes showing high expression levels in the tissues where GSI occurs.
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Affiliation(s)
- Bruno Aguiar
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 245, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, Porto, 4150-180, Portugal.
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 245, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, Porto, 4150-180, Portugal.
| | - Ana E Cunha
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 245, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, Porto, 4150-180, Portugal.
| | - Cristina P Vieira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 245, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, Porto, 4150-180, Portugal.
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16
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Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP. Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus. PLoS One 2015; 10:e0126138. [PMID: 25993016 PMCID: PMC4438004 DOI: 10.1371/journal.pone.0126138] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/30/2015] [Indexed: 12/24/2022] Open
Abstract
S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the Asteridae and Rosidae. This conclusion is based on the phylogenetic history of the S-RNase that determines pistil specificity. In Rosaceae, molecular characterizations of Prunus species, and species from the tribe Pyreae (i.e., Malus, Pyrus, Sorbus) revealed different numbers of genes determining S-pollen specificity. In Prunus only one pistil and pollen gene determine GSI, while in Pyreae there is one pistil but multiple pollen genes, implying different specificity recognition mechanisms. It is thus conceivable that within Rosaceae the genes involved in GSI in the two lineages are not orthologous but possibly paralogous. To address this hypothesis we characterised the S-RNase lineage and S-pollen lineage genes present in the genomes of five Rosaceae species from three genera: M. × domestica (apple, self-incompatible (SI); tribe Pyreae), P. persica (peach, self-compatible (SC); Amygdaleae), P. mume (mei, SI; Amygdaleae), Fragaria vesca (strawberry, SC; Potentilleae), and F. nipponica (mori-ichigo, SI; Potentilleae). Phylogenetic analyses revealed that the Malus and Prunus S-RNase and S-pollen genes belong to distinct gene lineages, and that only Prunus S-RNase and SFB-lineage genes are present in Fragaria. Thus, S-RNase based GSI system of Malus evolved independently from the ancestral system of Rosaceae. Using expression patterns based on RNA-seq data, the ancestral S-RNase lineage gene is inferred to be expressed in pistils only, while the ancestral S-pollen lineage gene is inferred to be expressed in tissues other than pollen.
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Affiliation(s)
- Bruno Aguiar
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Ana E. Cunha
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Nuno A. Fonseca
- CRACS-INESC Porto, Rua do Campo Alegre 1021/1055, 4169–007, Porto, Portugal
- European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, CB10 1SD, Cambridge, United Kingdom
| | - Amy Iezzoni
- Michigan State University, East Lansing, Michigan, United States of America
| | - Steve van Nocker
- Michigan State University, East Lansing, Michigan, United States of America
| | - Cristina P. Vieira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- * E-mail:
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17
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Mase N, Sawamura Y, Yamamoto T, Takada N, Nishio S, Saito T, Iketani H. A segmental duplication encompassing S-haplotype triggers pollen-part self-compatibility in Japanese pear ( Pyrus pyrifolia). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:117-128. [PMID: 24482602 PMCID: PMC3890579 DOI: 10.1007/s11032-013-9938-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/02/2013] [Indexed: 05/13/2023]
Abstract
Self-compatible mutants of self-incompatible crops have been extensively studied for research and agricultural purposes. Until now, the only known pollen-part self-compatible mutants in Rosaceae subtribe Pyrinae, which contains many important fruit trees, were polyploid. This study revealed that the pollen-part self-compatibility of breeding selection 415-1, a recently discovered mutant of Japanese pear (Pyrus pyrifolia) derived from γ-irradiated pollen, is caused by a duplication of an S-haplotype. In the progeny of 415-1, some plants had three S-haplotypes, two of which were from the pollen parent. Thus, 415-1 was able to produce pollen with two S-haplotypes, even though it was found to be diploid: the relative nuclear DNA content measured by flow cytometry showed no significant difference from that of a diploid cultivar. Inheritance patterns of simple sequence repeat (SSR) alleles in the same linkage group as the S-locus (LG 17) showed that some SSRs closely linked to S-haplotypes were duplicated in progeny containing the duplicated S-haplotype. These results indicate that the pollen-part self-compatibility of 415-1 is not caused by a mutation of pollen S factors in either one of the S-haplotypes, but by a segmental duplication encompassing the S-haplotype. Consequently, 415-1 can produce S-heteroallelic pollen grains that are capable of breaking down self-incompatibility (SI) by competitive interaction between the two different S factors in the pollen grain. 415-1 is the first diploid pollen-part self-compatible mutant with a duplicated S-haplotype to be discovered in the Pyrinae. The fact that 415-1 is not polyploid makes it particularly valuable for further studies of SI mechanisms.
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Affiliation(s)
- Nobuko Mase
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
| | - Yutaka Sawamura
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Toshiya Yamamoto
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
| | - Norio Takada
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Sogo Nishio
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Toshihiro Saito
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Hiroyuki Iketani
- NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
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Okada K, Moriya S, Haji T, Abe K. Isolation and characterization of multiple F-box genes linked to the S9- and S10-RNase in apple (Malus × domestica Borkh.). PLANT REPRODUCTION 2013; 26:101-111. [PMID: 23686223 DOI: 10.1007/s00497-013-0212-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/28/2013] [Indexed: 06/02/2023]
Abstract
Using 11 consensus primer pairs designed from S-linked F-box genes of apple and Japanese pear, 10 new F-box genes (MdFBX21 to 30) were isolated from the apple cultivar 'Spartan' (S(9)S(10)). MdFBX21 to 23 and MdFBX24 to 30 were completely linked to the S(9) -RNase and S(10-)RNase, respectively, and showed pollen-specific expression and S-haplotype-specific polymorphisms. Therefore, these 10 F-box genes are good candidates for the pollen determinant of self-incompatibility in apple. Phylogenetic analysis and comparison of deduced amino acid sequences of MdFBX21 to 30 with those of 25 S-linked F-box genes previously isolated from apple showed that a deduced amino acid identity of greater than 88.0 % can be used as the tentative criterion to classify F-box genes into one type. Using this criterion, 31 of 35 F-box genes of apple were classified into 11 types (SFBB1-11). All types included F-box genes derived from S(3-) and S(9-)haplotypes, and seven types included F-box genes derived from S(3-), S(9-), and S(10-)haplotypes. Moreover, comparison of nucleotide sequences of S-RNases and multiple F-box genes among S(3-), S(9-), and S(10-)haplotypes suggested that F-box genes within each type showed high nucleotide identity regardless of the identity of the S-RNase. The large number of F-box genes as candidates for the pollen determinant and the high degree of conservation within each type are consistent with the collaborative non-self-recognition model reported for Petunia. These findings support that the collaborative non-self-recognition system also exists in apple.
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Affiliation(s)
- Kazuma Okada
- Apple Research Station, NARO Institute of Fruit Tree Science, Morioka, Iwate, 020-0123, Japan.
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Aguiar B, Vieira J, Cunha AE, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Raspé O, Vieira CP. Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2423-34. [PMID: 23606363 PMCID: PMC3654429 DOI: 10.1093/jxb/ert098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
S-RNase-based gametophytic self-incompatibility evolved once before the split of the Asteridae and Rosidae. In Prunus (tribe Amygdaloideae of Rosaceae), the self-incompatibility S-pollen is a single F-box gene that presents the expected evolutionary signatures. In Malus and Pyrus (subtribe Pyrinae of Rosaceae), however, clusters of F-box genes (called SFBBs) have been described that are expressed in pollen only and are linked to the S-RNase gene. Although polymorphic, SFBB genes present levels of diversity lower than those of the S-RNase gene. They have been suggested as putative S-pollen genes, in a system of non-self recognition by multiple factors. Subsets of allelic products of the different SFBB genes interact with non-self S-RNases, marking them for degradation, and allowing compatible pollinations. This study performed a detailed characterization of SFBB genes in Sorbus aucuparia (Pyrinae) to address three predictions of the non-self recognition by multiple factors model. As predicted, the number of SFBB genes was large to account for the many S-RNase specificities. Secondly, like the S-RNase gene, the SFBB genes were old. Thirdly, amino acids under positive selection-those that could be involved in specificity determination-were identified when intra-haplotype SFBB genes were analysed using codon models. Overall, the findings reported here support the non-self recognition by multiple factors model.
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Affiliation(s)
- Bruno Aguiar
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150–180 Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150–180 Porto, Portugal
| | - Ana E. Cunha
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150–180 Porto, Portugal
| | - Nuno A. Fonseca
- CRACS-INESC Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal
| | - David Reboiro-Jato
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain
| | - Miguel Reboiro-Jato
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain
| | - Florentino Fdez-Riverola
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain
| | - Olivier Raspé
- National Botanic Garden of Belgium, Domein van Bouchout, B-1860 Meise, Belgium
| | - Cristina P. Vieira
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150–180 Porto, Portugal
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Miao H, Ye Z, Teixeira da Silva JA, Qin Y, Hu G. Identifying differentially expressed genes in pollen from self-incompatible "Wuzishatangju" and self-compatible "Shatangju" mandarins. Int J Mol Sci 2013; 14:8538-55. [PMID: 23595002 PMCID: PMC3645760 DOI: 10.3390/ijms14048538] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/02/2013] [Accepted: 04/07/2013] [Indexed: 02/05/2023] Open
Abstract
Self-incompatibility (SI) is one of the important factors that can result in seedless fruit in Citrus. However, the molecular mechanism of SI in Citrus is not yet clear. In this study, two suppression subtractive hybridization (SSH) libraries (forward, F and reverse, R) were constructed to isolate differentially expressed genes in pollen from "Wuzishatangju" (SI) and "Shatangju" (self-compatibility, SC) mandarins. Four hundred and sixty-eight differentially expressed cDNA clones from 2077 positive clones were sequenced and identified. Differentially expressed ESTs are possibly involved in the SI reaction of "Wuzishatangju" by regulating pollen development, kinase activity, ubiquitin pathway, pollen-pistil interaction, and calcium ion binding. Twenty five SI candidate genes were obtained, six of which displayed specific expression patterns in various organs and stages after self- and cross-pollination. The expression level of the F-box gene (H304) and S1 (F78) in the pollen of "Wuzishatangju" was 5-fold higher than that in "Shatangju" pollen. The F-box gene, S1, UBE2, UBE3, RNaseHII, and PCP were obviously up-regulated in pistils at 3 d after self-pollination of "Wuzishatangju", approximately 3-, 2-, 10-, 5-, 5-, and 2-fold higher, respectively than that at the same stage after cross-pollination of "Wuzishatangju" × "Shatangju" pistils. The potential involvement of these genes in the pollen SI reaction of "Wuzishatangju" is discussed.
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Affiliation(s)
- Hongxia Miao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; E-Mail:
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China of Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; E-Mail:
| | - Zixing Ye
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China of Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; E-Mail:
| | - Jaime A. Teixeira da Silva
- Faculty of Agriculture and Graduate School of Agriculture, Kagawa University, Ikenobe, Kagawa 761-0795, Japan; E-Mail:
| | - Yonghua Qin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China of Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; E-Mail:
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; E-Mail:
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China of Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; E-Mail:
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Xu C, Li M, Wu J, Guo H, Li Q, Zhang Y, Chai J, Li T, Xue Y. Identification of a canonical SCF(SLF) complex involved in S-RNase-based self-incompatibility of Pyrus (Rosaceae). PLANT MOLECULAR BIOLOGY 2013; 81:245-57. [PMID: 23263858 DOI: 10.1007/s11103-012-9995-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 12/05/2012] [Indexed: 05/10/2023]
Abstract
S-RNase-based self-incompatibility (SI) is an intraspecific reproductive barrier to prevent self-fertilization found in many species of the Solanaceae, Plantaginaceae and Rosaceae. In this system, S-RNase and SLF/SFB (S-locus F-box) genes have been shown to control the pistil and pollen SI specificity, respectively. Recent studies have shown that the SLF functions as a substrate receptor of a SCF (Skp1/Cullin1/F-box)-type E3 ubiquitin ligase complex to target S-RNases in Solanaceae and Plantaginaceae, but its role in Rosaceae remains largely undefined. Here we report the identification of two pollen-specific SLF-interacting Skp1-like (SSK) proteins, PbSSK1 and PbSSK2, in Pyrus bretschneideri from the tribe Pyreae of Rosaceae. Both yeast two-hybrid and pull-down assays demonstrated that they could connect PbSLFs to PbCUL1 to form a putative canonical SCF(SLF) (SSK/CUL1/SLF) complex in Pyrus. Furthermore, pull-down assays showed that the SSK proteins could bind SLF and CUL1 in a cross-species manner between Pyrus and Petunia. Additionally, phylogenetic analysis revealed that the SSK-like proteins from Solanaceae, Plantaginaceae and Rosaceae form a monoclade group, hinting their shared evolutionary origin. Taken together, with the recent identification of a canonical SCF(SFB) complex in Prunus of the tribe Amygdaleae of Rosaceae, our results show that a conserved canonical SCF(SLF/SFB) complex is present in Solanaceae, Plantaginaceae and Rosaceae, implying that S-RNase-based self-incompatibility shares a similar molecular and biochemical mechanism.
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Affiliation(s)
- Chi Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing 100101, China
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22
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Wang S, Kakui, H, Kikuchi S, Koba T, Sassa H. Interhaplotypic heterogeneity and heterochromatic features may contribute to recombination suppression at the S locus in apple (Malusxdomestica). JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4983-90. [PMID: 22760470 PMCID: PMC3428002 DOI: 10.1093/jxb/ers176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gametophytic self-incompatibility (GSI) is controlled by a complex S locus containing the pistil determinant S-RNase and pollen determinant SFB/SLF. Tight linkage of the pistil and pollen determinants is necessary to guarantee the self-incompatibility (SI) function. However, multiple probable pollen determinants of apple and Japanese pear, SFBBs (S locus F-box brothers), exist in each S haplotype, and how these multiple genes maintain the SI function remains unclear. It is shown here by high-resolution fluorescence in situ hybridization (FISH) that SFBB genes of the apple S9 haplotype are physically linked to the S9-RNase gene, and the S locus is located in the subtelomeric region. FISH analyses also determined the relative order of SFBB genes and S-RNase in the S9 haplotype, and showed that gene order differs between the S9 and S3 haplotypes. Furthermore, it is shown that the apple S locus is located in a knob-like large heterochromatin block where DNA is highly methylated. It is proposed that interhaplotypic heterogeneity and the heterochromatic nature of the S locus help to suppress recombination at the S locus in apple.
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Affiliation(s)
- Sanhong Wang
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
- Department of Horticulture, Nanjing Agricultural University210095, NanjingChina
| | - Hiroyuki Kakui,
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
| | - Takato Koba
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
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23
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Matsumoto D, Yamane H, Abe K, Tao R. Identification of a Skp1-like protein interacting with SFB, the pollen S determinant of the gametophytic self-incompatibility in Prunus. PLANT PHYSIOLOGY 2012; 159:1252-62. [PMID: 22548785 PMCID: PMC3387707 DOI: 10.1104/pp.112.197343] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 04/26/2012] [Indexed: 05/23/2023]
Abstract
Many species in Rosaceae, Solanaceae, and Plantaginaceae exhibit S-RNase-based self-incompatibility (SI). In this system, the pistil and pollen specificities are determined by S-RNase and the S locus F-box protein, respectively. The pollen S determinant F-box protein in Prunus (Rosaceae) is referred to by two different terms, SFB (for S-haplotype-specific F-box protein) and SLF (for S locus F box), whereas it is called SLF in Solanaceae and Plantaginaceae. Prunus SFB is thought to be a molecule indispensable for its cognate S-RNase to exert cytotoxicity and to arrest pollen tube growth in incompatible reactions. Although recent studies have demonstrated the molecular function of SCF(SLF) in the SI reaction of Solanaceae and Plantaginaceae, how SFB participates in the Prunus SI mechanism remains to be elucidated. Here we report the identification of sweet cherry (Prunus avium) SFB (PavSFB)-interacting Skp1-like1 (PavSSK1) using a yeast (Saccharomyces cerevisiae) two-hybrid screening against the pollen cDNA library. Phylogenetic analysis showed that PavSSK1 belongs to the same clade as Antirrhinum hispanicum SLF-interacting Skp1-like1 and Petunia hybrida SLF-interacting Skp1-like1 (PhSSK1). In yeast, PavSSK1 interacted not only with PavSFBs from different S haplotypes and Cullin1-likes (PavCul1s), but also with S-locus F-box-likes. A pull-down assay confirmed the interactions between PavSSK1 and PavSFB and between PavSSK1 and PavCul1s. These results collectively indicate that PavSSK1 could be a functional component of the SCF complex and that PavSFB may function as a component of the SCF complex. We discuss the molecular function of PavSFB in self-/nonself-recognition in the gametophytic SI of Prunus.
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De Franceschi P, Dondini L, Sanzol J. Molecular bases and evolutionary dynamics of self-incompatibility in the Pyrinae (Rosaceae). JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4015-32. [PMID: 22563122 DOI: 10.1093/jxb/ers108] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The molecular bases of the gametophytic self-incompatibility (GSI) system of species of the subtribe Pyrinae (Rosaceae), such as apple and pear, have been widely studied in the last two decades. The characterization of S-locus genes and of the mechanisms underlying pollen acceptance or rejection have been topics of major interest. Besides the single pistil-side S determinant, the S-RNase, multiple related S-locus F-box genes seem to be involved in the determination of pollen S specificity. Here, we collect and review the state of the art of GSI in the Pyrinae. We emphasize recent genomic data that have contributed to unveiling the S-locus structure of the Pyrinae, and discuss their consistency with the models of self-recognition that have been proposed for Prunus and the Solanaceae. Experimental data suggest that the mechanism controlling pollen-pistil recognition specificity of the Pyrinae might fit well with the collaborative 'non-self' recognition system proposed for Petunia (Solanaceae), whereas it presents relevant differences with the mechanism exhibited by the species of the closely related genus Prunus, which uses a single evolutionarily divergent F-box gene as the pollen S determinant. The possible involvement of multiple pollen S genes in the GSI system of Pyrinae, still awaiting experimental confirmation, opens up new perspectives to our understanding of the evolution of S haplotypes, and of the evolution of S-RNase-based GSI within the Rosaceae family. Whereas S-locus genes encode the players determining self-recognition, pollen rejection in the Pyrinae seems to involve a complex cascade of downstream cellular events with significant similarities to programmed cell death.
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Affiliation(s)
- Paolo De Franceschi
- Dipartimento di Colture Arboree (DCA), Università degli Studi di Bologna, Via Giuseppe Fanin 46, 40127 Bologna, Italy.
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25
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Iwano M, Takayama S. Self/non-self discrimination in angiosperm self-incompatibility. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:78-83. [PMID: 21968124 DOI: 10.1016/j.pbi.2011.09.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/11/2011] [Accepted: 09/13/2011] [Indexed: 05/22/2023]
Abstract
Self-incompatibility (SI) in angiosperms prevents inbreeding and promotes outcrossing to generate genetic diversity. In many angiosperms, self/non-self recognition in SI is accomplished by male-specificity and female-specificity determinants (S-determinants), encoded at the S-locus. Recent studies using genetic, molecular biological and biochemical approaches have revealed that angiosperms utilize diverse self/non-self discrimination systems, which can be classified into two fundamentally different systems, self-recognition and non-self recognition systems. The self-recognition system, adopted by Brassicaceae and Papaveraceae, depends on a specific interaction between male and female S-determinants derived from the same S-haplotype. The non-self recognition system, found in Solanaceae, depends on non-self (different S-haplotype)-specific interaction between male and female S-determinants, and the male S-determinant genes are duplicated to recognize diverse non-self female S-determinants.
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Affiliation(s)
- Megumi Iwano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan.
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Kakui H, Kato M, Ushijima K, Kitaguchi M, Kato S, Sassa H. Sequence divergence and loss-of-function phenotypes of S locus F-box brothers genes are consistent with non-self recognition by multiple pollen determinants in self-incompatibility of Japanese pear (Pyrus pyrifolia). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:1028-1038. [PMID: 21851432 DOI: 10.1111/j.1365-313x.2011.04752.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The S-RNase-based gametophytic self-incompatibility (SI) of Rosaceae, Solanaceae, and Plantaginaceae is controlled by at least two tightly linked genes located at the complex S locus; the highly polymorphic S-RNase for pistil specificity and the F-box gene (SFB/SLF) for pollen. Self-incompatibility in Prunus (Rosaceae) is considered to represent a 'self recognition by a single factor' system, because loss-of-function of SFB is associated with self-compatibility, and allelic divergence of SFB is high and comparable to that of S-RNase. In contrast, Petunia (Solanaceae) exhibits 'non-self recognition by multiple factors'. However, the distribution of 'self recognition' and 'non-self recognition' SI systems in different taxa is not clear. In addition, in 'non-self recognition' systems, a loss-of-function phenotype of pollen S is unknown. Here we analyze the divergence of SFBB genes, the multiple pollen S candidates, of a rosaceous plant Japanese pear (Pyrus pyrifolia) and show that intrahaplotypic divergence is high and comparable to the allelic diversity of S-RNase while interhaplotypic divergence is very low. Next, we analyzed loss-of-function of the SFBB1 type gene. Genetic analysis showed that pollen with the mutant haplotype S(4sm) lacking SFBB1-S(4) is rejected by pistils with an otherwise compatible S(1) while it is accepted by other non-self pistils. We found that the S(5) haplotype encodes a truncated SFBB1 protein, even though S(5) pollen is accepted normally by pistils with S(1) and other non-self haplotypes. These findings suggest that Japanese pear has a 'non-self recognition by multiple factors' SI system, although it is a species of Rosaceae to which Prunus also belongs.
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Affiliation(s)
- Hiroyuki Kakui
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
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Wang N, Kao TH. Self-incompatibility in Petunia: a self/nonself-recognition mechanism employing S-locus F-box proteins and S-RNase to prevent inbreeding. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:267-75. [PMID: 23801440 DOI: 10.1002/wdev.10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many flowering plants producing bisexual flowers have adopted self-incompatibility (SI), a reproductive strategy which allows pistils to distinguish between self and nonself pollen, and to only permit nonself pollen to effect fertilization. To date, three different SI mechanisms have been identified, and this article focuses on the S-RNase-based mechanism using Petunia (Solanaceae) as a model. The genetic basis of this type of SI was established nearly a century ago; the polymorphic S-locus specifies the genetic identity of pollen and the pistil. Molecular genetic studies carried out since the late 1980s have led to the identification of the polymorphic genes at the S-locus that control self/nonself-recognition between pollen and the pistil. The S-RNase gene, which controls pistil specificity, was identified first, and subsequent sequencing of the S-locus region containing S-RNase led to the identification of the S-locus F-box (SLF) gene (now named SLF1). A transgenic approach was used to show that S2-SLF1 (SLF1 of S2-halotype) of Petunia inflata controls pollen specificity. The S-locus contains additional pollen-expressed F-box genes that show sequence similarity with SLF1, and initially they were thought not to be involved in pollen specificity. However, further studies of SLF1 suggested that it is not the only pollen specificity gene. Indeed, it has recently been shown that two previously identified SLF-like genes in P. inflata (now named SLF2 and SLF3) and a yet unknown number of additional SLF-like genes (named SLF4, SLF5, etc.) collaboratively function to control pollen specificity. The significance and implications of this new finding are discussed.
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Affiliation(s)
- Ning Wang
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania, PA, USA
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