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Erez K, Jangid A, Feldheim ON, Friedlander T. The role of promiscuous molecular recognition in the evolution of RNase-based self-incompatibility in plants. Nat Commun 2024; 15:4864. [PMID: 38849350 PMCID: PMC11161657 DOI: 10.1038/s41467-024-49163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
How do biological networks evolve and expand? We study these questions in the context of the plant collaborative-non-self recognition self-incompatibility system. Self-incompatibility evolved to avoid self-fertilization among hermaphroditic plants. It relies on specific molecular recognition between highly diverse proteins of two families: female and male determinants, such that the combination of genes an individual possesses determines its mating partners. Though highly polymorphic, previous models struggled to pinpoint the evolutionary trajectories by which new specificities evolved. Here, we construct a novel theoretical framework, that crucially affords interaction promiscuity and multiple distinct partners per protein, as is seen in empirical findings disregarded by previous models. We demonstrate spontaneous self-organization of the population into distinct "classes" with full between-class compatibility and a dynamic long-term balance between class emergence and decay. Our work highlights the importance of molecular recognition promiscuity to network evolvability. Promiscuity was found in additional systems suggesting that our framework could be more broadly applicable.
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Affiliation(s)
- Keren Erez
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Amit Jangid
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Ohad Noy Feldheim
- The Einstein Institute of Mathematics, Faculty of Natural Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Tamar Friedlander
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel.
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2
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Hu J, Guo F, Du Z, Chen P, Shi C, Zhang J, Ye J, Deng X, Larkin RM, Jiao W, Lin Z, Bosch M, Chai L. A rare inter-haplotypic recombination at the S-locus contributed to the loss of self-incompatibility in trifoliate orange. PLANT COMMUNICATIONS 2024:100940. [PMID: 38715365 DOI: 10.1016/j.xplc.2024.100940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/20/2024] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Affiliation(s)
- Jianbing Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China.
| | - Furong Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Zezhen Du
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China
| | - Peng Chen
- Horticultural Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, P.R. China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jinzhi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China
| | - Wenbiao Jiao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China
| | - Zongcheng Lin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FL, UK
| | - Lijun Chai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China.
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3
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Castric V, Batista RA, Carré A, Mousavi S, Mazoyer C, Godé C, Gallina S, Ponitzki C, Theron A, Bellec A, Marande W, Santoni S, Mariotti R, Rubini A, Legrand S, Billiard S, Vekemans X, Vernet P, Saumitou-Laprade P. The homomorphic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene. Curr Biol 2024; 34:1967-1976.e6. [PMID: 38626763 DOI: 10.1016/j.cub.2024.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
In flowering plants, outcrossing is commonly ensured by self-incompatibility (SI) systems. These can be homomorphic (typically with many different allelic specificities) or can accompany flower heteromorphism (mostly with just two specificities and corresponding floral types). The SI system of the Oleaceae family is unusual, with the long-term maintenance of only two specificities but often without flower morphology differences. To elucidate the genomic architecture and molecular basis of this SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals and related them to a genetic map. The S-locus region proved to have a segregating 543-kb indel unique to one specificity, suggesting a hemizygous region, as observed in all distylous systems so far studied at the genomic level. Only one of the predicted genes in this indel region is found in the olive tree, Olea europaea, genome, also within a segregating indel. We describe complete association between the presence/absence of this gene and the SI types determined for individuals of seven distantly related Oleaceae species. This gene is predicted to be involved in catabolism of the gibberellic acid (GA) hormone, and experimental manipulation of GA levels in developing buds modified the male and female SI responses of the two specificities in different ways. Our results provide a unique example of a homomorphic SI system, where a single conserved gibberellin-related gene in a hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility.
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Affiliation(s)
- Vincent Castric
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Rita A Batista
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Amélie Carré
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Soraya Mousavi
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Clément Mazoyer
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Chloé Ponitzki
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Anthony Theron
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - Arnaud Bellec
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - William Marande
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - Sylvain Santoni
- UMR DIAPC Diversité et adaptation des plantes cultivées, F-34398 Montpellier, France
| | - Roberto Mariotti
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Andrea Rubini
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Sylvain Legrand
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Xavier Vekemans
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Philippe Vernet
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [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: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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5
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Wu J, Nan X, Zhang X, Xu W, Ma H, Yang Z, Wang C. The Identification and Analysis of the Self-Incompatibility Pollen Determinant Factor SLF in Lycium barbarum. PLANTS (BASEL, SWITZERLAND) 2024; 13:959. [PMID: 38611487 PMCID: PMC11013074 DOI: 10.3390/plants13070959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Self-incompatibility is a widespread genetic mechanism found in flowering plants. It plays a crucial role in preventing inbreeding and promoting outcrossing. The genes that control self-incompatibility in plants are typically determined by the S-locus female determinant factor and the S-locus male determinant factor. In the Solanaceae family, the male determinant factor is often the SLF gene. In this research, we cloned and analyzed 13 S2-LbSLF genes from the L. barbarum genome, which are located on chromosome 2 and close to the physical location of the S-locus female determinant factor S-RNase, covering a region of approximately 90.4 Mb. The amino acid sequence identity of the 13 S2-LbSLFs is 58.46%, and they all possess relatively conserved motifs and typical F-box domains, without introns. A co-linearity analysis revealed that there are no tandemly repeated genes in the S2-LbSLF genes, and that there are two pairs of co-linear genes between S2-LbSLF and the tomato, which also belongs to the Solanaceae family. A phylogenetic analysis indicates that the S2-LbSLF members can be divided into six groups, and it was found that the 13 S2-LbSLFs are clustered with the SLF genes of tobacco and Petunia inflata to varying degrees, potentially serving as pollen determinant factors regulating self-incompatibility in L. barbarum. The results for the gene expression patterns suggest that S2-LbSLF is only expressed in pollen tissue. The results of the yeast two-hybrid assay showed that the C-terminal region of S2-LbSLFs lacking the F-box domain can interact with S-RNase. This study provides theoretical data for further investigation into the functions of S2-LbSLF members, particularly for the identification of pollen determinant factors regulating self-incompatibility in L. barbarum.
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Affiliation(s)
- Jiali Wu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Xiongxiong Nan
- State Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, China
| | - Xin Zhang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
| | - Wendi Xu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
| | - Haijun Ma
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Ningxia Grape and Wine Innovation Center, North Minzu University, Yinchuan 750021, China
| | - Zijun Yang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Cuiping Wang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
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Zhang D, Li YY, Zhao X, Zhang C, Liu DK, Lan S, Yin W, Liu ZJ. Molecular insights into self-incompatibility systems: From evolution to breeding. PLANT COMMUNICATIONS 2024; 5:100719. [PMID: 37718509 PMCID: PMC10873884 DOI: 10.1016/j.xplc.2023.100719] [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: 03/29/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Plants have evolved diverse self-incompatibility (SI) systems for outcrossing. Since Darwin's time, considerable progress has been made toward elucidating this unrivaled reproductive innovation. Recent advances in interdisciplinary studies and applications of biotechnology have given rise to major breakthroughs in understanding the molecular pathways that lead to SI, particularly the strikingly different SI mechanisms that operate in Solanaceae, Papaveraceae, Brassicaceae, and Primulaceae. These best-understood SI systems, together with discoveries in other "nonmodel" SI taxa such as Poaceae, suggest a complex evolutionary trajectory of SI, with multiple independent origins and frequent and irreversible losses. Extensive exploration of self-/nonself-discrimination signaling cascades has revealed a comprehensive catalog of male and female identity genes and modifier factors that control SI. These findings also enable the characterization, validation, and manipulation of SI-related factors for crop improvement, helping to address the challenges associated with development of inbred lines. Here, we review current knowledge about the evolution of SI systems, summarize key achievements in the molecular basis of pollen‒pistil interactions, discuss potential prospects for breeding of SI crops, and raise several unresolved questions that require further investigation.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Weilun Yin
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Murase K, Takayama S, Isogai A. Molecular mechanisms of self-incompatibility in Brassicaceae and Solanaceae. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2024; 100:264-280. [PMID: 38599847 DOI: 10.2183/pjab.100.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Self-incompatibility (SI) is a mechanism for preventing self-fertilization in flowering plants. SI is controlled by a single S-locus with multiple haplotypes (S-haplotypes). When the pistil and pollen share the same S-haplotype, the pollen is recognized as self and rejected by the pistil. This review introduces our research on Brassicaceae and Solanaceae SI systems to identify the S-determinants encoded at the S-locus and uncover the mechanisms of self/nonself-discrimination and pollen rejection. The recognition mechanisms of SI systems differ between these families. A self-recognition system is adopted by Brassicaceae, whereas a collaborative nonself-recognition system is used by Solanaceae. Work by our group and subsequent studies indicate that plants have evolved diverse SI systems.
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Affiliation(s)
- Kohji Murase
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology
| | - Seiji Takayama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Akira Isogai
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
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8
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Moreels P, Bigot S, Defalque C, Correa F, Martinez JP, Lutts S, Quinet M. Intra- and inter-specific reproductive barriers in the tomato clade. FRONTIERS IN PLANT SCIENCE 2023; 14:1326689. [PMID: 38143584 PMCID: PMC10739309 DOI: 10.3389/fpls.2023.1326689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023]
Abstract
Tomato (Solanum lycopersicum L.) domestication and later introduction into Europe resulted in a genetic bottleneck that reduced genetic variation. Crosses with other wild tomato species from the Lycopersicon clade can be used to increase genetic diversity and improve important agronomic traits such as stress tolerance. However, many species in the Lycopersicon clade have intraspecific and interspecific incompatibility, such as gametophytic self-incompatibility and unilateral incompatibility. In this review, we provide an overview of the known incompatibility barriers in Lycopersicon. We begin by addressing the general mechanisms self-incompatibility, as well as more specific mechanisms in the Rosaceae, Papaveraceae, and Solanaceae. Incompatibility in the Lycopersicon clade is discussed, including loss of self-incompatibility, species exhibiting only self-incompatibility and species presenting both self-compatibility and self-incompatibility. We summarize unilateral incompatibility in general and specifically in Lycopersicon, with details on the 'self-compatible x self-incompatible' rule, implications of self-incompatibility in unilateral incompatibility and self-incompatibility-independent pathways of unilateral incompatibility. Finally, we discuss advances in the understanding of compatibility barriers and their implications for tomato breeding.
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Affiliation(s)
- Pauline Moreels
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Servane Bigot
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Corentin Defalque
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Francisco Correa
- Instituto de Investigaciones Agropecuarias (INIA-Rayentué), Rengo, Chile
| | | | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Muriel Quinet
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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9
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Bala M, Rehana S, Singh MP. Self-incompatibility: a targeted, unexplored pre-fertilization barrier in flower crops of Asteraceae. JOURNAL OF PLANT RESEARCH 2023; 136:587-612. [PMID: 37452973 DOI: 10.1007/s10265-023-01480-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Asteraceae (synonym as Compositae) is one of the largest angiosperm families among flowering plants comprising one-tenth of all agri-horticultural species grown across various habitats except in Antarctica. These are commercially utilized as cut and loose flowers as well as pot and bedding plants in landscape gardens due to their unique floral traits. Consequently, ineffective seed setting and presence of an intraspecific reproductive barrier known as self-incompatibility (SI) severely reduces the effectiveness of hybridization and self-fertilization by traditional crossing. There have been very few detailed studies of pollen-stigma interactions in this family. Moreover, about 63% of Aster species can barely self-fertilize due to self-incompatibility (SI). The chrysanthemum (Chrysanthemum × morifolium) is one of the most economically important ornamental plants in the Asteraceae family which hugely shows incompatibility. Reasons for the low fertility and reproductive capacity of species are still indefinite or not clear. Hence, the temporal pattern of inheritance of self-incompatibility and its effect on reproductive biology needs to be investigated further to improve the breeding efficiency. This review highlights the self-incompatible (SI) system operating in important Astraceous (ornamental) crops which are adversely affected by this mechanism along with different physiological and molecular techniques involved in breaking down self-incompatibility.
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Affiliation(s)
- Madhu Bala
- Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India.
| | - Shaik Rehana
- Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Mohini Prabha Singh
- Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
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Zakharova E, Khanina T, Knyazev A, Milyukova N, Kovaleva LV. Hormonal Signaling during dPCD: Cytokinin as the Determinant of RNase-Based Self-Incompatibility in Solanaceae. Biomolecules 2023; 13:1033. [PMID: 37509069 PMCID: PMC10377171 DOI: 10.3390/biom13071033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Research into molecular mechanisms of self-incompatibility (SI) in plants can be observed in representatives of various families, including Solanaceae. Earlier studies of the mechanisms of S-RNase-based SI in petunia (Petunia hybrida E. Vilm.) demonstrate that programmed cell death (PCD) is an SI factor. These studies suggest that the phytohormon cytokinin (CK) is putative activator of caspase-like proteases (CLPs). In this work, data confirming this hypothesis were obtained in two model objects-petunia and tomato (six Solanaceae representatives). The exogenous zeatin treatment of tomato and petunia stigmas before a compatible pollination activates CLPs in the pollen tubes in vivo, as shown via the intravital imaging of CLP activities. CK at any concentration slows down the germination and growth of petunia and tomato male gametophytes both in vitro and in vivo; shifts the pH of the cytoplasm (PHc) to the acid region, thereby creating the optimal conditions for CLP to function and inhibiting the F-actin formation and/or destructing the cytoskeleton in pollen tubes to point foci during SI-induced PCD; and accumulates in style tissues during SI response. The activity of the ISOPENTENYLTRANSFERASE 5 (IPT5) gene at this moment exceeds its activity in a cross-compatible pollination, and the levels of expression of the CKX1 and CKX2 genes (CK OXIDASE/DEHYDROGENASE) are significantly lower in self-incompatible pollination. All this suggests that CK plays a decisive role in the mechanism underlying SI-induced PCD.
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Affiliation(s)
- Ekaterina Zakharova
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Tatiana Khanina
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Andrey Knyazev
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Natalia Milyukova
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Lidia V Kovaleva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 191186 Moscow, Russia
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11
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Sun L, Cao S, Zheng N, Kao TH. Analyses of Cullin1 homologs reveal functional redundancy in S-RNase-based self-incompatibility and evolutionary relationships in eudicots. THE PLANT CELL 2023; 35:673-699. [PMID: 36478090 PMCID: PMC9940881 DOI: 10.1093/plcell/koac357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In Petunia (Solanaceae family), self-incompatibility (SI) is regulated by the polymorphic S-locus, which contains the pistil-specific S-RNase and multiple pollen-specific S-Locus F-box (SLF) genes. SLFs assemble into E3 ubiquitin ligase complexes known as Skp1-Cullin1-F-box complexes (SCFSLF). In pollen tubes, these complexes collectively mediate ubiquitination and degradation of all nonself S-RNases, but not self S-RNase, resulting in cross-compatible, but self-incompatible, pollination. Using Petunia inflata, we show that two pollen-expressed Cullin1 (CUL1) proteins, PiCUL1-P and PiCUL1-B, function redundantly in SI. This redundancy is lost in Petunia hybrida, not because of the inability of PhCUL1-B to interact with SSK1, but due to a reduction in the PhCUL1-B transcript level. This is possibly caused by the presence of a DNA transposon in the PhCUL1-B promoter region, which was inherited from Petunia axillaris, one of the parental species of Pe. hybrida. Phylogenetic and syntenic analyses of Cullin genes in various eudicots show that three Solanaceae-specific CUL1 genes share a common origin, with CUL1-P dedicated to S-RNase-related reproductive processes. However, CUL1-B is a dispersed duplicate of CUL1-P present only in Petunia, and not in the other species of the Solanaceae family examined. We suggest that the CUL1s involved (or potentially involved) in the SI response in eudicots share a common origin.
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Affiliation(s)
- Linhan Sun
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shiyun Cao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Teh-hui Kao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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12
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Ye C, He Z, Peng J, Wang R, Wang X, Fu M, Zhang Y, Wang A, Liu Z, Jia G, Chen Y, Tian B. Genomic and genetic advances of oiltea-camellia ( Camellia oleifera). FRONTIERS IN PLANT SCIENCE 2023; 14:1101766. [PMID: 37077639 PMCID: PMC10106683 DOI: 10.3389/fpls.2023.1101766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Oiltea-camellia (C. oleifera) is a widely cultivated woody oil crop in Southern China and Southeast Asia. The genome of oiltea-camellia was very complex and not well explored. Recently, genomes of three oiltea-camellia species were sequenced and assembled, multi-omic studies of oiltea-camellia were carried out and provided a better understanding of this important woody oil crop. In this review, we summarized the recent assembly of the reference genomes of oiltea-camellia, genes related to economic traits (flowering, photosynthesis, yield and oil component), disease resistance (anthracnose) and environmental stress tolerances (drought, cold, heat and nutrient deficiency). We also discussed future directions of integrating multiple omics for evaluating genetic resources and mining key genes of important traits, and the application of new molecular breeding and gene editing technologies to accelerate the breeding process of oiltea-camellia.
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Affiliation(s)
- Changrong Ye
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Zhilong He
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Jiayu Peng
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Rui Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Xiangnan Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Mengjiao Fu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Ying Zhang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Ai Wang
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Zhixian Liu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Gaofeng Jia
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Yongzhong Chen
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Bingchuan Tian
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
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13
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Kato M, Watanabe H, Hoshino Y. Evaluation of pollen tube growth ability in Petunia species having different style lengths. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:85-92. [PMID: 35937536 PMCID: PMC9300434 DOI: 10.5511/plantbiotechnology.21.1113a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/13/2021] [Indexed: 06/15/2023]
Abstract
Pollen tube growth is essential for the fertilization process in angiosperms. When pollen grains arrive on the stigma, they germinate, and the pollen tubes elongate through the styles of the pistils to deliver sperm cells into the ovules to produce the seeds. The relationship between the growth rate and style length remains unclear. In previous studies, we developed a liquid pollen germination medium for observing pollen tube growth. In this study, using this medium, we examined the pollen tube growth ability in Petunia axillaris subsp. axillaris, P. axillaris subsp. parodii, P. integrifolia, and P. occidentalis, which have different style lengths. Petunia occidentalis had the longest pollen tubes after 6 h of culture but had a relatively shorter style. Conversely, the pollination experiments revealed that P. axillaris subsp. parodii, which had the longest style, produced the longest pollen tubes in vivo. The results revealed no clear relationship between the style lengths and the growth rate of pollen tubes in vitro. Interspecific pollinations indicated that the styles affected pollen tube growth. We concluded that, in vitro, the pollen tubes grow without being affected by the styles, whereas, in vivo, the styles significantly affected pollen tube growth. Furthermore, interspecific pollination experiments implied that the pollen tube growth tended to be suppressed in the styles of self-incompatibility species. Finally, we discussed the pollen tube growth ability in relation to style lengths.
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Affiliation(s)
- Miyako Kato
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo, Hokkaido 060-0811, Japan
| | - Hitoshi Watanabe
- Center for Environment, Health and Field Sciences, Chiba University, 6-2-1 Kashiwano-ha, Kashiwa, Chiba 277-0882, Japan
| | - Yoichiro Hoshino
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo, Hokkaido 060-0811, Japan
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo, Hokkaido 060-0811, Japan
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14
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Lv S, Qiao X, Zhang W, Li Q, Wang P, Zhang S, Wu J. The origin and evolution of RNase T2 family and gametophytic self-incompatibility system in plants. Genome Biol Evol 2022; 14:6609977. [PMID: 35714207 PMCID: PMC9250077 DOI: 10.1093/gbe/evac093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Ribonuclease (RNase) T2 genes are found widely in both eukaryotes and prokaryotes, and genes from this family have been revealed to have various functions in plants. In particular, S-RNase is known to be the female determinant in the S-RNase-based gametophytic self-incompatibility (GSI) system. However, the origin and evolution of the RNase T2 gene family and GSI system are not well understood. In this study, 785 RNase T2 genes were identified in 81 sequenced plant genomes representing broad-scale diversity and divided into three subgroups (Class I, II, and III) based on phylogenetic and synteny network analysis. Class I was found to be of ancient origin and to emerge in green algae, Class II was shown to originate with the appearance of angiosperms, while Class III was discovered to be eudicot-specific. Each of the three major classes could be further classified into several subclasses of which some subclasses were found to be lineage-specific. Furthermore, duplication, deletion, or inactivation of the S/S-like-locus was revealed to be linked to repeated loss and gain of self-incompatibility in different species from distantly related plant families with GSI. Finally, the origin and evolutionary history of S-locus in Rosaceae species was unraveled with independent loss and gain of S-RNase occurred in different subfamilies of Rosaceae. Our findings provide insights into the origin and evolution of the RNase T2 family and the GSI system in plants.
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Affiliation(s)
- Shouzheng Lv
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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15
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Kardile HB, Yilma S, Sathuvalli V. Molecular Approaches to Overcome Self-Incompatibility in Diploid Potatoes. PLANTS 2022; 11:plants11101328. [PMID: 35631752 PMCID: PMC9143039 DOI: 10.3390/plants11101328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
There has been an increased interest in true potato seeds (TPS) as planting material because of their advantages over seed tubers. TPS produced from a tetraploid heterozygous bi-parental population produces non-uniform segregating progenies, which have had limited uniformity in yield and quality in commercial cultivation, and, thus, limited success. Inbreeding depression and self-incompatibility hamper the development of inbred lines in both tetraploid and diploid potatoes, impeding hybrid development efforts. Diploid potatoes have gametophytic self-incompatibility (SI) controlled by S-locus, harboring the male-dependent S-locus F-box (SLF/SFB) and female-dependent Stylar-RNase (S-RNase). Manipulation of these genes using biotechnological tools may lead to loss of self-incompatibility. Self-compatibility can also be achieved by the introgression of S-locus inhibitor (Sli) found in the self-compatible (SC) natural mutants of Solanum chacoense. The introgression of Sli through conventional breeding methods has gained much success. Recently, the Sli gene has been cloned from diverse SC diploid potato lines. It is expressed gametophytically and can overcome the SI in different diploid potato genotypes through conventional breeding or transgenic approaches. Interestingly, it has a 533 bp insertion in its promoter elements, a MITE transposon, making it a SC allele. Sli gene encodes an F-box protein PP2-B10, which consists of an F-box domain linked to a lectin domain. Interaction studies have revealed that the C-terminal region of Sli interacts with most of the StS-RNases, except StS-RNase 3, 9, 10, and 13, while full-length Sli cannot interact with StS-RNase 3, 9, 11, 13, and 14. Thus, Sli may play an essential role in mediating the interactions between pollen and stigma and function like SLFs to interact with and detoxify the S-RNases during pollen tube elongation to confer SC to SI lines. These advancements have opened new avenues in the diploid potato hybrid.
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Affiliation(s)
- Hemant Balasaheb Kardile
- Department of Crop and Soil Science, 109 Crop Science Building, Oregon State University, Corvallis, OR 97331, USA; (H.B.K.); (S.Y.)
- Division of Crop Improvement and Seed Technology, ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | - Solomon Yilma
- Department of Crop and Soil Science, 109 Crop Science Building, Oregon State University, Corvallis, OR 97331, USA; (H.B.K.); (S.Y.)
| | - Vidyasagar Sathuvalli
- Department of Crop and Soil Science, 109 Crop Science Building, Oregon State University, Corvallis, OR 97331, USA; (H.B.K.); (S.Y.)
- Hermiston Agricultural Research, and Extension Center, Hermiston, Department of Crop and Soil Science, Oregon State University, Hermiston, 2121 South 1st Street, Hermiston, OR 97838, USA
- Correspondence:
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16
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Laugerotte J, Baumann U, Sourdille P. Genetic control of compatibility in crosses between wheat and its wild or cultivated relatives. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:812-832. [PMID: 35114064 PMCID: PMC9055826 DOI: 10.1111/pbi.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/26/2021] [Accepted: 01/20/2022] [Indexed: 05/16/2023]
Abstract
In the recent years, the agricultural world has been progressing towards integrated crop protection, in the context of sustainable and reasoned agriculture to improve food security and quality, and to preserve the environment through reduced uses of water, pesticides, fungicides or fertilisers. For this purpose, one possible issue is to cross-elite varieties widely used in fields for crop productions with exotic or wild genetic resources in order to introduce new diversity for genes or alleles of agronomical interest to accelerate the development of new improved cultivars. However, crossing ability (or crossability) often depends on genetic background of the recipient varieties or of the donor, which hampers a larger use of wild resources in breeding programmes of many crops. In this review, we tried to provide a comprehensive summary of genetic factors controlling crossing ability between Triticeae species with a special focus on the crossability between wheat (Triticum aestivum L.) and rye (Secale cereale), which lead to the creation of Triticale (x Triticosecale Wittm.). We also discussed potential applications of newly identified genes or markers associated with crossability for accelerating wheat and Triticale improvement by application of modern genomics technologies in breeding programmes.
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Affiliation(s)
- Julie Laugerotte
- Genetics, Diversity and Ecophysiology of CerealsINRAEUniversité Clermont‐AuvergneClermont‐FerrandFrance
| | - Ute Baumann
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Pierre Sourdille
- Genetics, Diversity and Ecophysiology of CerealsINRAEUniversité Clermont‐AuvergneClermont‐FerrandFrance
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17
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Zhao H, Zhang Y, Zhang H, Song Y, Zhao F, Zhang Y, Zhu S, Zhang H, Zhou Z, Guo H, Li M, Li J, Gao Q, Han Q, Huang H, Copsey L, Li Q, Chen H, Coen E, Zhang Y, Xue Y. Origin, loss, and regain of self-incompatibility in angiosperms. THE PLANT CELL 2022; 34:579-596. [PMID: 34735009 PMCID: PMC8774079 DOI: 10.1093/plcell/koab266] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/26/2021] [Indexed: 06/02/2023]
Abstract
The self-incompatibility (SI) system with the broadest taxonomic distribution in angiosperms is based on multiple S-locus F-box genes (SLFs) tightly linked to an S-RNase termed type-1. Multiple SLFs collaborate to detoxify nonself S-RNases while being unable to detoxify self S-RNases. However, it is unclear how such a system evolved, because in an ancestral system with a single SLF, many nonself S-RNases would not be detoxified, giving low cross-fertilization rates. In addition, how the system has been maintained in the face of whole-genome duplications (WGDs) or lost in other lineages remains unclear. Here we show that SLFs from a broad range of species can detoxify S-RNases from Petunia with a high detoxification probability, suggestive of an ancestral feature enabling cross-fertilization and subsequently modified as additional SLFs evolved. We further show, based on its genomic signatures, that type-1 was likely maintained in many lineages, despite WGD, through deletion of duplicate S-loci. In other lineages, SI was lost either through S-locus deletions or by retaining duplications. Two deletion lineages regained SI through type-2 (Brassicaceae) or type-4 (Primulaceae), and one duplication lineage through type-3 (Papaveraceae) mechanisms. Thus, our results reveal a highly dynamic process behind the origin, maintenance, loss, and regain of SI.
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Affiliation(s)
- Hong Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Yanzhai Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu’e Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Sihui Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing 100101, China
| | - Hongkui Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing 100101, China
| | - Zhendiao Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing 100101, China
| | - Han Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junhui Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qianqian Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaqiu Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Qun Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Chen
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing 100101, China
| | | | - Yijing Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and the Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing 100101, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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18
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Broz AK, Miller CM, Baek YS, Tovar-Méndez A, Acosta-Quezada PG, Riofrío-Cuenca TE, Rusch DB, Bedinger PA. S-RNase Alleles Associated With Self-Compatibility in the Tomato Clade: Structure, Origins, and Expression Plasticity. Front Genet 2021; 12:780793. [PMID: 34938321 PMCID: PMC8685505 DOI: 10.3389/fgene.2021.780793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
The self-incompatibility (SI) system in the Solanaceae is comprised of cytotoxic pistil S-RNases which are countered by S-locus F-box (SLF) resistance factors found in pollen. Under this barrier-resistance architecture, mating system transitions from SI to self-compatibility (SC) typically result from loss-of-function mutations in genes encoding pistil SI factors such as S-RNase. However, the nature of these mutations is often not well characterized. Here we use a combination of S-RNase sequence analysis, transcript profiling, protein expression and reproductive phenotyping to better understand different mechanisms that result in loss of S-RNase function. Our analysis focuses on 12 S-RNase alleles identified in SC species and populations across the tomato clade. In six cases, the reason for gene dysfunction due to mutations is evident. The six other alleles potentially encode functional S-RNase proteins but are typically transcriptionally silenced. We identified three S-RNase alleles which are transcriptionally silenced under some conditions but actively expressed in others. In one case, expression of the S-RNase is associated with SI. In another case, S-RNase expression does not lead to SI, but instead confers a reproductive barrier against pollen tubes from other tomato species. In the third case, expression of S-RNase does not affect self, interspecific or inter-population reproductive barriers. Our results indicate that S-RNase expression is more dynamic than previously thought, and that changes in expression can impact different reproductive barriers within or between natural populations.
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Affiliation(s)
- Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Christopher M Miller
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - You Soon Baek
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, United States
| | - Patricia A Bedinger
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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19
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Harkness A, Brandvain Y. Non-self recognition-based self-incompatibility can alternatively promote or prevent introgression. THE NEW PHYTOLOGIST 2021; 231:1630-1643. [PMID: 33533069 DOI: 10.1111/nph.17249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Self-incompatibility alleles (S-alleles), which prevent self-fertilisation in plants, have historically been expected to benefit from negative frequency-dependent selection and invade when introduced to a new population through gene flow. However, the most taxonomically widespread form of self-incompatibility, the ribonuclease-based system ancestral to the core eudicots, functions through collaborative non-self recognition, which can affect both short-term patterns of gene flow and the long-term process of S-allele diversification. We analysed a model of S-allele evolution in two populations connected by migration, focussing on comparisons among the fates of S-alleles initially unique to each population and those shared among populations. We found that both shared and unique S-alleles from the population with more unique S-alleles were usually fitter compared with S-alleles from the population with fewer S-alleles. Resident S-alleles often became extinct and were replaced by migrant S-alleles, although this outcome could be averted by pollen limitation or biased migration. Collaborative non-self recognition will usually either result in the whole-sale replacement of S-alleles from one population with those from another or else disfavour introgression of S-alleles altogether.
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Affiliation(s)
- Alexander Harkness
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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20
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Ma L, Zhang C, Zhang B, Tang F, Li F, Liao Q, Tang D, Peng Z, Jia Y, Gao M, Guo H, Zhang J, Luo X, Yang H, Gao D, Lucas WJ, Li C, Huang S, Shang Y. A nonS-locus F-box gene breaks self-incompatibility in diploid potatoes. Nat Commun 2021; 12:4142. [PMID: 34230469 PMCID: PMC8260799 DOI: 10.1038/s41467-021-24266-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Potato is the third most important staple food crop. To address challenges associated with global food security, a hybrid potato breeding system, aimed at converting potato from a tuber-propagated tetraploid crop into a seed-propagated diploid crop through crossing inbred lines, is under development. However, given that most diploid potatoes are self-incompatible, this represents a major obstacle which needs to be addressed in order to develop inbred lines. Here, we report on a self-compatible diploid potato, RH89-039-16 (RH), which can efficiently induce a mating transition from self-incompatibility to self-compatibility, when crossed to self-incompatible lines. We identify the S-locusinhibitor (Sli) gene in RH, capable of interacting with multiple allelic variants of the pistil-specific S-ribonucleases (S-RNases). Further, Sli gene functions like a general S-RNase inhibitor, to impart SC to RH and other self-incompatible potatoes. Discovery of Sli now offers a path forward for the diploid hybrid breeding program. Diploid potatoes are typically self-incompatible, complicating efforts to breed diploid cultivars. Here the authors report map-based cloning of the S-locus inhibitor (Sli) gene in potato which encodes a non S-locus F-box protein that is expressed in pollen and can functions like a general S-RNase inhibitor to overcome self-incompatibility.
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Affiliation(s)
- Ling Ma
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Zhang
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Fei Tang
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Futing Li
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Die Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhen Peng
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Meng Gao
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jinzhe Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuming Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiqin Yang
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Dongli Gao
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - William J Lucas
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Canhui Li
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Yi Shang
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China.
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21
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Broz AK, Simpson-Van Dam A, Tovar-Méndez A, Hahn MW, McClure B, Bedinger PA. Spread of self-compatibility constrained by an intrapopulation crossing barrier. THE NEW PHYTOLOGIST 2021; 231:878-891. [PMID: 33864700 DOI: 10.1111/nph.17400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Mating system transitions from self-incompatibility (SI) to self-compatibility (SC) are common in plants. In the absence of high levels of inbreeding depression, SC alleles are predicted to spread due to transmission advantage and reproductive assurance. We characterized mating system and pistil-expressed SI factors in 20 populations of the wild tomato species Solanum habrochaites from the southern half of the species range. We found that a single SI to SC transition is fixed in populations south of the Rio Chillon valley in central Peru. In these populations, SC correlated with the presence of the hab-6 S-haplotype that encodes a low activity S-RNase protein. We identified a single population segregating for SI/SC and hab-6. Intrapopulation crosses showed that hab-6 typically acts in the expected codominant fashion to confer SC. However, we found one specific S-haplotype (hab-10) that consistently rejects pollen of the hab-6 haplotype, and results in SI hab-6/hab-10 heterozygotes. We suggest that the hab-10 haplotype could act as a genetic mechanism to stabilize mixed mating in this population by presenting a disadvantage for the hab-6 haplotype. This barrier may represent a mechanism allowing for the persistence of SI when an SC haplotype appears in or invades a population.
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Affiliation(s)
- Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | | | | | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Bruce McClure
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Patricia A Bedinger
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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22
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Vekemans X, Castric V, Hipperson H, Müller NA, Westerdahl H, Cronk Q. Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility. Mol Ecol 2021; 30:6072-6086. [PMID: 34137092 PMCID: PMC9290700 DOI: 10.1111/mec.16020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022]
Abstract
Whole‐genome sequencing of non‐model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data‐handling. Three such regions are the major histocompatibility complex (MHC), sex‐determining regions (SDRs) and the plant self‐incompatibility locus (S‐locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short‐read sequences against multiple alternative references improves genotyping comprehensiveness at the S‐locus thereby contributing to more accurate assessments of allelic frequencies. Long‐read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S‐locus haplotypes. These advances are adding value to short‐read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.
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Affiliation(s)
| | | | - Helen Hipperson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Helena Westerdahl
- Molecular Ecology and Evolution Laboratory, Department of Biology, Lund University, Lund, Sweden
| | - Quentin Cronk
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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23
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Abstract
Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.
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24
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Qin X, Chetelat RT. Ornithine decarboxylase genes contribute to S-RNase-independent pollen rejection. PLANT PHYSIOLOGY 2021; 186:452-468. [PMID: 33576789 PMCID: PMC8154068 DOI: 10.1093/plphys/kiab062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/23/2021] [Indexed: 05/14/2023]
Abstract
Unilateral incompatibility (UI) manifests as pollen rejection in the pistil, typically when self-incompatible (SI) species are pollinated by self-compatible (SC) relatives. In the Solanaceae, UI occurs when pollen lack resistance to stylar S-RNases, but other, S-RNase-independent mechanisms exist. Pistils of the wild tomato Solanum pennellii LA0716 (SC) lack S-RNase yet reject cultivated tomato (Solanum lycopersicum, SC) pollen. In this cross, UI results from low pollen expression of a farnesyl pyrophosphate synthase gene (FPS2) in S. lycopersicum. Using pollen from fps2-/- loss-of-function mutants in S. pennellii, we identified a pistil factor locus, ui3.1, required for FPS2-based pollen rejection. We mapped ui3.1 to an interval containing 108 genes situated on the IL 3-3 introgression. This region includes a cluster of ornithine decarboxylase (ODC2) genes, with four copies in S. pennellii, versus one in S. lycopersicum. Expression of ODC2 transcript was 1,034-fold higher in S. pennellii than in S. lycopersicum styles. Pistils of odc2-/- knockout mutants in IL 3-3 or S. pennellii fail to reject fps2 pollen and abolish transmission ratio distortion (TRD) associated with FPS2. Pollen of S. lycopersicum express low levels of FPS2 and are compatible on IL 3-3 pistils, but incompatible on IL 12-3 × IL 3-3 hybrids, which express both ODC2 and ui12.1, a locus thought to encode the SI proteins HT-A and HT-B. TRD observed in F2 IL 12-3 × IL 3-3 points to additional ODC2-interacting pollen factors on both chromosomes. Thus, ODC2 genes contribute to S-RNase independent UI and interact genetically with ui12.1 to strengthen pollen rejection.
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Affiliation(s)
- Xiaoqiong Qin
- Department of Plant Sciences (ms #3), University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Roger T Chetelat
- Department of Plant Sciences (ms #3), University of California, Davis, One Shields Avenue, Davis, California 95616
- Author for communication:
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25
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Fernandez i Marti A, Castro S, DeJong TM, Dodd RS. Evaluation of the S-locus in Prunus domestica, characterization, phylogeny and 3D modelling. PLoS One 2021; 16:e0251305. [PMID: 33983990 PMCID: PMC8118244 DOI: 10.1371/journal.pone.0251305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Self-compatibility has become the primary objective of most prune (Prunus domestica) breeding programs in order to avoid the problems related to the gametophytic self-incompatibility (GSI) system present in this crop. GSI is typically under the control of a specific locus., known as the S-locus., which contains at least two genes. The first gene encodes glycoproteins with RNase activity in the pistils., and the second is an SFB gene expressed in the pollen. There is limited information on genetics of SI/SC in prune and in comparison., with other Prunus species, cloning., sequencing and discovery of different S-alleles is very scarce. Clear information about S-alleles can be used for molecular identification and characterization of the S-haplotypes. We determined the S-alleles of 36 cultivars and selections using primers that revealed 17 new alleles. In addition, our study describes for the first time the association and design of a molecular marker for self-compatibility in P. domestica. Our phylogenetic tree showed that the S-alleles are spread across the phylogeny, suggesting that like previous alleles detected in the Rosaceae., they were of trans-specific origin. We provide for the first time 3D models for the P. domestica SI RNase alleles as well as in other Prunus species, including P. salicina (Japanese plum), P. avium (cherry), P. armeniaca (apricot), P. cerasifera and P. spinosa.
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Affiliation(s)
- Angel Fernandez i Marti
- Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
- * E-mail:
| | - Sarah Castro
- Plant Science, University of California, Davis, California, United States of America
| | - Theodore M. DeJong
- Plant Science, University of California, Davis, California, United States of America
| | - Richard S. Dodd
- Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
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26
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Zakharova EV, Timofeeva GV, Fateev AD, Kovaleva LV. Caspase-like proteases and the phytohormone cytokinin as determinants of S-RNAse-based self-incompatibility-induced PCD in Petunia hybrida L. PROTOPLASMA 2021; 258:573-586. [PMID: 33230626 DOI: 10.1007/s00709-020-01587-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/18/2020] [Indexed: 06/11/2023]
Abstract
S-RNAse-based self-incompatibility (SI) in petunia (Petunia hybrida L.) is a self-/non-self-recognition system underlying the pistil rejection of self-pollen. Using different methods, including a TUNEL assay, we have recently shown that programmed cell death (PCD) is a factor of the SI in petunia. Here, we show that the growth of self-incompatible pollen tubes in the style tissues during 4 h after pollination is accompanied by five-sixfold increase in a caspase-like protease (CLP) activity. Exogenous cytokinin (CK) inhibits the pollen tube growth and stimulates the CLP activity in compatible pollen tubes. The actin depolymerization with latrunculin B induces a sharp drop in the CLP activity in self-incompatible pollen tubes and its increase in compatible pollen tubes. Altogether, our results suggest that a CLP is involved in the SI-induced PCD and that CK is a putative activator of the CLP. We assume that CK provokes acidification of the cytosol and thus promotes the activation of a CLP. Thus, our results suggest that CK and CLP are involved in the S-RNAse-based SI-induced PCD in petunia. Potential relations between these components in PCD signaling are discussed.
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Affiliation(s)
| | - Galina V Timofeeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Arseny D Fateev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Lidia V Kovaleva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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27
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Harkness A, Goldberg EE, Brandvain Y. Diversification or Collapse of Self-Incompatibility Haplotypes as a Rescue Process. Am Nat 2021; 197:E89-E109. [DOI: 10.1086/712424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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28
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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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29
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Florez-Rueda AM, Scharmann M, Roth M, Städler T. Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages. FRONTIERS IN PLANT SCIENCE 2021; 12:624442. [PMID: 33815438 PMCID: PMC8018279 DOI: 10.3389/fpls.2021.624442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.
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30
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Wu L, Williams JS, Sun L, Kao TH. Sequence analysis of the Petunia inflata S-locus region containing 17 S-Locus F-Box genes and the S-RNase gene involved in self-incompatibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1348-1368. [PMID: 33048387 DOI: 10.1111/tpj.15005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Self-incompatibility in Petunia is controlled by the polymorphic S-locus, which contains S-RNase encoding the pistil determinant and 16-20 S-locus F-box (SLF) genes collectively encoding the pollen determinant. Here we sequenced and assembled approximately 3.1 Mb of the S2 -haplotype of the S-locus in Petunia inflata using bacterial artificial chromosome clones collectively containing all 17 SLF genes, SLFLike1, and S-RNase. Two SLF pseudogenes and 28 potential protein-coding genes were identified, 20 of which were also found at the S-loci of both the S6a -haplotype of P. inflata and the SN -haplotype of self-compatible Petunia axillaris, but not in the S-locus remnants of self-compatible potato (Solanum tuberosum) and tomato (Solanum lycopersicum). Comparative analyses of S-locus sequences of these three S-haplotypes revealed potential genetic exchange in the flanking regions of SLF genes, resulting in highly similar flanking regions between different types of SLF and between alleles of the same type of SLF of different S-haplotypes. The high degree of sequence similarity in the flanking regions could often be explained by the presence of similar long terminal repeat retroelements, which were enriched at the S-loci of all three S-haplotypes and in the flanking regions of all S-locus genes examined. We also found evidence of the association of transposable elements with SLF pseudogenes. Based on the hypothesis that SLF genes were derived by retrotransposition, we identified 10 F-box genes as putative SLF parent genes. Our results shed light on the importance of non-coding sequences in the evolution of the S-locus, and on possible evolutionary mechanisms of generation, proliferation, and deletion of SLF genes.
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Affiliation(s)
- Lihua Wu
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Justin S Williams
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Linhan Sun
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Teh-Hui Kao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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31
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Clot CR, Polzer C, Prodhomme C, Schuit C, Engelen CJM, Hutten RCB, van Eck HJ. The origin and widespread occurrence of Sli-based self-compatibility in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2713-2728. [PMID: 32514711 PMCID: PMC7419354 DOI: 10.1007/s00122-020-03627-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/26/2020] [Indexed: 05/06/2023]
Abstract
Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k-mer tables. Set algebra and depth filtering were used to identify bulk-specific k-mers. Coupling and repulsion phase k-mers, transmitted from the SC parent, mapped in both populations to the distal end of chromosome 12. Intersection between the k-mers from both populations, in coupling phase with SC, exposed a shared haplotype of approximately 1.5 Mb. Subsequently, we screened read archives of potatoes and wild relatives for k-mers specific to this haplotype. The well-known SC clones US-W4 and RH89-039-16, but surprisingly, also S. chacoense clone M6 were positives. Hence, the S. tuberosum source of SC seems identical to Sli. Furthermore, the candidate region drastically reduced to 333 kb. Haplotype-specific KASP markers were designed and validated on a panel of diploid clones including another renown SC dihaploid G254. Interestingly, k-mers specific to the SC haplotype were common in tetraploid varieties. Pedigree information suggests that the SC haplotype was introduced into tetraploid varieties via the founder "Rough Purple Chili". We show that Sli is surprisingly widespread and indigenous to the cultivated gene pool of potato.
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Affiliation(s)
- Corentin R Clot
- Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Clara Polzer
- Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Aardevo B.V., Johannes Postweg 8, 8308 PB, Nagele, The Netherlands
| | - Charlotte Prodhomme
- Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- La Fédération Nationale des Producteurs de Plants de Pomme de Terre (FN3PT), Agrocampus Ouest, UMR IGEPP, 29260, Ploudaniel, France
| | - Cees Schuit
- Bejo Zaden B.V., Trambaan 1, 1749 CZ, Warmenhuizen, The Netherlands
| | - Christel J M Engelen
- Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Ronald C B Hutten
- Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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Cruz-Zamora Y, Nájera-Torres E, Noriega-Navarro R, Torres-Rodríguez MD, Bernal-Gracida LA, García-Valdés J, Juárez-Díaz JA, Cruz-García F. NaStEP, an essential protein for self-incompatibility in Nicotiana, performs a dual activity as a proteinase inhibitor and as a voltage-dependent channel blocker. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:352-361. [PMID: 32272353 DOI: 10.1016/j.plaphy.2020.03.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/18/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
The S-specific pollen rejection response in Nicotiana depends on the interaction between S-RNase and a suite of SLF proteins. However, the biochemical pathway requires other essential proteins. One of them is the stigmatic protein NaStEP, which belongs to the Kunitz-type protease inhibitor family. Within the pollen tubes, NaStEP is a positive regulator of HT-B stability, likely inhibiting its degradation and, additionally, interacts with NaSIPP, a mitochondrial phosphate carrier. To gain a deeper understanding of the biochemical role of NaStEP in pollen rejection, we evaluated whether the activity of NaStEP as protease inhibitor is specific to a particular type of protease and whether it has the function of a voltage-dependent channel (VDC) blocker. Our findings indicate that, in vitro, NaStEP inhibits a subtilisin-like protease in an irreversible manner, but not other proteases, such as thermolysin and papain. Furthermore, we found that subtilisin processes the native NaStEP (24 kDa) into two lower molecular weight peptides of 21 and 14 kDa. Moreover, when we incubated NaStEP along with Xenopus leavis oocytes expressing the voltage-dependent potassium channel Kv 1.3, the current was blocked, indicating that NaStEP acts as a VDC blocker. These data allow us to propose NaStEP acts as a key molecule with two functions, one protecting HT-B from degradation by inhibiting a subtilisin-like protease and the second one by forming a complex with a mitochondrial VDC that could destabilize the mitochondria to trigger cell death, which would reinforce S-specific pollen rejection in Nicotiana.
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Affiliation(s)
- Y Cruz-Zamora
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - E Nájera-Torres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - R Noriega-Navarro
- Departamento de Química Analítica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - M D Torres-Rodríguez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - L A Bernal-Gracida
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - J García-Valdés
- Departamento de Química Analítica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - J A Juárez-Díaz
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico
| | - F Cruz-García
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Mx, 04510, Mexico.
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Jewell CP, Zhang SV, Gibson MJS, Tovar-Méndez A, McClure B, Moyle LC. Intraspecific Genetic Variation Underlying Postmating Reproductive Barriers between Species in the Wild Tomato Clade (Solanum sect. Lycopersicon). J Hered 2020; 111:216-226. [PMID: 32072169 DOI: 10.1093/jhered/esaa003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/11/2020] [Indexed: 12/29/2022] Open
Abstract
A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated with this variation in UI, but the mechanistic connection between these intra- and inter-specific pollen rejection behaviors is poorly understood in most instances. We generated an F2 population between SI and SC genotypes of a single species, Solanum pennellii, to examine the genetic basis of intraspecific variation in UI against other species, and to determine whether loci underlying SI are genetically associated with this variation. We found that F2 individuals vary in the rate at which UI rejection occurs. One large effect QTL detected for this trait co-localized with the SI-determining S-locus. Moreover, individuals that expressed S-RNase-the S-locus protein involved in SI pollen rejection-in their styles had much more rapid UI responses compared with those without S-RNase protein. Our analysis shows that intraspecific variation at mate choice loci-in this case at loci that prevent self-fertilization-can contribute to variation in the expression of interspecific isolation, including postmating prezygotic barriers. Understanding the nature of such intraspecific variation can provide insight into the accumulation of these barriers between diverging lineages.
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Affiliation(s)
| | - Simo V Zhang
- Department of Biology, Indiana University, Bloomington, IN
| | | | | | - Bruce McClure
- Department of Biochemistry, University of Missouri, Columbia, MO
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN
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34
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Jewell CP, Zhang SV, Gibson MJS, Tovar-Méndez A, McClure B, Moyle LC. Intraspecific Genetic Variation Underlying Postmating Reproductive Barriers between Species in the Wild Tomato Clade (Solanum sect. Lycopersicon). J Hered 2020. [PMID: 32072169 DOI: 10.1101/718544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated with this variation in UI, but the mechanistic connection between these intra- and inter-specific pollen rejection behaviors is poorly understood in most instances. We generated an F2 population between SI and SC genotypes of a single species, Solanum pennellii, to examine the genetic basis of intraspecific variation in UI against other species, and to determine whether loci underlying SI are genetically associated with this variation. We found that F2 individuals vary in the rate at which UI rejection occurs. One large effect QTL detected for this trait co-localized with the SI-determining S-locus. Moreover, individuals that expressed S-RNase-the S-locus protein involved in SI pollen rejection-in their styles had much more rapid UI responses compared with those without S-RNase protein. Our analysis shows that intraspecific variation at mate choice loci-in this case at loci that prevent self-fertilization-can contribute to variation in the expression of interspecific isolation, including postmating prezygotic barriers. Understanding the nature of such intraspecific variation can provide insight into the accumulation of these barriers between diverging lineages.
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Affiliation(s)
| | - Simo V Zhang
- Department of Biology, Indiana University, Bloomington, IN
| | | | | | - Bruce McClure
- Department of Biochemistry, University of Missouri, Columbia, MO
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN
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Liang M, Cao Z, Zhu A, Liu Y, Tao M, Yang H, Xu Q, Wang S, Liu J, Li Y, Chen C, Xie Z, Deng C, Ye J, Guo W, Xu Q, Xia R, Larkin RM, Deng X, Bosch M, Franklin-Tong VE, Chai L. Evolution of self-compatibility by a mutant S m-RNase in citrus. NATURE PLANTS 2020; 6:131-142. [PMID: 32055045 PMCID: PMC7030955 DOI: 10.1038/s41477-020-0597-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 01/08/2020] [Indexed: 05/07/2023]
Abstract
Self-incompatibility (SI) is an important mechanism that prevents self-fertilization and inbreeding in flowering plants. The most widespread SI system utilizes S ribonucleases (S-RNases) and S-locus F-boxes (SLFs) as S determinants. In citrus, SI is ancestral, and Citrus maxima (pummelo) is self-incompatible, while Citrus reticulata (mandarin) and its hybrids are self-compatible (SC). Here, we identify nine highly polymorphic pistil-specific, developmentally expressed S-RNases from pummelo that segregate with S haplotypes in a gametophytic manner and cluster with authentic S-RNases. We provide evidence that these S-RNases function as the female S determinants in citrus. Moreover, we show that each S-RNase is linked to approximately nine SLFs. In an analysis of 117 citrus SLF and SFL-like (SLFL) genes, we reveal that they cluster into 12 types and that the S-RNases and intra-haplotypic SLF and SLFL genes co-evolved. Our data support the notion that citrus have a S locus comprising a S-RNase and several SLFs that fit the non-self-recognition model. We identify a predominant single nucleotide mutation, Sm-RNase, in SC citrus, which provides a 'natural' loss of function. We show that SI-SC transitions due to the Sm-RNase initially arose in mandarin, spreading to its hybrids and became fixed. Identification of an evolutionarily distant new genus utilizing the S-RNase-based SI system, >100 million years separated from the nearest S-RNase family, is a milestone for evolutionary comparative studies.
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Affiliation(s)
- Mei Liang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Zonghong Cao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, P. R. China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, P. R. China
| | - Mengqin Tao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Huayan Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Shaohua Wang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Kunming, P. R. China
| | - Junjie Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Yongping Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Chuanwu Chen
- Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, P. R. China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Chongling Deng
- Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, P. R. China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, P. R. China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
| | - Vernonica E Franklin-Tong
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China.
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Kovaleva LV, Zakharova EV, Timofeeva GV, Andreev IM, Golivanov YY, Bogoutdinova LR, Baranova EN, Khaliluev MR. Aminooxyacetic acid (АОА), inhibitor of 1-aminocyclopropane-1-carboxilic acid (AСС) synthesis, suppresses self-incompatibility-induced programmed cell death in self-incompatible Petunia hybrida L. pollen tubes. PROTOPLASMA 2020; 257:213-227. [PMID: 31410589 DOI: 10.1007/s00709-019-01430-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Self-incompatibility (SI) is genetically determined reproductive barrier preventing inbreeding and thereby providing the maintenance of plant species diversity. At present, active studies of molecular bases of SI mechanisms are underway. S-RNAse-based SI in Petunia hybrida L. is a self-/non-self recognition system that allows the pistil to reject self pollen and to accept non-self pollen for outcrossing. In the present work, using fluorescent methods including the TUNEL method allowed us to reveal the presence of markers of programmed cell death (PCD), such as DNA fragmentation, in growing in vivo petunia pollen tubes during the passage of the SI reaction. The results of statistical analysis reliably proved that PCD is the factor of S-RNAse-based SI. It was found that preliminary treatment before self-pollination of stigmas of petunia self-incompatible line with aminooxyacetic acid (AOA), inhibitor of ACC synthesis, led to stimulation of pollen tubes growth when the latter did not exhibit any hallmarks of PCD. These data argue in favor of assumption that ethylene controls the passage of PCD in incompatible pollen tubes in the course of S-RNAse-based SI functioning. The involvement of the hormonal regulation in SI mechanism in P. hybrida L. is the finding observed by us for the first time.
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Affiliation(s)
- L V Kovaleva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya st. 35, Moscow, 127276, Russia.
| | - E V Zakharova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya st. 42, Moscow, 127550, Russia
- Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya st. 49, Moscow, 127550, Russia
| | - G V Timofeeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya st. 35, Moscow, 127276, Russia
| | - I M Andreev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya st. 35, Moscow, 127276, Russia
| | - Ya Yu Golivanov
- Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya st. 49, Moscow, 127550, Russia
| | - L R Bogoutdinova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya st. 42, Moscow, 127550, Russia
- Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya st. 49, Moscow, 127550, Russia
| | - E N Baranova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya st. 42, Moscow, 127550, Russia
| | - M R Khaliluev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya st. 42, Moscow, 127550, Russia
- Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya st. 49, Moscow, 127550, Russia
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37
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Muñoz-Sanz JV, Zuriaga E, Cruz-García F, McClure B, Romero C. Self-(In)compatibility Systems: Target Traits for Crop-Production, Plant Breeding, and Biotechnology. FRONTIERS IN PLANT SCIENCE 2020; 11:195. [PMID: 32265945 PMCID: PMC7098457 DOI: 10.3389/fpls.2020.00195] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/10/2020] [Indexed: 05/13/2023]
Abstract
Self-incompatibility (SI) mechanisms prevent self-fertilization in flowering plants based on specific discrimination between self- and non-self pollen. Since this trait promotes outcrossing and avoids inbreeding it is a widespread mechanism of controlling sexual plant reproduction. Growers and breeders have effectively exploited SI as a tool for manipulating domesticated crops for thousands of years. However, only within the past thirty years have studies begun to elucidate the underlying molecular features of SI. The specific S-determinants and some modifier factors controlling SI have been identified in the sporophytic system exhibited by Brassica species and in the two very distinct gametophytic systems present in Papaveraceae on one side and in Solanaceae, Rosaceae, and Plantaginaceae on the other. Molecular level studies have enabled SI to SC transitions (and vice versa) to be intentionally manipulated using marker assisted breeding and targeted approaches based on transgene integration, silencing, and more recently CRISPR knock-out of SI-related factors. These scientific advances have, in turn, provided a solid basis to implement new crop production and plant breeding practices. Applications of self-(in)compatibility include widely differing objectives such as crop yield and quality improvement, marker-assisted breeding through SI genotyping, and development of hybrids for overcoming intra- and interspecific reproductive barriers. Here, we review scientific progress as well as patented applications of SI, and also highlight future prospects including further elucidation of SI systems, deepening our understanding of SI-environment relationships, and new perspectives on plant self/non-self recognition.
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Affiliation(s)
| | - Elena Zuriaga
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Felipe Cruz-García
- Departmento de Bioquímica, Facultad de Química, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Bruce McClure
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Carlos Romero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat Politécnica de València (UPV), Valencia, Spain
- *Correspondence: Carlos Romero,
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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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Matsumoto D, Tao R. Recognition of S-RNases by an S locus F-box like protein and an S haplotype-specific F-box like protein in the Prunus-specific self-incompatibility system. PLANT MOLECULAR BIOLOGY 2019; 100:367-378. [PMID: 30937702 DOI: 10.1007/s11103-019-00860-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
S-RNase was demonstrated to be predominantly recognized by an S locus F-box-like protein and an S haplotype-specific F-box-like protein in compatible pollen tubes of sweet cherry. Self-incompatibility (SI) is a reproductive barrier that rejects self-pollen and inhibits self-fertilization to promote outcrossing. In Solanaceae and Rosaceae, S-RNase-based gametophytic SI (GSI) comprises S-RNase and F-box protein(s) as the pistil and pollen S determinants, respectively. Compatible pollen tubes are assumed to detoxify the internalized cytotoxic S-RNases to maintain growth. S-RNase detoxification is conducted by the Skp1-cullin1-F-box protein complex (SCF) formed by pollen S determinants, S locus F-box proteins (SLFs), in Solanaceae. In Prunus, the general inhibitor (GI), but not pollen S determinant S haplotype-specific F-box protein (SFB), is hypothesized to detoxify S-RNases. Recently, SLF-like proteins 1-3 (SLFL1-3) were suggested as GI candidates, although it is still possible that other proteins function predominantly in GI. To identify the other GI candidates, we isolated four other pollen-expressed SLFL and SFB-like (SFBL) proteins PavSLFL6, PavSLFL7A, PavSFBL1, and PavSFBL2 in sweet cherry. Binding assays with four PavS-RNases indicated that PavSFBL2 bound to PavS1, 6-RNase while the others bound to nothing. PavSFBL2 was confirmed to form an SCF complex in vitro. A co-immunoprecipitation assay using the recombinant PavS6-RNase as bait against pollen extracts and a mass spectrometry analysis identified the SCF complex components of PavSLFLs and PavSFBL2, M-locus-encoded glutathione S-transferase (MGST), DnaJ-like protein, and other minor proteins. These results suggest that SLFLs and SFBLs could act as predominant GIs in Prunus-specific S-RNase-based GSI.
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Affiliation(s)
- Daiki Matsumoto
- Laboratory of Pomology, 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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40
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Guo H, Halitschke R, Wielsch N, Gase K, Baldwin IT. Mate Selection in Self-Compatible Wild Tobacco Results from Coordinated Variation in Homologous Self-Incompatibility Genes. Curr Biol 2019; 29:2020-2030.e5. [PMID: 31178322 DOI: 10.1016/j.cub.2019.05.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/16/2019] [Accepted: 05/17/2019] [Indexed: 11/22/2022]
Abstract
In flowering plants, intraspecific mate preference is frequently related to mating systems: the rejection of self pollen in self-incompatible (SI) plants that prevents inbreeding is one of the best described examples. However, in other mating systems, more nuanced patterns of pollen rejection occur. In the self-compatible (SC) Nicotiana attenuata, in which SI is not found and all crosses are compatible, certain pollen genotypes are consistently selected in mixed pollinations. However, the molecular mechanisms of this polyandrous mate selection remain unknown. Style-expressed NaS-like-RNases and pollen-expressed NaSLF-like genes, homologous to SI factors in Solanaceae, were identified and examined for a role in N. attenuata's mate selection. A comparison of two NaS-like-RNases and six NaSLF-like genes among 26 natural accessions revealed specific combinations of co-expression and direct protein-protein interactions. To evaluate their role in mate selection, we silenced the expression of specific NaS-like-RNases and NaSLF-like proteins and conducted diagnostic binary mixed pollinations and mixed pollinations with 14 different non-self pollen donors. Styles expressing particular combinations of NaS-like-RNases selected mates from plants with corresponding NaS-like-RNase expression patterns, while styles lacking NaS-like-RNase expression were non-selective in their fertilizations, which reflected the genotype ratios of pollen mixtures deposited on the stigmas. DNA methylation could account for some of the observed variation in stylar NaS-like-RNase patterns. We conclude that the S-RNase-SLF recognition mechanism plays a central role in polyandrous mate selection in this self-compatible species. These results suggest that after the SI-SC transition, natural variation of SI homologous genes was repurposed to mediate intraspecific mate selection.
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Affiliation(s)
- Han Guo
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, DE-07745 Jena, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, DE-07745 Jena, Germany
| | - Natalie Wielsch
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, DE-07745 Jena, Germany
| | - Klaus Gase
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, DE-07745 Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, DE-07745 Jena, Germany.
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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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Li M, Zhang D, Gao Q, Luo Y, Zhang H, Ma B, Chen C, Whibley A, Zhang Y, Cao Y, Li Q, Guo H, Li J, Song Y, Zhang Y, Copsey L, Li Y, Li X, Qi M, Wang J, Chen Y, Wang D, Zhao J, Liu G, Wu B, Yu L, Xu C, Li J, Zhao S, Zhang Y, Hu S, Liang C, Yin Y, Coen E, Xue Y. Genome structure and evolution of Antirrhinum majus L. NATURE PLANTS 2019; 5:174-183. [PMID: 30692677 PMCID: PMC6784882 DOI: 10.1038/s41477-018-0349-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/14/2018] [Indexed: 05/18/2023]
Abstract
Snapdragon (Antirrhinum majus L.), a member of the Plantaginaceae family, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a near-complete genome assembly of A. majus cultivar JI7 (A. majus cv.JI7) comprising 510 Megabases (Mb) of genomic sequence and containing 37,714 annotated protein-coding genes. Scaffolds covering 97.12% of the assembled genome were anchored on eight chromosomes. Comparative and evolutionary analyses revealed that a whole-genome duplication event occurred in the Plantaginaceae around 46-49 million years ago (Ma). We also uncovered the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility, identifying a unique duplication of TCP family genes dated to around 46-49 Ma and reconstructing a near-complete ψS-locus of roughly 2 Mb. The genome sequence obtained in this study not only provides a representative genome sequenced from the Plantaginaceae but also brings the popular plant model system of Antirrhinum into the genomic age.
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Affiliation(s)
- Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongfen Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Luo
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | | | | | - Yu'e Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yinghao Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qun Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Han Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junhui Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanzhai Song
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiuxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ming Qi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Wang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | | | | | | - Bin Wu
- BGI-Shenzhen, Shenzhen, China
| | - Lili Yu
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, China.
| | | | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
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44
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Li M, Zhang D, Gao Q, Luo Y, Zhang H, Ma B, Chen C, Whibley A, Zhang Y, Cao Y, Li Q, Guo H, Li J, Song Y, Zhang Y, Copsey L, Li Y, Li X, Qi M, Wang J, Chen Y, Wang D, Zhao J, Liu G, Wu B, Yu L, Xu C, Li J, Zhao S, Zhang Y, Hu S, Liang C, Yin Y, Coen E, Xue Y. Genome structure and evolution of Antirrhinum majus L. NATURE PLANTS 2019. [PMID: 30692677 DOI: 10.1038/s41477-018-0349-349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Snapdragon (Antirrhinum majus L.), a member of the Plantaginaceae family, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a near-complete genome assembly of A. majus cultivar JI7 (A. majus cv.JI7) comprising 510 Megabases (Mb) of genomic sequence and containing 37,714 annotated protein-coding genes. Scaffolds covering 97.12% of the assembled genome were anchored on eight chromosomes. Comparative and evolutionary analyses revealed that a whole-genome duplication event occurred in the Plantaginaceae around 46-49 million years ago (Ma). We also uncovered the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility, identifying a unique duplication of TCP family genes dated to around 46-49 Ma and reconstructing a near-complete ψS-locus of roughly 2 Mb. The genome sequence obtained in this study not only provides a representative genome sequenced from the Plantaginaceae but also brings the popular plant model system of Antirrhinum into the genomic age.
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Affiliation(s)
- Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongfen Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Luo
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | | | | | - Yu'e Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yinghao Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qun Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Han Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junhui Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanzhai Song
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiuxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ming Qi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Wang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | | | | | | - Bin Wu
- BGI-Shenzhen, Shenzhen, China
| | - Lili Yu
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, China.
| | | | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering and National Center of Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
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45
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Enciso-Rodriguez F, Manrique-Carpintero NC, Nadakuduti SS, Buell CR, Zarka D, Douches D. Overcoming Self-Incompatibility in Diploid Potato Using CRISPR-Cas9. FRONTIERS IN PLANT SCIENCE 2019; 10:376. [PMID: 31001300 PMCID: PMC6454193 DOI: 10.3389/fpls.2019.00376] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/12/2019] [Indexed: 05/19/2023]
Abstract
Potato breeding can be redirected to a diploid inbred/F1 hybrid variety breeding strategy if self-compatibility can be introduced into diploid germplasm. However, the majority of diploid potato clones (Solanum spp.) possess gametophytic self-incompatibility that is primarily controlled by a single multiallelic locus called the S-locus which is composed of tightly linked genes, S-RNase (S-locus RNase) and multiple SLFs (S-locus F-box proteins), which are expressed in the style and pollen, respectively. Using S-RNase genes known to function in the Solanaceae gametophytic SI mechanism, we identified S-RNase alleles with flower-specific expression in two diploid self-incompatible potato lines using genome resequencing data. Consistent with the location of the S-locus in potato, we genetically mapped the S-RNase gene using a segregating population to a region of low recombination within the pericentromere of chromosome 1. To generate self-compatible diploid potato lines, a dual single-guide RNA (sgRNA) strategy was used to target conserved exonic regions of the S-RNase gene and generate targeted knockouts (KOs) using a Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (Cas9) approach. Self-compatibility was achieved in nine S-RNase KO T0 lines which contained bi-allelic and homozygous deletions/insertions in both genotypes, transmitting self compatibility to T1 progeny. This study demonstrates an efficient approach to achieve stable, consistent self-compatibility through S-RNase KO for use in diploid potato breeding approaches.
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Affiliation(s)
- Felix Enciso-Rodriguez
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - Satya Swathi Nadakuduti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
- AgBioResearch, Michigan State University, East Lansing, MI, United States
| | - Daniel Zarka
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - David Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- AgBioResearch, Michigan State University, East Lansing, MI, United States
- *Correspondence: David Douches,
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46
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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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Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Nonself-Recognition System. Genetics 2018; 209:861-883. [PMID: 29716955 DOI: 10.1534/genetics.118.300748] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/28/2018] [Indexed: 11/18/2022] Open
Abstract
Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self-recognition (SR) and nonself-recognition (NSR). Most work has focused on diversification within SR systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic NSR [SRNase/S Locus F-box (SLF)] SI system. For this model, the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and, in general, is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate-to-high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a NSR SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a recognition system common in flowering plants.
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Chen Q, Meng D, Gu Z, Li W, Yuan H, Duan X, Yang Q, Li Y, Li T. SLFL Genes Participate in the Ubiquitination and Degradation Reaction of S-RNase in Self-compatible Peach. FRONTIERS IN PLANT SCIENCE 2018; 9:227. [PMID: 29520292 PMCID: PMC5826962 DOI: 10.3389/fpls.2018.00227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/07/2018] [Indexed: 05/23/2023]
Abstract
It has been proved that the gametophytic self-incompatibility (GSI), mainly exists in Rosaceae and Solanaceae, is controlled by S genes, which are two tightly linked genes located at highly polymorphic S-locus: the S-RNase for pistil specificity and the F-box gene (SFB/SLF) for pollen specificity, respectively. However, the roles of those genes in SI of peach are still a subject of extensive debate. In our study, we selected 37 representative varieties according to the evolution route of peach and identified their S genotypes. We cloned pollen determinant genes mutated PperSFB1m, PperSFB2m, PperSFB4m, and normal PperSFB2, and style determinant genes PperS1-RNase, PperS2-RNase, PperS2m-RNase, and PperS4-RNase. The mutated PperSFBs encode truncated SFB proteins due to a fragment insertion. The truncated PperSFBs and normal PperSFB2 interacted with PperS-RNases demonstrated by Y2H. Normal PperSFB2 was divided into four parts: box, box-V1, V1-V2, and HVa-HVb. The box domain of PperSFB2 did not interact with PperS-RNases, both of the box-V1 and V1-V2 had interactions with PperS-RNases, while the hypervariable region of PperSFB2 HVa-HVb only interacted with PperS2-RNase showed by Y2H and BiFC assay. Bioinformatics analysis of peach genome revealed that there were other F-box genes located at S-locus, and of which three F-box genes were specifically expressed in pollen, named as PperSLFL1, PperSLFL2, and PperSLFL3, respectively. In phylogenetic analysis PperSLFLs clustered with Maloideae SFBB genes, and PperSFB genes were clustered into the other group with other SFB genes of Prunus. Protein interaction analysis revealed that the three PperSLFLs interacted with PperSSK1 and PperS-RNases with no allelic specificity. In vitro ubiquitination assay showed that PperSLFLs could tag ubiquitin molecules onto PperS-RNases. The above results suggest that three PperSLFLs are the appropriate candidates for the "general inhibitor," which would inactivate the S-RNases in pollen tubes, involved in the self-incompatibility of peach.
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Qin X, Li W, Liu Y, Tan M, Ganal M, Chetelat RT. A farnesyl pyrophosphate synthase gene expressed in pollen functions in S-RNase-independent unilateral incompatibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:417-430. [PMID: 29206320 DOI: 10.1111/tpj.13796] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 05/25/2023]
Abstract
Multiple independent and overlapping pollen rejection pathways contribute to unilateral interspecific incompatibility (UI). In crosses between tomato species, pollen rejection usually occurs when the female parent is self-incompatible (SI) and the male parent self-compatible (SC) (the 'SI × SC rule'). Additional, as yet unknown, UI mechanisms are independent of self-incompatibility and contribute to UI between SC species or populations. We identified a major quantitative trait locus on chromosome 10 (ui10.1) which affects pollen-side UI responses in crosses between cultivated tomato, Solanum lycopersicum, and Solanum pennelliiLA0716, both of which are SC and lack S-RNase, the pistil determinant of S-specificity in Solanaceae. Here we show that ui10.1 is a farnesyl pyrophosphate synthase gene (FPS2) expressed in pollen. Expression is about 18-fold higher in pollen of S. pennellii than in S. lycopersicum. Pollen with the hypomorphic S. lycopersicum allele is selectively eliminated on pistils of the F1 hybrid, leading to transmission ratio distortion in the F2 progeny. CRISPR/Cas9-generated knockout mutants (fps2) in S. pennelliiLA0716 are self-sterile due to pollen rejection, but mutant pollen is fully functional on pistils of S. lycopersicum. F2 progeny of S. lycopersicum × S. pennellii (fps2) show reversed transmission ratio distortion due to selective elimination of pollen bearing the knockout allele. Overexpression of FPS2 in S. lycopersicum pollen rescues the pollen elimination phenotype. FPS2-based pollen selectivity does not involve S-RNase and has not been previously linked to UI. Our results point to an entirely new mechanism of interspecific pollen rejection in plants.
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Affiliation(s)
- Xiaoqiong Qin
- Department of Plant Sciences (ms #3), One Shields Ave., University of California, Davis, CA, 95616, USA
| | - Wentao Li
- Department of Plant Sciences (ms #3), One Shields Ave., University of California, Davis, CA, 95616, USA
| | - Yang Liu
- Department of Plant Sciences (ms #3), One Shields Ave., University of California, Davis, CA, 95616, USA
| | - Meilian Tan
- Department of Plant Sciences (ms #3), One Shields Ave., University of California, Davis, CA, 95616, USA
| | - Martin Ganal
- Trait Genetics GmbH, Am Schwabeplan 1B, 06466, Gatersleben, Germany
| | - Roger T Chetelat
- Department of Plant Sciences (ms #3), One Shields Ave., University of California, Davis, CA, 95616, USA
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50
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Wu L, Williams JS, Wang N, Khatri WA, San Román D, Kao TH. Use of Domain-Swapping to Identify Candidate Amino Acids Involved in Differential Interactions between Two Allelic Variants of Type-1 S-Locus F-Box Protein and S3-RNase in Petunia inflata. PLANT & CELL PHYSIOLOGY 2018; 59:234-247. [PMID: 29149301 DOI: 10.1093/pcp/pcx176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/11/2017] [Indexed: 06/07/2023]
Abstract
Petunia inflata possesses a self-incompatibility (SI) mechanism, which involves S-RNase and multiple S-locus F-box (SLF) genes at the polymorphic S-locus. For a given S-haplotype, each SLF is thought to interact with some of its non-self S-RNases, but not with its self S-RNase. In this work, we studied an allelic pair of SLF1, S2-SLF1 and S3-SLF1, which differ in 44 amino acids and show differential interactions with S3-RNase. We first used an in vivo transgenic assay to determine whether four chimeric proteins of S2-SLF1 and S3-SLF1, each with one of the three functional domains swapped, interact with S3-RNase. The results narrowed the candidate amino acids for specific interaction of S2-SLF1 with S3-RNase to the 16 in domain FD3. We then examined seven additional chimeric proteins by dividing FD3 into two subdomains and four mini-domains (A, B, C and D). The results further narrowed the candidate amino acids to four in mini-domain A and four in mini-domain D. Molecular modeling of interactions between S3-RNase and S2-SLF1 revealed that three of these eight are at the interaction surface, and all three are conserved in S1-SLF1 and S6a-SLF1, both of which interact with S3-RNase based on the in vivo transgenic assay. Three of the chimeric proteins were used for the in vivo transgenic assay to determine whether FD3 alone contains the amino acids required for S2-SLF1 to interact with S7-RNase and S13-RNase. The results revealed the diversity and complexity of interactions between SLF proteins and S-RNases.
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Affiliation(s)
- Lihua Wu
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Justin S Williams
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ning Wang
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wasi A Khatri
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Daniele San Román
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Teh-Hui Kao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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