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Jay P, Leroy M, Le Poul Y, Whibley A, Arias M, Chouteau M, Joron M. Association mapping of colour variation in a butterfly provides evidence that a supergene locks together a cluster of adaptive loci. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210193. [PMID: 35694756 PMCID: PMC9189503 DOI: 10.1098/rstb.2021.0193] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between sets of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining a landmark-free phenotyping algorithm with multivariate genome-wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We show that the supergene controlling the striking wing pattern polymorphism displayed by this species contains several independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are, however, associated with colour variations only in a subset of morphs where the phenotype is controlled by derived inversion forms, indicating that they were recruited after the formation of the inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Paul Jay
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Manon Leroy
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Yann Le Poul
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Mónica Arias
- CIRAD, UMR PHIM, F-34398 Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, CEDEX 5, 34398 Montpellier, France
| | - Mathieu Chouteau
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France.,LEEISA, USR 63456, Université de Guyane, CNRS, IFREMER, 275 route de Montabo, 797334 Cayenne, French Guiana
| | - Mathieu Joron
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
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2
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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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An Ancient and Eroded Social Supergene Is Widespread across Formica Ants. Curr Biol 2020; 30:304-311.e4. [PMID: 31902719 DOI: 10.1016/j.cub.2019.11.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/10/2019] [Accepted: 11/11/2019] [Indexed: 12/25/2022]
Abstract
Supergenes, clusters of tightly linked genes, play a key role in the evolution of complex adaptive variation [1, 2]. Although supergenes have been identified in many species, we lack an understanding of their origin, evolution, and persistence [3]. Here, we uncover 20-40 Ma of evolutionary history of a supergene associated with polymorphic social organization in Formica ants [4]. We show that five Formica species exhibit homologous divergent haplotypes spanning 11 Mbp on chromosome 3. Despite the supergene's size, only 142 single nucleotide polymorphisms (SNPs) consistently distinguish alternative supergene haplotypes across all five species. These conserved trans-species SNPs are localized in a small number of disjunct clusters distributed across the supergene. This unexpected pattern of divergence indicates that the Formica supergene does not follow standard models of sex chromosome evolution, in which distinct evolutionary strata reflect an expanding region of suppressed recombination [5]. We propose an alternative "eroded strata model" in which clusters of conserved trans-species SNPs represent functionally important areas maintained by selection in the face of rare recombination between ancestral haplotypes. The comparison of whole-genome sequences across 10 additional Formica species reveals that the most conserved region of the supergene contains a transcription factor essential for motor neuron development in Drosophila [6]. The discovery that a very small portion of this large and ancient supergene harbors conserved trans-species SNPs linked to colony social organization suggests that the ancestral haplotypes have been eroded by recombination, with selection preserving differentiation at one or a few genes generating alternative social organization.
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4
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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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5
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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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6
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Wang F, Zhong X, Wang H, Song A, Chen F, Fang W, Jiang J, Teng N. Investigation of Differences in Fertility among Progenies from Self-Pollinated Chrysanthemum. Int J Mol Sci 2018. [PMID: 29533976 PMCID: PMC5877693 DOI: 10.3390/ijms19030832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Most chrysanthemum cultivars are self-incompatible, so it is very difficult to create pure lines that are important in chrysanthemum breeding and theoretical studies. In our previous study, we obtained a self-compatible chrysanthemum cultivar and its self-pollinated seed set was 56.50%. It was interesting that the seed set of its ten progenies ranged from 0% to 37.23%. Examination of the factors causing the differences in the seed set will lead to an improved understanding of chrysanthemum self-incompatibility, and provide valuable information for creating pure lines. Pollen morphology, pollen germination percentage, pistil receptivity and embryo development were investigated using the in vitro culture method, the paraffin section technique, scanning electron microscopy and transmission electron microscopy. Moreover, RNA sequencing and bioinformatics were applied to analyzing the transcriptomic profiles of mature stigmas and anthers. It was found that the self-pollinated seed set of "Q10-33-1①","Q10-33-1③","Q10-33-1④" and "Q10-33-1⑩" were 37.23%, 26.77%, 7.97% and 0%, respectively. The differences in fertility among four progenies were mainly attributable to differences in pollen germination percentage and pistil receptivity. Failure of the seed set in "Q10-33-1⑩" was possibly due to self-incompatibility. In the transcriptomic files, 22 potential stigma S genes and 8 potential pollen S genes were found out.
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Affiliation(s)
- Fan Wang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Xinghua Zhong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
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Qu H, Guan Y, Wang Y, Zhang S. PLC-Mediated Signaling Pathway in Pollen Tubes Regulates the Gametophytic Self-incompatibility of Pyrus Species. FRONTIERS IN PLANT SCIENCE 2017; 8:1164. [PMID: 28729872 PMCID: PMC5498517 DOI: 10.3389/fpls.2017.01164] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 06/16/2017] [Indexed: 05/27/2023]
Abstract
Among the Rosaceae species, the gametophytic self-incompatibility (GSI) is controlled by a single multi-allelic S locus, which is composed of the pistil-S and pollen-S genes. The pistil-S gene encodes a polymorphic ribonuclease (S-RNase), which is essential for identifying self-pollen. However, the S-RNase system has not been fully characterized. In this study, the self-S-RNase inhibited the Ca2+-permeable channel activity at pollen tube apices and the selectively decreased phospholipase C (PLC) activity in the plasma membrane of Pyrus pyrifolia pollen tubes. Self-S-RNase decreased the Ca2+ influx through a PLC-mediated signaling pathway. Phosphatidylinositol-specific PLC has a 26-amino acid insertion in pollen tubes of the 'Jinzhuili' cultivar, which is a spontaneous self-compatible mutant of the 'Yali' cultivar. 'Yali' plants exhibit a typical S-RNase-based GSI. Upon self-pollination, PLC gene expression is significantly higher in 'Jinzhuili' pollen tubes than that in 'Yali' pollen tubes. Moreover, the PLC in pollen tubes can only interact with one of the two types of S-RNase from the style. In the Pyrus x bretschneideri Rehd, the PLC directly interacted with the S7-RNase in the pollen tube, but not with the S34-RNase. Collectively, our results reveal that the effects of S-RNase on PLC activity are required for S-specific pollen rejection, and that PLC-IP3 participates in the self-incompatibility reaction of Pyrus species.
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Affiliation(s)
- Haiyong Qu
- College of Horticulture, Qingdao Agricultural UniversityQingdao, China
| | - Yaqin Guan
- College of Horticulture, Qingdao Agricultural UniversityQingdao, China
| | - Yongzhang Wang
- College of Horticulture, Qingdao Agricultural UniversityQingdao, China
| | - Shaolin Zhang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
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8
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Hybrid Sterility in Rice (Oryza sativa L.) Involves the Tetratricopeptide Repeat Domain Containing Protein. Genetics 2016; 203:1439-51. [PMID: 27182946 DOI: 10.1534/genetics.115.183848] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/20/2016] [Indexed: 11/18/2022] Open
Abstract
Intersubspecific hybrid sterility is a common form of reproductive isolation in rice (Oryza sativa L.), which significantly hampers the utilization of heterosis between indica and japonica varieties. Here, we elucidated the mechanism of S7, which specially causes Aus-japonica/indica hybrid female sterility, through cytological and genetic analysis, map-based cloning, and transformation experiments. Abnormal positioning of polar nuclei and smaller embryo sac were observed in F1 compared with male and female parents. Female gametes carrying S7(cp) and S7(i) were aborted in S7(ai)/S7(cp) and S7(ai)/S7(i), respectively, whereas they were normal in both N22 and Dular possessing a neutral allele, S7(n) S7 was fine mapped to a 139-kb region in the centromere region on chromosome 7, where the recombination was remarkably suppressed due to aggregation of retrotransposons. Among 16 putative open reading frames (ORFs) localized in the mapping region, ORF3 encoding a tetratricopeptide repeat domain containing protein was highly expressed in the pistil. Transformation experiments demonstrated that ORF3 is the candidate gene: downregulated expression of ORF3 restored spikelet fertility and eliminated absolutely preferential transmission of S7(ai) in heterozygote S7(ai)/S7(cp); sterility occurred in the transformants Cpslo17-S7(ai) Our results may provide implications for overcoming hybrid embryo sac sterility in intersubspecific hybrid rice and utilization of hybrid heterosis for cultivated rice improvement.
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9
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Abstract
Understanding the molecular underpinnings of evolutionary adaptations is a central focus of modern evolutionary biology. Recent studies have uncovered a panoply of complex phenotypes, including locally adapted ecotypes and cryptic morphs, divergent social behaviours in birds and insects, as well as alternative metabolic pathways in plants and fungi, that are regulated by clusters of tightly linked loci. These 'supergenes' segregate as stable polymorphisms within or between natural populations and influence ecologically relevant traits. Some supergenes may span entire chromosomes, because selection for reduced recombination between a supergene and a nearby locus providing additional benefits can lead to locus expansions with dynamics similar to those known for sex chromosomes. In addition to allowing for the co-segregation of adaptive variation within species, supergenes may facilitate the spread of complex phenotypes across species boundaries. Application of new genomic methods is likely to lead to the discovery of many additional supergenes in a broad range of organisms and reveal similar genetic architectures for convergently evolved phenotypes.
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Affiliation(s)
- Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Romain Libbrecht
- Laboratory of Insect Social Evolution, Rockefeller University, New York 10065, USA
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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10
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Sakai S, Wakoh H. Initial invasion of gametophytic self-incompatibility alleles in the absence of tight linkage between pollen and pistil S alleles. Am Nat 2014; 184:248-57. [PMID: 25058284 DOI: 10.1086/676942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In homomorphic self-incompatibility (SI) systems of plants, the loci controlling the pollen and pistil types are tightly linked, and this prevents the generation of compatible combinations of alleles expressing pollen and pistil types, which would result in self-fertilization. We modeled the initial invasion of the first pollen and pistil alleles in gametophytic SI to determine whether these alleles can stably coexist in a population without tight linkage. We assume pollen and pistil loci each carry an incompatibility allele S and an allele without an incompatibility function N. We assume that pollen with an S allele are incompatible with pistils carrying S alleles, whereas other crosses are compatible. Ovules in pistils carrying an S allele suffer viability costs because recognition consumes resources. We found that the cost of carrying a pistil S allele allows pollen and pistil S alleles to coexist in a stable equilibrium if linkage is partial. This occurs because parents that carry pistil S alleles but are homozygous for pollen N alleles cannot avoid self-fertilization; however, they suffer viability costs. Hence, pollen N alleles are selected again. When pollen and pistil S alleles can coexist in a polymorphic equilibrium, selection will favor tighter linkage.
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Affiliation(s)
- Satoki Sakai
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University Aoba, Sendai 980-8578, Japan
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Gonthier L, Blassiau C, Mörchen M, Cadalen T, Poiret M, Hendriks T, Quillet MC. High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2103-21. [PMID: 23689744 DOI: 10.1007/s00122-013-2122-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/08/2013] [Indexed: 05/14/2023]
Abstract
High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.
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Affiliation(s)
- Lucy Gonthier
- Université de Lille, UMR INRA-Lille 1 1281, Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d'Ascq, France
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12
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Wang S, Kakui, H, Kikuchi S, Koba T, Sassa H. Interhaplotypic heterogeneity and heterochromatic features may contribute to recombination suppression at the S locus in apple (Malusxdomestica). JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4983-90. [PMID: 22760470 PMCID: PMC3428002 DOI: 10.1093/jxb/ers176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gametophytic self-incompatibility (GSI) is controlled by a complex S locus containing the pistil determinant S-RNase and pollen determinant SFB/SLF. Tight linkage of the pistil and pollen determinants is necessary to guarantee the self-incompatibility (SI) function. However, multiple probable pollen determinants of apple and Japanese pear, SFBBs (S locus F-box brothers), exist in each S haplotype, and how these multiple genes maintain the SI function remains unclear. It is shown here by high-resolution fluorescence in situ hybridization (FISH) that SFBB genes of the apple S9 haplotype are physically linked to the S9-RNase gene, and the S locus is located in the subtelomeric region. FISH analyses also determined the relative order of SFBB genes and S-RNase in the S9 haplotype, and showed that gene order differs between the S9 and S3 haplotypes. Furthermore, it is shown that the apple S locus is located in a knob-like large heterochromatin block where DNA is highly methylated. It is proposed that interhaplotypic heterogeneity and the heterochromatic nature of the S locus help to suppress recombination at the S locus in apple.
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Affiliation(s)
- Sanhong Wang
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
- Department of Horticulture, Nanjing Agricultural University210095, NanjingChina
| | - Hiroyuki Kakui,
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
| | - Takato Koba
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba UniversityMatsudo, Chiba 271-8510Japan
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Fan C, Walling JG, Zhang J, Hirsch CD, Jiang J, Wing RA. Conservation and purifying selection of transcribed genes located in a rice centromere. THE PLANT CELL 2011; 23:2821-30. [PMID: 21856794 PMCID: PMC3180794 DOI: 10.1105/tpc.111.085605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recombination is strongly suppressed in centromeric regions. In chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. Surprisingly, the centromere of chromosome8 (Cen8) of rice (Oryza sativa) contains several transcribed genes. However, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in Cen8. Sequencing of orthologous Cen8 regions from two additional Oryza species, Oryza glaberrima and Oryza brachyantha, which diverged from O. sativa 1 and 10 million years ago, respectively, revealed a set of seven transcribed Cen8 genes conserved across all three species. Chromatin immunoprecipitation analysis with the centromere-specific histone CENH3 confirmed that the sequenced orthologous regions are part of the functional centromere. All seven Cen8 genes have undergone purifying selection, representing a striking phenomenon of active gene survival within a recombination-free zone over a long evolutionary time. The coding sequences of the Cen8 genes showed sequence divergence and mutation rates that were significantly reduced from those of genes located on the chromosome arms. This suggests that Oryza has a mechanism to maintain the fidelity and functionality of Cen8 genes, even when embedded in a sea of repetitive sequences and transposable elements.
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MESH Headings
- Base Sequence
- Centromere/genetics
- Chromatin Immunoprecipitation
- Chromosomes, Plant/genetics
- DNA Transposable Elements
- DNA, Plant/genetics
- Evolution, Molecular
- Genes, Plant/genetics
- Genetic Variation/genetics
- Genome, Plant/genetics
- Molecular Sequence Data
- Mutation Rate
- Oryza/classification
- Oryza/genetics
- Polymorphism, Single Nucleotide
- Repetitive Sequences, Nucleic Acid
- Selection, Genetic
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- Chuanzhu Fan
- Arizona Genomics Institute, School of Plant Sciences, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Jason G. Walling
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Cory D. Hirsch
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
- Address correspondence to
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Casey NM, Milbourne D, Barth S, Febrer M, Jenkins G, Abberton MT, Jones C, Thorogood D. The genetic location of the self-incompatibility locus in white clover (Trifolium repens L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:567-576. [PMID: 20383486 DOI: 10.1007/s00122-010-1330-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 03/26/2010] [Indexed: 05/29/2023]
Abstract
White clover (Trifolium repens L.) is a forage legume of considerable economic importance in temperate agricultural systems. It has a strong self-incompatibility system. The molecular basis of self-incompatibility in T. repens is unknown, but it is under the control of a single locus, which is expressed gametophytically. To locate the self-incompatibility locus (S locus) in T. repens, we carried out cross-pollination experiments in an F(1) mapping population and constructed a genetic linkage map using amplified fragment length polymorphism and simple sequence repeat markers. As the first step in a map-based cloning strategy, we locate for the first time the S locus in T. repens on a genetic linkage map, on the homoeologous linkage group pair 1 (E), which is broadly syntenic to Medicago truncatula L. chromosome 1. On the basis of this syntenic relationship, the possibility that the S locus may or may not possess an S-RNase gene is discussed.
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Affiliation(s)
- Nora M Casey
- Teagasc Crops Research Centre, Oak Park, County Carlow, Ireland
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Bernhardt SA, Blair C, Sylla M, Bosio C, Black WC. Evidence of multiple chromosomal inversions in Aedes aegypti formosus from Senegal. INSECT MOLECULAR BIOLOGY 2009; 18:557-569. [PMID: 19754736 DOI: 10.1111/j.1365-2583.2009.00895.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Chromosomal inversions are prevalent in mosquito species but polytene chromosomes are difficult to prepare and visualize in members of the tribe Aedinii and thus there exists only indirect evidence of inversions. We constructed an F(1) intercross family using a P(1) female from a laboratory strain of Aedes aegypti aegypti (Aaa) and a P(1) male Aedes aegypti formosus (Aaf) from a strain collected from south-eastern Senegal. Recombination rates in the F(2) offspring were severely reduced and genotype ratios suggested a deleterious recessive allele on chromosome 3. The F(2) linkage map was incongruent in most respects with the established map for Aaa. Furthermore, no increased recombination was detected in F(5) offspring. Recombination rates and gene order were consistent with the presence in Aaf of at least four large inversions on chromosome 1, a single small inversion on chromosome 2 and three inversions on chromosome 3.
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Affiliation(s)
- S A Bernhardt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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Xue Y, Zhang Y, Yang Q, Li Q, Cheng Z, Dickinson HG. Genetic features of a pollen-part mutation suggest an inhibitory role for the Antirrhinum pollen self-incompatibility determinant. PLANT MOLECULAR BIOLOGY 2009; 70:499-509. [PMID: 19360476 DOI: 10.1007/s11103-009-9487-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 03/29/2009] [Indexed: 05/27/2023]
Abstract
Self-incompatibility (SI), an important barrier to inbreeding in flowering plants, is controlled in many species by a single polymorphic S-locus. In the Solanaceae, two tightly linked S-locus genes, S-RNase and SLF (S-locus F-box)/SFB (S-haplotype-specific F-box), control SI expression in pistil and pollen, respectively. The pollen S-determinant appears to function to inhibit all but self S-RNase in the Solanaceae, but its genetic function in the closely-related Plantaginaceae remains equivocal. We have employed transposon mutagenesis in a member of the Plantaginaceae (Antirrhinum) to generate a pollen-part SI-breakdown mutant Pma1 (Pollen-part mutation in Antirrhinum1). Molecular genetic analyses showed that an extra telocentric chromosome containing AhSLF-S ( 1 ) is present in its self-compatible but not in its SI progeny. Furthermore, analysis of the effects of selection revealed positive selection acting on both SLFs and SFBs, but with a stronger purifying selection on SLFs. Taken together, our results suggest an inhibitor role of the pollen S in the Plantaginaceae (as represented by Antirrhinum), similar to that found in the Solanaceae. The implication of these findings is discussed in the context of S-locus evolution in flowering plants.
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Affiliation(s)
- Yongbiao Xue
- Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, West Lincui Road, Chaoyang District, Beijing, China.
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Evolutionary strata in a small mating-type-specific region of the smut fungus Microbotryum violaceum. Genetics 2009; 182:1391-6. [PMID: 19448270 DOI: 10.1534/genetics.109.103192] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA sequence analysis and genetic mapping of loci from mating-type-specific chromosomes of the smut fungus Microbotryum violaceum demonstrated that the nonrecombining mating-type-specific region in this species comprises approximately 25% ( approximately 1 Mb) of the chromosome length. Divergence between homologous mating-type-linked genes in this region varies between 0 and 8.6%, resembling the evolutionary strata of vertebrate and plant sex chromosomes.
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Hudson A, Critchley J, Erasmus Y. The genus antirrhinum (snapdragon): a flowering plant model for evolution and development. Cold Spring Harb Protoc 2008; 2008:pdb.emo100. [PMID: 21356683 DOI: 10.1101/pdb.emo100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
INTRODUCTIONThe Antirrhinum species group comprises approximately 20 morphologically diverse members that are able to form fertile hybrids. It includes the cultivated snapdragon Antirrhinum majus, which has been used as a model for biochemical and developmental genetics for more than 75 yr. The research infrastructure for A. majus, together with the interfertility of the species group, allows Antirrhinum to be used to examine the genetic basis for plant diversity.
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Affiliation(s)
- Andrew Hudson
- University of Edinburgh, Institute of Molecular Plant Sciences, Edinburgh EH9 3JH, United Kingdom
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