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Hobza R, Bačovský V, Čegan R, Horáková L, Hubinský M, Janíček T, Janoušek B, Jedlička P, Kružlicová J, Kubát Z, Rodríguez Lorenzo JL, Novotná P, Hudzieczek V. Sexy ways: approaches to studying plant sex chromosomes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5204-5219. [PMID: 38652048 PMCID: PMC11389836 DOI: 10.1093/jxb/erae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the specific genetic and epigenetic mechanisms responsible for shaping distinct sexes in plants. While the fundamental methods of molecular biology and genomics are generally employed for the analysis of sex chromosomes, it is often necessary to modify classical procedures not only to simplify and expedite analyses but sometimes to make them possible at all. In this review, we demonstrate how, at the level of structural and functional genetics, cytogenetics, and bioinformatics, it is essential to adapt established procedures for sex chromosome analysis.
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Affiliation(s)
- Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Lucie Horáková
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marcel Hubinský
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Bohuslav Janoušek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Pavel Jedlička
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jana Kružlicová
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - José Luis Rodríguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Pavla Novotná
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
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He L, Wang Y, Wang Y, Zhang RG, Wang Y, Hörandl E, Ma T, Mao YF, Mank JE, Ming R. Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes. Nat Commun 2024; 15:6893. [PMID: 39134553 PMCID: PMC11319354 DOI: 10.1038/s41467-024-51158-3] [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: 03/13/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yuàn Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuán Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Tao Ma
- Key Laboratory for Bio‑Resource and Eco‑Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yan-Fei Mao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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3
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Ortiz AJ, Sharbrough J. Genome-wide patterns of homoeologous gene flow in allotetraploid coffee. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11584. [PMID: 39184198 PMCID: PMC11342229 DOI: 10.1002/aps3.11584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/11/2024] [Accepted: 01/25/2024] [Indexed: 08/27/2024]
Abstract
Premise Allopolyploidy-a hybridization-induced whole-genome duplication event-has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages. Methods The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid Coffea arabica. Results We found that HGF is abundant in the C. arabica genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted-but not mitochondrial-targeted-genes, as would be expected if plastid-nuclear incompatibilities exist between the two parent species. Discussion Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid-nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.
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Affiliation(s)
- Andre J. Ortiz
- Department of BiologyNew Mexico Institute of Mining and TechnologySocorroNew MexicoUSA
| | - Joel Sharbrough
- Department of BiologyNew Mexico Institute of Mining and TechnologySocorroNew MexicoUSA
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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024:elae017. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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Yamano K, Haseda A, Iwabuchi K, Osabe T, Sudo Y, Pachakkil B, Tanaka K, Suzuki Y, Toyoda A, Hirakawa H, Onodera Y. QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules. PLoS One 2024; 19:e0296675. [PMID: 38394294 PMCID: PMC10890751 DOI: 10.1371/journal.pone.0296675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/15/2023] [Indexed: 02/25/2024] Open
Abstract
Although spinach is predominantly dioecious, monoecious plants with varying proportions of female and male flowers are also present. Recently, monoecious inbred lines with highly female and male conditions have been preferentially used as parents for F1-hybrids, rather than dioecious lines. Accordingly, identifying the loci for monoecism is an important issue for spinach breeding. We here used long-read sequencing and Hi-C technology to construct SOL_r2.0_pseudomolecule, a set of six pseudomolecules of spinach chromosomes (total length: 879.2 Mb; BUSCO complete 97.0%) that are longer and more genetically complete than our previous version of pseudomolecules (688.0 Mb; 81.5%). Three QTLs, qFem2.1, qFem3.1, and qFem6.1, responsible for monoecism were mapped to SOL_r2.0_pseudomolecule. qFem3.1 had the highest LOD score and corresponded to the M locus, which was previously identified as a determinant of monoecious expression, by genetic analysis of progeny from female and monoecious plants. The other QTLs were shown to modulate the ratio of female to male flowers in monoecious plants harboring a dominant allele of the M gene. Our findings will enable breeders to efficiently produce highly female- and male-monoecious parental lines for F1-hybrids by pyramiding the three QTLs. Through fine-mapping, we narrowed the candidate region for the M locus to a 19.5 kb interval containing three protein-coding genes and one long non-coding RNA gene. Among them, only RADIALIS-like-2a showed a higher expression in the reproductive organs, suggesting that it might play a role in reproductive organogenesis. However, there is no evidence that it is involved in the regulation of stamen and pistil initiation, which are directly related to the floral sex differentiation system in spinach. Given that auxin is involved in reproductive organ formation in many plant species, genes related to auxin transport/response, in addition to floral organ formation, were identified as candidates for regulators of floral sex-differentiation from qFem2.1 and qFem6.1.
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Affiliation(s)
- Kaoru Yamano
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Akane Haseda
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Keisuke Iwabuchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takayuki Osabe
- School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yuki Sudo
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Babil Pachakkil
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
- Department of Informatics, Tokyo University of Information Sciences, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Hideki Hirakawa
- The Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yasuyuki Onodera
- The Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Feng YY, Du H, Huang KY, Ran JH, Wang XQ. Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce. Commun Biol 2024; 7:114. [PMID: 38242964 PMCID: PMC10799047 DOI: 10.1038/s42003-024-05786-6] [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: 07/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Sun P, Nishiyama S, Li H, Mai Y, Han W, Suo Y, Liang C, Du H, Diao S, Wang Y, Yuan J, Zhang Y, Tao R, Li F, Fu J. Genetic insights into the dissolution of dioecy in diploid persimmon Diospyros oleifera Cheng. BMC PLANT BIOLOGY 2023; 23:606. [PMID: 38030968 PMCID: PMC10688080 DOI: 10.1186/s12870-023-04610-3] [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: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Dioecy, a sexual system of single-sexual (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sexual individuals. RESULTS In this study, co-sexual expression (monoecy and hermaphroditic development), previously thought to be polyploid-specific in Diospyros species, was identified in the diploid D. oleifeara historically. We characterized potential genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions of Diospyros oleifera. We found all co-sexual plants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant gene OGI, implying the presence of genetic factors controlling gynoecia development in genetically male D. oleifera. Importantly, discrepancies in the OGI/MeGI module were found in diploid monoecious D. oleifera compared with polyploid monoecious D. kaki, including no Kali insertion on the promoter of OGI, no different abundance of smRNAs targeting MeGI (a counterpart of OGI), and no different expression of MeGI between female and male floral buds. On the contrary, in both single- and co-sexual plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and a DUF247 gene cluster strongly associated with the monoecious phenotype and several regions that may contribute to andromonoecy. CONCLUSIONS Collectively, our findings demonstrate stable breakdown of the dioecious system in D. oleifera, presumably also a result of genomic features of the Y-linked region.
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Affiliation(s)
- Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Soichiro Nishiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan.
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
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8
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Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [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: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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9
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Wang Q, Qu Y, Yu Y, Mao X, Fu X. Genome-wide identification and comparative analysis of DNA methyltransferase and demethylase gene families in two ploidy Cyclocarya paliurus and their potential function in heterodichogamy. BMC Genomics 2023; 24:287. [PMID: 37248459 DOI: 10.1186/s12864-023-09383-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND DNA methylation is one of the most abundant epigenetic modifications, which plays important roles in flower development, sex differentiation, and regulation of flowering time. Its pattern is affected by cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase). At present, there are no reports on C5-MTase and dMTase genes in heterodichogamous Cyclocarya paliurus. RESULTS In this study, 6 CpC5-MTase and 3 CpdMTase genes were identified in diploid (2n = 2 × = 32) C. paliurus, while 20 CpC5-MTase and 13 CpdMTase genes were identified in autotetraploid (2n = 4 × = 64). 80% of identified genes maintained relatively fixed positions on chromosomes during polyploidization. In addition, we found that some DRM subfamily members didn't contain the UBA domain. The transcript abundance of CpC5-MTase and CpdMTase in male and female flowers of two morphs (protandry and protogyny) from diploidy was analyzed. Results showed that all genes were significantly up-regulated at the stage of floral bud break (S2), but significantly down-regulated at the stage of flower maturation (S4). At S2, some CpC5-MTase genes showed higher expression levels in PG-M than in PG-F, whereas some CpdMTase genes showed higher expression levels in PA-M than in PA-F. In addition, these genes were significantly associated with gibberellin synthesis-related genes (e.g. DELLA and GID1), suggesting that DNA methylation may play a role in the asynchronous floral development process through gibberellin signal. CONCLUSIONS These results broaden our understanding of the CpC5-MTase and CpdMTase genes in diploid and autotetraploid C. paliurus, and provide a novel insight into regulatory mechanisms of DNA methylation in heterodichogamy.
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Affiliation(s)
- Qian Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yinquan Qu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Yanhao Yu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xia Mao
- Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, 212400, Jiangsu, China
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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10
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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11
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Mai Y, Sun P, Suo Y, Li H, Han W, Diao S, Wang L, Yuan J, Wang Y, Ye L, Zhang Y, Li F, Fu J. Regulatory mechanism of MeGI on sexuality in Diospyros oleifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1046235. [PMID: 36909399 PMCID: PMC9994623 DOI: 10.3389/fpls.2023.1046235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Dioecy system is an important strategy for maintaining genetic diversity. The transcription factor MeGI, contributes to dioecy by promoting gynoecium development in Diospyros lotus and D. kaki. However, the function of MeGI in D. oleifera has not been identified. In this study, we confirmed that MeGI, cloned from D. oleifera, repressed the androecium development in Arabidopsis thaliana. Subsequently, chromatin immunoprecipitation-sequencing (ChIP-seq), DNA affinity purification-sequencing (DAP-seq), and RNA-seq were used to uncover the gene expression response to MeGI. The results showed that the genes upregulated and downregulated in response to MeGI were mainly enriched in the circadian rhythm-related and flavonoid biosynthetic pathways, respectively. Additionally, the WRKY DNA-binding protein 28 (WRKY28) gene, which was detected by ChIP-seq, DAP-seq, and RNA-seq, was emphasized. WRKY28 has been reported to inhibit salicylic acid (SA) biosynthesis and was upregulated in MeGI-overexpressing A. thaliana flowers, suggesting that MeGI represses the SA level by increasing the expression level of WRKY28. This was confirmed that SA level was lower in D. oleifera female floral buds than male. Overall, our findings indicate that the MeGI mediates its sex control function in D. oleifera mainly by regulating genes in the circadian rhythm, SA biosynthetic, and flavonoid biosynthetic pathways.
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Affiliation(s)
- Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Liyuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Chinese Academy of Sciences (CAS) Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Lingshuai Ye
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
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12
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Akagi T, Jung K, Masuda K, Shimizu KK. Polyploidy before and after domestication of crop species. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102255. [PMID: 35870416 DOI: 10.1016/j.pbi.2022.102255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/01/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Katharina Jung
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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13
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Tonosaki K, Fujimoto R, Dennis ES, Raboy V, Osabe K. Will epigenetics be a key player in crop breeding? FRONTIERS IN PLANT SCIENCE 2022; 13:958350. [PMID: 36247549 PMCID: PMC9562705 DOI: 10.3389/fpls.2022.958350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Victor Raboy
- Independent Researcher Portland, Portland, OR, United States
| | - Kenji Osabe
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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14
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He L, Hörandl E. Does polyploidy inhibit sex chromosome evolution in angiosperms? FRONTIERS IN PLANT SCIENCE 2022; 13:976765. [PMID: 36212292 PMCID: PMC9541106 DOI: 10.3389/fpls.2022.976765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Dioecy is rare in flowering plants (5-6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany
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15
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Zhang X, Pan L, Guo W, Li Y, Wang W. A convergent mechanism of sex determination in dioecious plants: Distinct sex-determining genes display converged regulation on floral B-class genes. FRONTIERS IN PLANT SCIENCE 2022; 13:953445. [PMID: 36092432 PMCID: PMC9459113 DOI: 10.3389/fpls.2022.953445] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 06/12/2023]
Abstract
Sex determination in dioecious plants has been broadly and progressively studied with the blooming of genome sequencing and editing techniques. This provides us with a great opportunity to explore the evolution and genetic mechanisms underlining the sex-determining system in dioecious plants. In this study, comprehensively reviewing advances in sex-chromosomes, sex-determining genes, and floral MADS-box genes in dioecious plants, we proposed a convergent model that governs plant dioecy across divergent species using a cascade regulation pathway connecting sex-determining genes and MADS-box genes e.g., B-class genes. We believe that this convergent mechanism of sex determination in dioecious plants will shed light on our understanding of gene regulation and evolution of plant dioecy. Perspectives concerning the evolutionary pathway of plant dioecy are also suggested.
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Affiliation(s)
- Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Department of Molecular of Biology, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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16
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Cauret CMS, Mortimer SME, Roberti MC, Ashman TL, Liston A. Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 (BETHESDA, MD.) 2022; 12:6603112. [PMID: 35666193 PMCID: PMC9339316 DOI: 10.1093/g3journal/jkac139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/19/2022] [Indexed: 01/07/2023]
Abstract
When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
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Affiliation(s)
- Caroline M S Cauret
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sebastian M E Mortimer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marcelina C Roberti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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17
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Wang L, Li H, Suo Y, Han W, Diao S, Mai Y, Wang Y, Yuan J, Ye L, Pu T, Zhang Q, Sun P, Li F, Fu J. Effects of Different Chemicals on Sexual Regulation in Persimmon ( Diospyros kaki Thunb.) Flowers. FRONTIERS IN PLANT SCIENCE 2022; 13:876086. [PMID: 35693185 PMCID: PMC9179176 DOI: 10.3389/fpls.2022.876086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/28/2022] [Indexed: 06/02/2023]
Abstract
Research on crop sexuality is important for establishing systems for germplasm innovation and cultivating improved varieties. In this study, androecious persimmon trees were treated with various concentrations of ethrel (100, 500, and 1,000 mg/L) and zeatin (1, 5, and 10 mg/L) to investigate the morphological, physiological, and molecular characteristics of persimmon. Ethrel at 1,000 mg/L and zeatin at 10 mg/L both significantly reduced the stamen length and pollen grain diameter in androecious trees. Ethrel treatment also led to reduced stamen development with degenerated cellular contents; zeatin treatment promoted the development of arrested pistils via maintaining relatively normal mitochondrial morphology. Both treatments altered carbohydrate, amino acid, and endogenous phytohormone contents, as well as genes associated with hormone production and floral organ development. Thereafter, we explored the combined effects of four chemicals, including ethrel and zeatin, as well as zebularine and 5-azacytidine, both of which are DNA methylation inhibitors, on androecious persimmon flower development. Morphological comparisons showed that stamen length, pollen viability, and pollen grain diameter were significantly inhibited after combined treatment. Large numbers of genes involving in carbohydrate metabolic, mitogen-activated protein kinase (MAPK) signaling, and ribosome pathways, and metabolites including uridine monophosphate (UMP) and cyclamic acid were identified in response to the treatment, indicating complex regulatory mechanisms. An association analysis of transcriptomic and metabolomic data indicated that ribosomal genes have distinct effects on UMP and cyclamic acid metabolites, explaining how male floral buds of androecious persimmon trees respond to these exogenous chemicals. These findings extend the knowledge concerning sexual differentiation in persimmon; they also provide a theoretical basis for molecular breeding, high-yield cultivation, and quality improvement in persimmon.
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Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R. Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2354-2368. [PMID: 35045170 DOI: 10.1093/jxb/erab538] [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: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined the differences between females and androhermaphrodites in their placenta and ovule organization. Our results reveal the regulatory pathways potentially involved in sex-specific flower development in the classical model of dioecy, S. latifolia. These pathways include previously hypothesized and unknown female-regulator genes that act on the factors that determine the flower boundaries, and a negative regulator of anther development, SUPERMAN-like (SlSUP).
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Eva Tihlaříková
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vilém Neděla
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Lubomír Smrža
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Vladimír Beneš
- EMBL Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, D-69117 Heidelberg, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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Sharbrough J, Conover JL, Fernandes Gyorfy M, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms. Mol Biol Evol 2022; 39:msac074. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L. Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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20
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Masuda K, Ikeda Y, Matsuura T, Kawakatsu T, Tao R, Kubo Y, Ushijima K, Henry IM, Akagi T. Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon. NATURE PLANTS 2022; 8:217-224. [PMID: 35301445 DOI: 10.1038/s41477-022-01107-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 05/29/2023]
Abstract
In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems1. Polyploidizations are often associated with this plasticity in sexual systems2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- JST-PRESTO, Saitama, Japan.
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21
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Rodriguez-Granados NY, Ramirez-Prado JS, Brik-Chaouche R, An J, Manza-Mianza D, Sircar S, Troadec C, Hanique M, Soulard C, Costa R, Dogimont C, Latrasse D, Raynaud C, Boualem A, Benhamed M, Bendahmane A. CmLHP1 proteins play a key role in plant development and sex determination in melon (Cucumis melo). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1213-1228. [PMID: 34897855 DOI: 10.1111/tpj.15627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.
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Affiliation(s)
- Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Juan Sebastian Ramirez-Prado
- Centre of Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Jing An
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Sanchari Sircar
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Christelle Troadec
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Melissa Hanique
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Camille Soulard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Rafael Costa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Catherine Dogimont
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, BP 94, F-84143, Montfavet, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
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22
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Li SF, Lv CC, Lan LN, Jiang KL, Zhang YL, Li N, Deng CL, Gao WJ. DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus. HORTICULTURE RESEARCH 2021; 8:198. [PMID: 34465747 PMCID: PMC8408194 DOI: 10.1038/s41438-021-00633-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 05/04/2023]
Abstract
DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus. Compared with male flowers, female flowers at the same stages showed higher levels of DNA methylation. Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages. Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation. Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus. The upregulated genes AoMS1, AoLAP3, AoAMS, and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus. Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation. In addition, the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome, implying that DNA methylation might have been involved in Y chromosome evolution. These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Can-Can Lv
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Kai-Lu Jiang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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23
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Masuda K, Yamamoto E, Shirasawa K, Onoue N, Kono A, Ushijima K, Kubo Y, Tao R, Henry IM, Akagi T. Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon. DNA Res 2021; 27:5858979. [PMID: 32761076 PMCID: PMC7406971 DOI: 10.1093/dnares/dsaa012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 11/17/2022] Open
Abstract
Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Eiji Yamamoto
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Atsushi Kono
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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24
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Cascales J, Acevedo RM, Paiva DI, Gottlieb AM. Differential DNA methylation and gene expression during development of reproductive and vegetative organs in Ilex species. JOURNAL OF PLANT RESEARCH 2021; 134:559-575. [PMID: 33759060 DOI: 10.1007/s10265-021-01279-3] [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: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Differential epigenetic (DNA cytosine methylation) and gene expression patterns were investigated in reproductive and vegetative organs from Ilex paraguariensis and I. dumosa, at distinct developmental stages. We aimed at contributing towards elucidating major molecular changes underlying the sexual differentiation processes which, in these dioecious species, are completely unknown. Simultaneously, as a first step towards the development of an early sexing system, we searched for promising molecular markers. This was assessed through Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism on cDNA (cDNA-AFLP) techniques, applying discriminant multivariate analyses, and bioinformatic characterization of differential fragments. A significant positive correlation was found between epigenetic and indirect 'genetic' information for both species, indicating influence of the genetic background on the epigenetic variation. Higher epigenetic than genetic diversities were estimated. Our outcomes showed up to 1.86 times more representation of mCG subepiloci than mCCG in all organs sampled. Along the maturing stages of floral buds, the frequency of mCG evidenced an incremental trend, whereas mCCG and unmethylated conditions showed opposite tendencies. Reproductive and vegetative samples tended to cluster apart based on epigenetic patterns; at gene expression level, organs exhibited clear-cut distinctive patterns, nonetheless profiles of young leaves and floral primordia resemble. Epigenetic and expression data allowed discrimination of I. dumosa´s samples according to the gender of the donor; more elusive patterns were observed for I. paraguariensis. In total, 102 differentially methylated and expressed fragments were characterized bioinformatically. Forty-three were annotated in various functional categories; four candidate markers were validated through qPCR, finding statistical differences among organs but not among sexes. The methylation condition of epilocus C13m33 appears as indicative of gender in both species. Thirty-three organ-specific and 34 gender-specific methylated markers were discriminated and deserve further research, particularly those expressed in leaves. Our study contributes concrete candidate markers with potential for practical application.
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Affiliation(s)
- Jimena Cascales
- Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, CONICET-UBA), Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Raúl Maximiliano Acevedo
- Laboratorio de Biotecnología Aplicada y Genómica Funcional, Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE, UNNE-CONICET), Universidad Nacional del Nordeste, Sargento Juan Bautista Cabral 2131, Corrientes, W3402BKG, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Daniela Ivana Paiva
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Montecarlo (INTA EEA Montecarlo), Av. El Libertador 2472, Misiones, N3384, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Alexandra Marina Gottlieb
- Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, CONICET-UBA), Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina.
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25
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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26
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Renner SS, Müller NA. Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration. NATURE PLANTS 2021; 7:392-402. [PMID: 33782581 DOI: 10.1038/s41477-021-00884-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/18/2021] [Indexed: 05/17/2023]
Abstract
Hundreds of land plant lineages have independently evolved separate sexes in either gametophytes (dioicy) or sporophytes (dioecy), but 43% of all dioecious angiosperms are found in just 34 entirely dioecious clades, suggesting that their mode of sex determination evolved a long time ago. Here, we review recent insights on the molecular mechanisms that underlie the evolutionary change from individuals that each produce male and female gametes to individuals specializing in the production of just one type of gamete. The canonical model of sex chromosome evolution in plants predicts that two sex-determining genes will become linked in a sex-determining region (SDR), followed by expanding recombination suppression, chromosome differentiation and, ultimately, degeneration. Experimental work, however, is showing that single genes function as master regulators in model systems, such as the liverwort Marchantia and the angiosperms Diospyros and Populus. In Populus, this type of regulatory function has been demonstrated by genome editing. In other systems, including Actinidia, Asparagus and Vitis, two coinherited factors appear to independently regulate female and male function, yet sex chromosome differentiation has remained low. We discuss the best-understood systems and evolutionary pathways to dioecy, and present a meta-analysis of the sizes and ages of SDRs. We propose that limited sexual conflict explains why most SDRs are small and sex chromosomes remain homomorphic. It appears that models of increasing recombination suppression with age do not apply because selection favours mechanisms in which sex determination depends on minimal differences, keeping it surgically precise.
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Affiliation(s)
- Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany.
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
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27
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Wu M, Haak DC, Anderson GJ, Hahn MW, Moyle LC, Guerrero RF. Inferring the Genetic Basis of Sex Determination from the Genome of a Dioecious Nightshade. Mol Biol Evol 2021; 38:2946-2957. [PMID: 33769517 PMCID: PMC8233512 DOI: 10.1093/molbev/msab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dissecting the genetic mechanisms underlying dioecy (i.e., separate female and male individuals) is critical for understanding the evolution of this pervasive reproductive strategy. Nonetheless, the genetic basis of sex determination remains unclear in many cases, especially in systems where dioecy has arisen recently. Within the economically important plant genus Solanum (∼2,000 species), dioecy is thought to have evolved independently at least 4 times across roughly 20 species. Here, we generate the first genome sequence of a dioecious Solanum and use it to ascertain the genetic basis of sex determination in this species. We de novo assembled and annotated the genome of Solanum appendiculatum (assembly size: ∼750 Mb scaffold N50: 0.92 Mb; ∼35,000 genes), identified sex-specific sequences and their locations in the genome, and inferred that males in this species are the heterogametic sex. We also analyzed gene expression patterns in floral tissues of males and females, finding approximately 100 genes that are differentially expressed between the sexes. These analyses, together with observed patterns of gene-family evolution specific to S. appendiculatum, consistently implicate a suite of genes from the regulatory network controlling pectin degradation and modification in the expression of sex. Furthermore, the genome of a species with a relatively young sex-determination system provides the foundational resources for future studies on the independent evolution of dioecy in this clade.
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Affiliation(s)
- Meng Wu
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Gregory J Anderson
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Rafael F Guerrero
- Department of Computer Science, Indiana University, Bloomington, IN, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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28
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Li H, Wang L, Mai Y, Han W, Suo Y, Diao S, Sun P, Fu J. Phytohormone and integrated mRNA and miRNA transcriptome analyses and differentiation of male between hermaphroditic floral buds of andromonoecious Diospyros kaki Thunb. BMC Genomics 2021; 22:203. [PMID: 33757427 PMCID: PMC7986387 DOI: 10.1186/s12864-021-07514-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 03/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Persimmon (Diospyros kaki Thunb.) has various labile sex types, and studying its sex differentiation can improve breeding efficiency. However, studies on sexual regulation patterns in persimmon have focused mainly on monoecy and dioecy, whereas little research has been published on andromonoecy. In order to reveal the sex differentiation regulation mechanism of andromonoecious persimmon, we performed histological and cytological observations, evaluated OGI and MeGI expression and conducted phytohormones assays and mRNA and small RNA transcriptome analyses of the male and hermaphroditic floral buds of the andromonoecious persimmon 'Longyanyeshi 1'. RESULTS Stages 2 and 4 were identified as the critical morphological periods for sex differentiation of 'Longyanyeshi 1' by histological and cytological observation. At both stages, OGI was differentially expressed in male and hermaphroditic buds, but MeGI was not. This was different from their expressions in dioecious and monoecious persimmons. Meantime, the results of phytohormones assays showed that high IAA, ABA, GA3, and JA levels at stage 2 may have promoted male floral bud differentiation. However, high JA levels at stage 4 and high ZT levels at stages 2 and 4 may have promoted hermaphroditic floral bud differentiation. In these phytohormone biosynthesis and signaling pathways, 52 and 54 differential expression genes (including Aux/IAA, ARFs, DELLA, AHP, A-ARR, B-ARR, CYP735A, CRE1, PP2C, JAZ, MYC2, COI1, CTR1, SIMKK, ACO, and MPK6) were identified, respectively. During the development of male floral buds, five metacaspases genes may have been involved in pistil abortion. In addition, MYB, FAR1, bHLH, WRKY, and MADS transcription factors might play important roles in persimmon floral bud sex differentiation. Noteworthy, miR169v_1, miR169e_3, miR319_1, and miR319 were predicted to contribute to phytohormone biosynthesis and signaling pathways and floral organogenesis and may also regulate floral bud sex differentiation. CONCLUSION The present study revealed the differences in morphology and phytohormones content between male and hermaphroditic floral buds of 'Longyanyeshi 1' during the process of sex differentiation, and identified a subset of candidate genes and miRNAs putatively associated with its sex differentiation. These findings can provide a foundation for molecular regulatory mechanism researching on andromonoecious persimmon.
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Affiliation(s)
- Huawei Li
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Liyuan Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yini Mai
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Weijuan Han
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Yujing Suo
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Songfeng Diao
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Peng Sun
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
| | - Jianmin Fu
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- National Innovation Alliance of Persimmon Industry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
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Wang L, Han W, Diao S, Suo Y, Li H, Mai Y, Wang Y, Sun P, Fu J. Study of Sexual-Linked Genes ( OGI and MeGI) on the Performance of Androecious Persimmons ( Diospyros kaki Thunb.). PLANTS 2021; 10:plants10020390. [PMID: 33670570 PMCID: PMC7922513 DOI: 10.3390/plants10020390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 11/25/2022]
Abstract
It is reported that the production of floral sexual phenotype in hexaploid monoecious persimmon (Diospyros kaki) is closely related to a pseudogene called OGI, and a short interspersed nuclear element (SINE)-like insertion (named Kali) in the OGI promoter leads to the gene silence. As a result, DNA methylation level of MeGI promoter determines the development of male or female flowers. However, the molecular mechanism in androecious D. kaki, which only bear male flowers, remains elusive. Here, real-time quantitative polymerase chain reaction (RT-qPCR), molecular cloning, and bisulfite PCR sequencing technique were carried out using 87 materials, including 56 androecious resources, 15 monoecious, and 16 gynoecious cultivars, to investigate the performance of OGI and MeGI on the specific androecious type of D. kaki in China. In conclusion, the Kali insertion was exactly located in the OGI promoter region, and the OGI gene and the Kali sequence were existing and conserved in androecious D. kaki. Meanwhile, we also demonstrated that the MeGI gene was widespread in our investigated samples. Ultimately, our result convincingly provided evidence that the low expression of OGI is probably ascribed to the presence of Kali displaying strong methylation in the OGI promoter, and low expression of MeGI, as well as high DNA methylation level, in the promoter was closely connected with the production of male flowers; this result was consistent with the monoecious persimmon model. Our findings provide predominant genetic aspects for investigation into androecious D. kaki, and future perfecting the sex-determining mechanisms in persimmon.
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Affiliation(s)
- Liyuan Wang
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Weijuan Han
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
| | - Songfeng Diao
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
| | - Yujing Suo
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
| | - Huawei Li
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
| | - Yini Mai
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
| | - Yiru Wang
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
| | - Peng Sun
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
- Correspondence: (P.S.); (J.F.); Tel.: +86-371-65996829 (P.S.); Fax: +86-371-65953628 (P.S.)
| | - Jianmin Fu
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Non-Timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; (L.W.); (W.H.); (S.D.); (Y.S.); (H.L.); (Y.M.); (Y.W.)
- Correspondence: (P.S.); (J.F.); Tel.: +86-371-65996829 (P.S.); Fax: +86-371-65953628 (P.S.)
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Leite Montalvão AP, Kersten B, Fladung M, Müller NA. The Diversity and Dynamics of Sex Determination in Dioecious Plants. FRONTIERS IN PLANT SCIENCE 2021; 11:580488. [PMID: 33519840 PMCID: PMC7843427 DOI: 10.3389/fpls.2020.580488] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/23/2020] [Indexed: 05/03/2023]
Abstract
The diversity of inflorescences among flowering plants is captivating. Such charm is not only due to the variety of sizes, shapes, colors, and flowers displayed, but also to the range of reproductive systems. For instance, hermaphrodites occur abundantly throughout the plant kingdom with both stamens and carpels within the same flower. Nevertheless, 10% of flowering plants have separate unisexual flowers, either in different locations of the same individual (monoecy) or on different individuals (dioecy). Despite their rarity, dioecious plants provide an excellent opportunity to investigate the mechanisms involved in sex expression and the evolution of sex-determining regions (SDRs) and sex chromosomes. The SDRs and the evolution of dioecy have been studied in many species ranging from Ginkgo to important fruit crops. Some of these studies, for example in asparagus or kiwifruit, identified two sex-determining genes within the non-recombining SDR and may thus be consistent with the classical model for the evolution of dioecy from hermaphroditism via gynodioecy, that predicts two successive mutations, the first one affecting male and the second one female function, becoming linked in a region of suppressed recombination. On the other hand, aided by genome sequencing and gene editing, single factor sex determination has emerged in other species, such as persimmon or poplar. Despite the diversity of sex-determining mechanisms, a tentative comparative analysis of the known sex-determining genes and candidates in different species suggests that similar genes and pathways may be employed repeatedly for the evolution of dioecy. The cytokinin signaling pathway appears important for sex determination in several species regardless of the underlying genetic system. Additionally, tapetum-related genes often seem to act as male-promoting factors when sex is determined via two genes. We present a unified model that synthesizes the genetic networks of sex determination in monoecious and dioecious plants and will support the generation of hypothesis regarding candidate sex determinants in future studies.
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Affiliation(s)
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, Großhansdorf, Germany
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31
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Masuda K, Fujita N, Yang HW, Ushijima K, Kubo Y, Tao R, Akagi T. Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon. FRONTIERS IN PLANT SCIENCE 2020; 11:567249. [PMID: 33414795 PMCID: PMC7783364 DOI: 10.3389/fpls.2020.567249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Sex expression in plants is often flexible and contributes to the maintenance of genetic diversity within a species. In diploid persimmons (the genus Diospyros), the sexuality is controlled by the Y chromosome-encoded small-RNA gene, OGI, and its autosomal counterpart, MeGI. Hexaploid Oriental persimmon (Diospyros kaki) evolved more flexible sex expression, where genetically male individuals carrying OGI can produce both male and female flowers (monoecy). This is due to (semi-)inactivation of OGI by the Kali-SINE retrotransposon insertion on the promoter region and the resultant DNA methylations. Instead, flower sex determination in Oriental persimmon is also dependent on DNA methylation states of MeGI. Here, we focused on a cultivar, Kumemaru, which shows stable male flower production. Our results demonstrated that cv. Kumemaru carries OGI with Kali-SINE, which was highly methylated as well as in other monoecious cultivars; nevertheless, OGI gene could have a basal expression level. Transcriptomic analysis between cv. Kumemaru and 14 cultivars that predominantly produce female flowers showed differentially expressed genes (DEGs) specific to cv. Kumemaru, which is mainly involved in stress responses. Co-expression gene networks focusing on the DEGs also suggested the involvement of stress signals, mainly via gibberellin (GA), salicylic acid (SA), and especially jasmonic acid (JA) signal pathways. We also identified potential regulators of this co-expression module, represented by the TCP4 transcription factor. Furthermore, we attempted to identify cv. Kumemaru-specific transcript polymorphisms potentially contributing to derepressed OGI expression by cataloging subsequences (k-mers) in the transcriptomic reads from cv. Kumemaru and the other 14 female cultivars. Overall, although the direct genetic factor to activate OGI remains to be solved, our results implied the involvement of stress signals in the release of silenced OGI and the resultant continuous male production.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Naoko Fujita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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32
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Bondada R, Somasundaram S, Marimuthu MP, Badarudeen MA, Puthiyaveedu VK, Maruthachalam R. Natural epialleles of Arabidopsis SUPERMAN display superwoman phenotypes. Commun Biol 2020; 3:772. [PMID: 33319840 PMCID: PMC7738503 DOI: 10.1038/s42003-020-01525-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/25/2020] [Indexed: 01/07/2023] Open
Abstract
Epimutations are heritable changes in gene function due to loss or gain of DNA cytosine methylation or chromatin modifications without changes in the DNA sequence. Only a few natural epimutations displaying discernible phenotypes are documented in plants. Here, we report natural epimutations in the cadastral gene, SUPERMAN(SUP), showing striking phenotypes despite normal transcription, discovered in a natural tetraploid, and subsequently in eleven diploid Arabidopsis genetic accessions. This natural lois lane(lol) epialleles behave as recessive mendelian alleles displaying a spectrum of silent to strong superwoman phenotypes affecting only the carpel whorl, in contrast to semi-dominant superman or supersex features manifested by induced epialleles which affect both stamen and carpel whorls. Despite its unknown origin, natural lol epialleles are subjected to the same epigenetic regulation as induced clk epialleles. The existence of superwoman epialleles in diverse wild populations is interpreted in the light of the evolution of unisexuality in plants. Ramesh Bondada et al. report natural epimutations in the Arabidopsis SUPERMAN gene from tetraploid and diploid accessions. The existence of these epialleles in diverse wild populations have the potential to shed light on the evolution of unisexuality in plants.
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Affiliation(s)
- Ramesh Bondada
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Saravanakumar Somasundaram
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | | | - Mohammed Afsal Badarudeen
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Vaishak Kanjirakol Puthiyaveedu
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Ravi Maruthachalam
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India.
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Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol 2020; 21:223. [PMID: 32892750 PMCID: PMC7487632 DOI: 10.1186/s13059-020-02131-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
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Affiliation(s)
- Hélène Badouin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| | - Amandine Velt
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - François Gindraud
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Timothée Flutre
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Vincent Dumas
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Jonathan Corbi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérémy Ganofsky
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Santoni
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Hélène Berges
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Eric Duchêne
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Raquel Tavares
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Roberto Bacilieri
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Camille Rustenholz
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France.
| | - Gabriel A B Marais
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
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Zhou P, Zhang X, Fatima M, Ma X, Fang H, Yan H, Ming R. DNA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya. HORTICULTURE RESEARCH 2020; 7:81. [PMID: 32528693 PMCID: PMC7261803 DOI: 10.1038/s41438-020-0298-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 05/21/2023]
Abstract
Separate sexes in dioecious plants display different morphology and physiological characteristics. The differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype, which is genetically determined and epigenetically modified. In dioecious papaya (Carica papaya L.), global comparisons of epigenetic DNA methylation and gene expressions were still limited. We conducted bisulfite sequencing of early-stage flowers grown in three seasons (spring, summer and winter) and compared their methylome and transcriptome profiles to investigate the differential characteristics of male and female in papaya. Methylation variances between female and male papaya were conserved among three different seasons. However, combined genome-scale transcriptomic evidence revealed that most methylation variances did not have influence on the expression profiles of neighboring genes, and the differentially expressed genes were most overrepresented in phytohormone signal transduction pathways. Further analyses showed diverse stress-responsive methylation alteration in male and female flowers. Male flower methylation was more responsive to stress whereas female flower methylation varied less under stress. Early flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific hypomethylation. These findings provide insights into the sex-specific DNA methylation and gene expression landscapes of dioecious papaya and a foundation to investigate the correlation between differentiated floral characteristics and their candidate genes.
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Affiliation(s)
- Ping Zhou
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, Fujian China
| | - Xiaodan Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Xinyi Ma
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Hongkun Fang
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Hansong Yan
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Ray Ming
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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35
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Harkess A, Huang K, van der Hulst R, Tissen B, Caplan JL, Koppula A, Batish M, Meyers BC, Leebens-Mack J. Sex Determination by Two Y-Linked Genes in Garden Asparagus. THE PLANT CELL 2020; 32:1790-1796. [PMID: 32220850 PMCID: PMC7268802 DOI: 10.1105/tpc.19.00859] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/24/2020] [Accepted: 03/26/2020] [Indexed: 05/20/2023]
Abstract
The origin and early evolution of sex chromosomes have been hypothesized to involve the linkage of factors with antagonistic effects on male and female function. Garden asparagus (Asparagus officinalis) is an ideal species to investigate this hypothesis, as the X and Y chromosomes are cytologically homomorphic and evolved from an ancestral autosome pair in association with a shift from hermaphroditism to dioecy. Mutagenesis screens paired with single-molecule fluorescence in situ hybridization directly implicate Y-specific genes that respectively suppress female (pistil) development and are necessary for male (anther) development. Comparison of contiguous X and Y chromosome assemblies shows that hemizygosity underlies the loss of recombination between the genes suppressing female organogenesis (SUPPRESSOR OF FEMALE FUNCTION) and promoting male function (TAPETAL DEVELOPMENT AND FUNCTION1 [aspTDF1]). We also experimentally demonstrate the function of aspTDF1. These findings provide direct evidence that sex chromosomes can function through linkage of two sex determination genes.
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Affiliation(s)
- Alex Harkess
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Kun Huang
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716
| | | | - Bart Tissen
- Limgroup B.V., 5961 NV Horst, The Netherlands
| | - Jeffrey L Caplan
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716
| | - Aakash Koppula
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware 19716
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware 19716
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
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36
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A cross population between D. kaki and D. virginiana shows high variability for saline tolerance and improved salt stress tolerance. PLoS One 2020; 15:e0229023. [PMID: 32097425 PMCID: PMC7041798 DOI: 10.1371/journal.pone.0229023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
Persimmon (Diospyros kaki Thunb.) production is facing important problems related to climate change in the Mediterranean areas. One of them is soil salinization caused by the decrease and change of the rainfall distribution. In this context, there is a need to develop cultivars adapted to the increasingly challenging soil conditions. In this study, a backcross between (D. kaki x D. virginiana) x D. kaki was conducted, to unravel the mechanism involved in salinity tolerance of persimmon. The backcross involved the two species most used as rootstock for persimmon production. Both species are clearly distinct in their level of tolerance to salinity. Variables related to growth, leaf gas exchange, leaf water relations and content of nutrients were significantly affected by saline stress in the backcross population. Water flow regulation appears as a mechanism of salt tolerance in persimmon via differences in water potential and transpiration rate, which reduces ion entrance in the plant. Genetic expression of eight putative orthologous genes involved in different mechanisms leading to salt tolerance was analyzed. Differences in expression levels among populations under saline or control treatment were found. The ‘High affinity potassium transporter’ (HKT1-like) reduced its expression levels in the roots in all studied populations. Results obtained allowed selection of tolerant rootstocks genotypes and describe the hypothesis about the mechanisms involved in salt tolerance in persimmon that will be useful for breeding salinity tolerant rootstocks.
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37
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Zhou R, Macaya-Sanz D, Carlson CH, Schmutz J, Jenkins JW, Kudrna D, Sharma A, Sandor L, Shu S, Barry K, Tuskan GA, Ma T, Liu J, Olson M, Smart LB, DiFazio SP. A willow sex chromosome reveals convergent evolution of complex palindromic repeats. Genome Biol 2020; 21:38. [PMID: 32059685 PMCID: PMC7023750 DOI: 10.1186/s13059-020-1952-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.
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Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.,Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Aditi Sharma
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.
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38
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Masuda K, Akagi T, Esumi T, Tao R. Epigenetic Flexibility Underlies Somaclonal Sex Conversions in Hexaploid Persimmon. PLANT & CELL PHYSIOLOGY 2020; 61:393-402. [PMID: 31693144 DOI: 10.1093/pcp/pcz207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Epigenetic regulation adds a flexible layer to genetic variations, potentially enabling long-term, but reversible, changes to a trait, while maintaining genetic information. In the hexaploid Oriental persimmon (Diospyros kaki), genetically monoecious cultivars bearing male flowers require the Y-encoded small RNA (smRNA) gene, OGI. This gene represses the expression of its autosomal counterpart gene, MeGI, as part of the canonical male production system. However, a D. kaki cultivar, Saijo, which lacks the OGI gene and originally bears only female flowers, occasionally produces somaclonal mutant male and revertant female (RF) branches. In this study, we investigated the mechanisms underlying these somaclonal sex conversions in persimmon. Specifically, we aimed to unravel how a genetically female tree without the OGI gene can produce male flowers and RF flowers. Applying multi-omics approaches, we revealed that this noncanonical male production system is basically consistent with the canonical system, in which the accumulation of smRNA targeting MeGI and the considerable DNA methylation of MeGI are involved. The epigenetic status of MeGI on CGN and CHG was synchronized to the genome-wide methylation patterns, both in transition to and from the male production system. These results suggest that the somaclonal sex conversions in persimmon are driven by the genome-wide epigenetic regulatory activities. Moreover, flexibility in the epigenetic layers of long-lived plant species (e.g. trees) is important for overcoming genetic robustness.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi-shi, Saitama, 332-0012 Japan
| | - Tomoya Esumi
- Academic Assembly Institute of Agricultural and Life Sciences, Shimane University, Matsue, 690-8504, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
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39
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Maeda H, Akagi T, Onoue N, Kono A, Tao R. Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon. PLANT & CELL PHYSIOLOGY 2019; 60:2464-2477. [PMID: 31350891 PMCID: PMC6839372 DOI: 10.1093/pcp/pcz139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.
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Affiliation(s)
- Haruka Maeda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Akagi
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, Japan
| | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan
| | - Atsushi Kono
- Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan
| | - Ryutaro Tao
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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40
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Akagi T, Charlesworth D. Pleiotropic effects of sex-determining genes in the evolution of dioecy in two plant species. Proc Biol Sci 2019; 286:20191805. [PMID: 31615362 PMCID: PMC6834047 DOI: 10.1098/rspb.2019.1805] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/23/2019] [Indexed: 01/28/2023] Open
Abstract
One reason for studying sex chromosomes of flowering plants is that they have often evolved separate sexes recently, and the genomes of dioecious species may not yet have evolved adaptations to their changes from the ancestral state. An unstudied question concerns the relative importance of such adaptation, versus the effects of the mutations that led to separate sexes in the first place. Theoretical models for such an evolutionary change make the prediction that the mutations that created males must have sexually antagonistic effects, not only abolishing female functions, but also increasing male functions relative to the ancestral functional hermaphrodites. It is important to test this critical assumption. Moreover, the involvement of sexual antagonism also implies that plant sex-determining genes may directly cause some of the sexual dimorphisms observed in dioecious plants. Sex-determining genes are starting to be uncovered in plants, including species in the genera Diospyros and Actinidia (families Ebenaceae and Actinidiaceae, respectively). Here, we describe transgenic experiments in which the effects of the very different male-determining genes of these two dioecious species were studied in a non-dioecious plant, Nicotiana tabacum. The results indeed support the critical assumption outlined above.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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41
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Dong Z, Xiao Y, Govindarajulu R, Feil R, Siddoway ML, Nielsen T, Lunn JE, Hawkins J, Whipple C, Chuck G. The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression. Nat Commun 2019; 10:3810. [PMID: 31444327 PMCID: PMC6707278 DOI: 10.1038/s41467-019-11774-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/05/2019] [Indexed: 01/08/2023] Open
Abstract
Many domesticated crop plants have been bred for increased apical dominance, displaying greatly reduced axillary branching compared to their wild ancestors. In maize, this was achieved through selection for a gain-of-function allele of the TCP transcription factor teosinte branched1 (tb1). The mechanism for how a dominant Tb1 allele increased apical dominance, is unknown. Through ChIP seq, RNA seq, hormone and sugar measurements on 1 mm axillary bud tissue, we identify the genetic pathways putatively regulated by TB1. These include pathways regulating phytohormones such as gibberellins, abscisic acid and jasmonic acid, but surprisingly, not auxin. In addition, metabolites involved in sugar sensing such as trehalose 6-phosphate were increased. This suggests that TB1 induces bud suppression through the production of inhibitory phytohormones and by reducing sugar levels and energy balance. Interestingly, TB1 also putatively targets several other domestication loci, including teosinte glume architecture1, prol1.1/grassy tillers1, as well as itself. This places tb1 on top of the domestication hierarchy, demonstrating its critical importance during the domestication of maize from teosinte. The TB1 transcription factor was selected for the increased apical dominance of maize compared to its ancestor teosinte. A metabolic and genomic analysis of domesticated axillary buds suggest that TB1 achieved this by regulating phytohormone signaling, sugar metabolism and other domestication genes.
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Affiliation(s)
- Zhaobin Dong
- Plant Gene Expression Center/USDA, University of California, Berkeley, Albany, CA, 94710, USA
| | - Yuguo Xiao
- Brigham Young University, Provo, UT, 84602, USA
| | | | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Muehlenberg, 14476, Potsdam-Golm, Germany
| | | | | | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Muehlenberg, 14476, Potsdam-Golm, Germany
| | | | | | - George Chuck
- Plant Gene Expression Center/USDA, University of California, Berkeley, Albany, CA, 94710, USA.
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42
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Bačovský V, Houben A, Kumke K, Hobza R. The distribution of epigenetic histone marks differs between the X and Y chromosomes in Silene latifolia. PLANTA 2019; 250:487-494. [PMID: 31069521 DOI: 10.1007/s00425-019-03182-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/03/2019] [Indexed: 05/18/2023]
Abstract
Contrasting patterns of histone modifications between the X and Y chromosome in Silene latifolia show euchromatic histone mark depletion on the Y chromosome and indicate hyperactivation of one X chromosome in females. Silene latifolia (white campion) is a dioecious plant with heteromorphic sex chromosomes (24, XX in females and 24, XY in males), and a genetically degenerated Y chromosome that is 1.4 times larger than the X chromosome. Although the two sex chromosomes differ in their DNA content, information about epigenetic histone marks and evidence of their function are scarce. We performed immunolabeling experiments using antibodies specific for active and suppressive histone modifications as well as pericentromere-specific histone modifications. We show that the Y chromosome is partially depleted of histone modifications important for transcriptionally active chromatin, and carries these marks only in the pseudo-autosomal region, but that it is not enriched for suppressive and pericentromere histone marks. We also show that two of the active marks are specifically enriched in one of the X chromosomes in females and in the X chromosome in males. Our data support recent findings that genetic imprinting mediates dosage compensation of sex chromosomes in S. latifolia.
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.
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43
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Akagi T, Pilkington SM, Varkonyi-Gasic E, Henry IM, Sugano SS, Sonoda M, Firl A, McNeilage MA, Douglas MJ, Wang T, Rebstock R, Voogd C, Datson P, Allan AC, Beppu K, Kataoka I, Tao R. Two Y-chromosome-encoded genes determine sex in kiwifruit. NATURE PLANTS 2019; 5:801-809. [PMID: 31383971 DOI: 10.1038/s41477-019-0489-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/02/2019] [Indexed: 05/20/2023]
Abstract
Dioecy, the presence of male and female individuals, has evolved independently in multiple flowering plant lineages1-3. Although theoretical models for the evolution of dioecy, such as the 'two-mutations' model, are well established4,5, little is known about the specific genes determining sex and their evolutionary history3. Kiwifruit, a major tree crop consumed worldwide, is a dioecious species. In kiwifruit we previously identified a Y-encoded sex-determinant candidate gene acting as the suppressor of feminization (SuF), named Shy Girl (SyGI)6. Here, we identify a second Y-encoded sex-determinant that we named Friendly Boy (FrBy), which exhibits strong expression in tapetal cells. Gene-editing and complementation analyses in Arabidopsis thaliana and Nicotiana tabacum indicated that FrBy acts for the maintenance of male (M) functions, independently of SyGI, and that these functions are conserved across angiosperm species. We further characterized the genomic architecture of the small (<1 megabase pairs (Mb)) male-specific region of the Y chromosome (MSY), which harbours only two genes expressed extensively in developing gynoecia and androecia, respectively: SyGI and FrBy. Re-sequencing of the genome of a natural hermaphrodite kiwifruit revealed that this individual is genetically male but carries deletion(s) of parts of the Y chromosome, including SyGI. Additionally, expression of FrBy in female kiwifruit resulted in hermaphrodite plants. These results clearly indicate that Y-encoded SyGI and FrBy act independently as the SuF and M factors in kiwifruit, respectively, and provide insight into not only the evolutionary path leading to a two-factor sex-determination system, but also a new breeding approach for dioecious species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- JST, PRESTO, Kawaguchi-shi, Saitama, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Sarah M Pilkington
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Shigeo S Sugano
- JST, PRESTO, Kawaguchi-shi, Saitama, Japan
- R-GIRO, Ritsumeikan University, Shiga, Japan
| | - Minori Sonoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Alana Firl
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Mark A McNeilage
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Mikaela J Douglas
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Paul Datson
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kenji Beppu
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ikuo Kataoka
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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44
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Kawakatsu T, Ecker JR. Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding. BREEDING SCIENCE 2019; 69:191-204. [PMID: 31481828 PMCID: PMC6711733 DOI: 10.1270/jsbbs.19005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/18/2019] [Indexed: 05/17/2023]
Abstract
DNA methylation is an epigenetic modification that can affect gene expression and transposable element (TE) activities. Because cytosine DNA methylation patterns are inherited through both mitotic and meiotic cell divisions, differences in these patterns can contribute to phenotypic variability. Advances in high-throughput sequencing technologies have enabled the generation of abundant DNA sequence data. Integrated analyses of genome-wide gene expression patterns and DNA methylation patterns have revealed the underlying mechanisms and functions of DNA methylation. Moreover, associations between DNA methylation and agronomic traits have also been uncovered. The resulting information may be useful for future applications of natural epigenomic variation, for crop breeding. Additionally, artificial epigenome editing may be an attractive new plant breeding technique for generating novel varieties with improved agronomic traits.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
1-2 Owashi Tsukuba, Ibaraki 305-8634,
Japan
- Corresponding author (e-mail: )
| | - Joseph R. Ecker
- Howard Hughes Medical Institute,
10010 North Torrey Pines Road, La Jolla, CA 92037,
USA
- The Salk Institute for Biological Studies,
10010 North Torrey Pines Road, La Jolla, CA 92037,
USA
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45
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Liu M, Li W, Zhao G, Fan X, Long H, Fan Y, Shi M, Tan X, Zhang L. New Insights of Salicylic Acid Into Stamen Abortion of Female Flowers in Tung Tree ( Vernicia fordii). Front Genet 2019; 10:316. [PMID: 31024626 PMCID: PMC6460477 DOI: 10.3389/fgene.2019.00316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/21/2019] [Indexed: 12/03/2022] Open
Abstract
Tung tree (Vernicia fordii), an economically important woody oil plant, is a monoecious and diclinous species with male and female flowers on the same inflorescence. The extremely low proportion of female flowers leads to low fruit yield in tung orchards. The female flower normally develops along with stamen abortion; otherwise sterile ovules will be produced. However, little knowledge is known about the molecular basis of the female flower development in tung tree. In this study, integrated analyses of morphological and cytological observations, endogenous phytohormone assay and RNA-seq were conducted to understand the molecular mechanism of the female flower development in tung tree. Cytological observation suggested that the abortion of stamens in female flowers (SFFs) belongs to the type of programmed cell death (PCD), which was caused by tapetum degeneration at microspore mother cell stage. A total of 1,366 differentially expressed genes (DEGs) were identified in female flowers by RNA-seq analysis, of which 279 (20.42%) DEGs were significantly enriched in phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Stage-specific transcript identification detected dynamically expressed genes of important transcription regulators in female flowers that may be involved in PCD and floral organ development. Gene expression patterns revealed that 17 anther and pollen development genes and 37 PCD-related genes might be involved in the abortion of SFF. Further analyses of phytohormone levels and co-expression networks suggested that salicylic acid (SA) accumulation could trigger PCD and inhibit the development of SFF in tung tree. This study provides new insights into the role of SA in regulating the abortion of SFF to develop normal female flowers.
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Affiliation(s)
- Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Guang Zhao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Xiaoming Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Hongxu Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yanru Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Mingwang Shi
- Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
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46
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Yang H, Akagi T, Kawakatsu T, Tao R. Gene networks orchestrated by MeGI: a single-factor mechanism underlying sex determination in persimmon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:97-111. [PMID: 30556936 PMCID: PMC6850717 DOI: 10.1111/tpj.14202] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 05/20/2023]
Abstract
Separating male and female sex organs is one of the main strategies used to maintain genetic diversity within a species. However, the genetic determinants and their regulatory mechanisms have been identified in only a few species. In dioecious persimmons, the homeodomain transcription factor, MeGI, which is the target of a Y chromosome-encoded small-RNA, OGI, can determine floral sexuality. The basic features of this system are conserved in the monoecious hexaploid Oriental persimmon, in which an additional epigenetic regulation of MeGI determines floral sexuality. The downstream regulatory pathways of MeGI remain uncharacterized. In this study, we examined transcriptomic data for male and female flowers from monoecious persimmon cultivars to unveil the gene networks orchestrated by MeGI. A network visualization and cistrome assessment suggested that class-1 KNOTTED-like homeobox (KNOX)/ovate family protein (OFP)/growth regulating factors (GRFs) and short vegetative phase (SVP) genes mediate the differences in gynoecium and androecium development between male and female flowers, respectively. The expression of these genes is directly controlled by MeGI. The gene networks also suggested that some cytokinin, auxin, and gibberellin signaling genes function cooperatively in the KNOX/OFP/GRF pathway during gynoecium differentiation. Meanwhile, SVP may repress PI expression in developing androecia. Overall, our results suggest that MeGI evolved the ability to promote gynoecium development and suppress androecium development by regulating KNOX/OFP/GRF and SVP expression levels, respectively. These insights may help to clarify the molecular mechanism underlying the production of unisexual flowers, while also elucidating the physiological background enabling a single-factor system to establish dioecy in plants.
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Affiliation(s)
- Ho‐Wen Yang
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
| | - Takashi Akagi
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
- Japan Science and Technology Agency (JST)PRESTOKawaguchi‐shiSaitama332‐0012Japan
| | - Taiji Kawakatsu
- Division of BiotechnologyInstitute of Agrobiological SciencesNational Agriculture and Food Research OrganizationTsukubaIbaraki305‐8602Japan
| | - Ryutaro Tao
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
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47
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Lai YS, Zhang W, Zhang X, Shen D, Wang H, Qiu Y, Song J, Li X. Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression. G3 (BETHESDA, MD.) 2018; 8:3981-3991. [PMID: 30377155 PMCID: PMC6288824 DOI: 10.1534/g3.118.200755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022]
Abstract
The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7-52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression.
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Affiliation(s)
- Yun-Song Lai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611180, China
| | - Wei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Di Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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48
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Sollars ESA, Buggs RJA. Genome-wide epigenetic variation among ash trees differing in susceptibility to a fungal disease. BMC Genomics 2018; 19:502. [PMID: 29954338 PMCID: PMC6022711 DOI: 10.1186/s12864-018-4874-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background European ash trees (Fraxinus excelsior) are currently threatened by ash dieback (ADB) caused by the fungus Hymenoscyphus fraxineus but a small percentage of the population possesses natural low susceptibility. The genome of a European ash tree has recently been sequenced. Here, we present whole genome DNA methylation data for two F. excelsior genotypes with high susceptibility to ADB, and two genotypes with low susceptibility, each clonally replicated. We also include two genotypes of Manchurian ash (F. mandshurica), an ash species which has co-evolved with H. fraxineus and also has low susceptibility to ADB. Results In F. excelsior, we find an average methylation level of 76.2% in the CG context, 52.0% in the CHG context, and 13.9% in the CHH context; similar levels to those of tomato. We find higher methylation in transposable elements as opposed to non-mobile elements, and high densities of Non-Differentially Methylation Positions (N-DMPs) in genes with housekeeping functions. Of genes putatively duplicated in whole genome duplication (WGD) events, an average of 25.9% are differentially methylated in at least one cytosine context, potentially indicative of unequal silencing. Variability in methylation patterns exists among clonal replicates, and this is only slightly less than the variability found between different genotypes. Of twenty genes previously found to have expression levels associated with ADB susceptibility, we find only two of these have differential methylation between high and low susceptibility F. excelsior trees. In addition, we identify 1683 significant Differentially Methylated Regions (DMRs) (q-value< 0.001) between the high and low susceptibility genotypes of F. excelsior trees, of which 665 remain significant when F. mandshurica samples are added to the low susceptibility group. Conclusions We find a higher frequency of differentially methylated WGD-derived gene duplicates in ash than other plant species previously studied. We also identify a set of genes with differential methylation between genotypes and species with high versus low susceptibility to ADB. This provides valuable foundational data for future work on the role that epigenetics may play in gene dosage compensation and susceptibility to ADB in ash. Electronic supplementary material The online version of this article (10.1186/s12864-018-4874-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth S A Sollars
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK. .,Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK.
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49
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Henry IM, Akagi T, Tao R, Comai L. One Hundred Ways to Invent the Sexes: Theoretical and Observed Paths to Dioecy in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:553-575. [PMID: 29719167 DOI: 10.1146/annurev-arplant-042817-040615] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dioecy, the presence of male and female flowers on separate individuals, is both widespread and uncommon within flowering plants, with only a few percent of dioecious species spread across most major phylogenetic taxa. It is therefore safe to assume that dioecy evolved independently in these different groups, which allows us to ask questions regarding the molecular and developmental mechanisms underlying these independent transitions to dioecy. We start this review by examining the problem from the standpoint of a genetic engineer trying to develop dioecy, discuss various potential solutions, and compare them to models proposed in the past and based on genetic and evolutionary considerations. Next, we present recent information regarding candidate sex determinants in three species, acquired using newly established genomic approaches. Although such specific information is still scarce, it is slowly becoming apparent that various genes or pathways can be altered to evolve dioecy.
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Affiliation(s)
- Isabelle M Henry
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
| | - Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Luca Comai
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
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50
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Akagi T, Henry IM, Ohtani H, Morimoto T, Beppu K, Kataoka I, Tao R. A Y-Encoded Suppressor of Feminization Arose via Lineage-Specific Duplication of a Cytokinin Response Regulator in Kiwifruit. THE PLANT CELL 2018; 30:780-795. [PMID: 29626069 PMCID: PMC5969274 DOI: 10.1105/tpc.17.00787] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/13/2018] [Accepted: 04/05/2018] [Indexed: 05/19/2023]
Abstract
Dioecy, the presence of male and female flowers on distinct individuals, has evolved independently in multiple plant lineages, and the genes involved in this differential development are just starting to be uncovered in a few species. Here, we used genomic approaches to investigate this pathway in kiwifruits (genus Actinidia). Genome-wide cataloging of male-specific subsequences, combined with transcriptome analysis, led to the identification of a type-C cytokinin response regulator as a potential sex determinant gene in this genus. Functional transgenic analyses in two model systems, Arabidopsis thaliana and Nicotiana tabacum, indicated that this gene acts as a dominant suppressor of carpel development, prompting us to name it Shy Girl (SyGI). Evolutionary analyses in a panel of Actinidia species revealed that SyGI is located in the Y-specific region of the genome and probably arose from a lineage-specific gene duplication. Comparisons with the duplicated autosomal counterpart, and with orthologs from other angiosperms, suggest that the SyGI-specific duplication and subsequent evolution of cis-elements may have played a key role in the acquisition of separate sexes in this species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, California 95616
| | - Haruka Ohtani
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takuya Morimoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kenji Beppu
- Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Ikuo Kataoka
- Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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