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Akagi T, Sugano SS. Random epigenetic inactivation of the X-chromosomal HaMSter gene causes sex ratio distortion in persimmon. NATURE PLANTS 2024:10.1038/s41477-024-01805-w. [PMID: 39333352 DOI: 10.1038/s41477-024-01805-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/06/2024] [Indexed: 09/29/2024]
Abstract
In contrast to the recent progress in the genome sequencing of plant sex chromosomes, the functional contribution of the genes in sex chromosomes remains little known1. They were classically thought to be related to sexual dimorphism, which is beneficial to male or female functions, including segregation ratios. Here we focused on the functional evolution of the sex ratio distortion-related locus Half Male Sterile/Inviable (HaMSter), which is located in the short sex-linked region in diploid persimmon (Diospyros lotus). The expression of HaMSter, encoding a plant1589-like undefined protein, is necessary for production of viable seeds. Notably, only X-allelic HaMSter is substantially expressed and half of the maternal X alleles of HaMSter is randomly inactivated, which results in sex ratio distortion in seeds. Genome-wide DNA methylome analyses revealed endosperm-specific DNA hypermethylation, especially in the X-linked region. The maintenance/release of this hypermethylation is linked to inactivation/activation of HaMSter expression, respectively, which determines the sex ratio distortion pattern.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, Japan.
| | - Shigeo S Sugano
- Bioproduction Research Institute, The National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Nashiki A, Matsuo H, Takano K, Fitriyah F, Isobe S, Shirasawa K, Yoshioka Y. Identification of novel sex determination loci in Japanese weedy melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:136. [PMID: 37231314 DOI: 10.1007/s00122-023-04381-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE Japanese weedy melon exhibits unique sex expression with interactions between previously reported sex determination genes and two novel loci. Sex expression contributes to fruit quality and yield in the Cucurbitaceae. In melon, orchestrated regulation by sex determination genes explains the mechanism of sex expression, resulting in a great variety of sexual morphologies. In this study, we examined the Japanese weedy melon UT1, which does not follow the reported model of sex expression. We conducted QTL analysis using F2 plants for flower sex on the main stem and the lateral branch and mapped "occurrence of pistil-bearing flower on the main stem" locus on Chr. 3 (Opbf3.1) and "type of pistil-bearing flower" (female or bisexual) loci on Chr. 2 (tpbf2.1) and Chr. 8 (tpbf8.1). The Opbf3.1 included the known sex determination gene CmACS11. Sequence comparison of CmACS11 between parental lines revealed three nonsynonymous SNPs. A CAPS marker developed from one of the SNPs was closely linked to the occurrence of pistil-bearing flowers on the main stem in two F2 populations with different genetic backgrounds. The UT1 allele on Opbf3.1 was dominant in F1 lines from crosses between UT1 and diverse cultivars and breeding lines. This study suggests that Opbf3.1 and tpbf8.1 may promote the development of pistil and stamen primordia by inhibiting CmWIP1 and CmACS-7 functions, respectively, making the UT1 plants hermaphrodite. The results of this study provide new insights into the molecular mechanisms of sex determination in melons and considerations for the application of femaleness in melon breeding.
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Affiliation(s)
- Akito Nashiki
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroki Matsuo
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kota Takano
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Fauziatul Fitriyah
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Yosuke Yoshioka
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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He L, Fan Y, Zhang Z, Wei X, Yu J. Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach. Genes (Basel) 2023; 14:661. [PMID: 36980934 PMCID: PMC10048520 DOI: 10.3390/genes14030661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers' morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.
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Affiliation(s)
| | | | - Zhao Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
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Harnessing epigenetic variability for crop improvement: current status and future prospects. Genes Genomics 2021; 44:259-266. [PMID: 34807374 DOI: 10.1007/s13258-021-01189-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/07/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that supplements the genetics-based view of complex life phenomena. In crop breeding, the decrease in genetic diversity due to artificial selection of conventional breeding methods has been a long-standing concern. Therefore, the epigenetic diversity has been proposed as a new resource for future crop breeding, which will be hereinafter referred to as epibreeding. DISCUSSION The induction of methylome changes has been performed in plants by several methods including chemical drugs treatment and tissue culture. Target-specific epigenetic engineering has been also attempted by exogenous RNAi mediated by virus-induced gene silencing and grafting. Importantly, the new and innovative techniques including the CRISPR-Cas9 system have recently been adopted in epigenetic engineering of plant genomes, facilitating the efforts for epibreeding. CONCLUSION In this review, we introduce several examples of natural and induced epigenetic changes impacting on agronomic traits and discuss the methods for generating epigenomic diversity and site-specific epigenetic engineering.
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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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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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Mochida K, Nishii R, Hirayama T. Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. PLANT & CELL PHYSIOLOGY 2020; 61:1408-1418. [PMID: 32392328 PMCID: PMC7434589 DOI: 10.1093/pcp/pcaa064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/26/2020] [Indexed: 05/16/2023]
Abstract
To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants' later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant-environment interactions by elucidating plants' temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant-environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Corresponding author: E-mail, ; Fax, +81-45-503-9609
| | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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