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Soorni A, Rezvani M, Bigdeli H. Transcriptome-guided selection of stable reference genes for expression analysis in spinach. Sci Rep 2024; 14:22113. [PMID: 39333266 PMCID: PMC11436919 DOI: 10.1038/s41598-024-73444-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Accurate measurement of gene expression levels is vital for advancing plant biology research. This study explores the identification and validation of stable reference genes (RGs) for gene expression analysis in Spinacia oleracea. Leveraging transcriptome data from various developmental stages, we employed rigorous statistical analyses to identify potential RGs. A total of 1196 candidate genes were initially screened based on expression variability, with subsequent refinement using criteria such as low variance and stability. Among 12 commonly used candidate RGs, EF1α and H3 emerged as the most stable across diverse experimental conditions, while GRP and PPR exhibited lower stability. These findings were further validated through qRT-PCR assays and comprehensive statistical analyses, including geNorm, NormFinder, BestKeeper, and RefFinder. Our study underscores the importance of systematic RG selection to ensure accurate normalization in gene expression studies, particularly in the context of S. oleracea developmental stages and physiological processes like flowering. These validated RGs provide a robust foundation for future gene expression analysis in S. oleracea and contribute to the advancement of molecular research in plant biology.
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Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | - Maryam Rezvani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Haniye Bigdeli
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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2
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Fatima M, Ma X, Zhang J, Ming R. Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach. Sci Rep 2024; 14:18635. [PMID: 39128921 PMCID: PMC11317516 DOI: 10.1038/s41598-024-68965-9] [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: 09/13/2023] [Accepted: 07/30/2024] [Indexed: 08/13/2024] Open
Abstract
Evolution of unisexual flowers involves extreme changes in floral development. Spinach is one of the species to discern the formation and evolution of dioecy. MADS-box gene family is involved in regulation of floral organ identity and development and in many other plant developmental processes. However, there is no systematic analysis of MADS-box family genes in spinach. A comprehensive genome-wide analysis and transcriptome profiling of MADS-box genes were undertaken to understand their involvement in unisexual flower development at different stages in spinach. In total, 54 MADS-box genes found to be unevenly located across 6 chromosomes and can be divided into type I and type II genes. Twenty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups. While thirty-four type II SoMADSs consist of 3 MIKC*, and 31 MIKCC -type genes including sixteen floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in spinach. Gene structure, motif distribution, physiochemical properties, gene duplication and collinearity analyses for these genes are performed in detail. Promoters of both types of SoMADS genes contain mainly MeJA and ABA response elements. Expression profiling indicated that MIKCc genes exhibited more dynamic and intricate expression patterns compared to M-type genes and the majority of type-II genes AP1, SVP, and SOC1 sub-groups showed female flower-biased expression profiles, suggesting their role in carpel development, while PI showed male-biased expression throughout flower developmental stages, suggesting their role in stamen development. These results provide genomic resources and insights into spinach dioecious flower development and expedite spinach improvement.
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Affiliation(s)
- Mahpara Fatima
- College of Life Science, FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaokai Ma
- College of Life Science, FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jisen Zhang
- College of Life Science, FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Ray Ming
- College of Life Science, FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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3
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She H, Liu Z, Xu Z, Zhang H, Wu J, Wang X, Cheng F, Charlesworth D, Qian W. Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra. THE NEW PHYTOLOGIST 2024; 243:477-494. [PMID: 38715078 DOI: 10.1111/nph.19799] [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: 02/12/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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4
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Nguyen-Hoang A, Sandell FL, Himmelbauer H, Dohm JC. Spinach genomes reveal migration history and candidate genes for important crop traits. NAR Genom Bioinform 2024; 6:lqae034. [PMID: 38633427 PMCID: PMC11023180 DOI: 10.1093/nargab/lqae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.
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Affiliation(s)
- An Nguyen-Hoang
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Felix L Sandell
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
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5
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Ma Y, Fu W, Wan S, Li Y, Mao H, Khalid E, Zhang W, Ming R. Gene Regulatory Network Controlling Flower Development in Spinach ( Spinacia oleracea L.). Int J Mol Sci 2024; 25:6127. [PMID: 38892313 PMCID: PMC11173220 DOI: 10.3390/ijms25116127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as the differences in the regulatory mechanisms of floral organ development of dioecious and monoecious flowers. We compared transcriptional-level differences between different genders and identified differentially expressed genes (DEGs) related to spinach floral development, as well as sex-biased genes to investigate the flower development mechanisms in spinach. In this study, 9189 DEGs were identified among the different genders. DEG analysis showed the participation of four main transcription factor families, MIKC_MADS, MYB, NAC, and bHLH, in spinach flower development. In our key findings, abscisic acid (ABA) and gibberellic acid (GA) signal transduction pathways play major roles in male flower development, while auxin regulates both male and female flower development. By constructing a gene regulatory network (GRN) for floral organ development, core transcription factors (TFs) controlling organ initiation and growth were discovered. This analysis of the development of female, male, and monoecious flowers in spinach provides new insights into the molecular mechanisms of floral organ development and sexual differentiation in dioecious and monoecious plants in spinach.
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Affiliation(s)
- Yaying Ma
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.M.); (W.F.)
- 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; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Wenhui Fu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.M.); (W.F.)
| | - Suyan Wan
- 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; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Yikai Li
- 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; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Haoming Mao
- 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; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Ehsan Khalid
- 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; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Wenping Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - 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; (S.W.); (Y.L.); (H.M.); (E.K.)
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Zhang YL, Wang LY, Yang Y, Zhao X, Zhu HW, You C, Chen N, Wei SJ, Li SF, Gao WJ. Gibberellins regulate masculinization through the SpGAI-SpSTM module in dioecious spinach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1907-1921. [PMID: 38491869 DOI: 10.1111/tpj.16717] [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: 04/26/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3, showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.
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Affiliation(s)
- Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yi Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xu Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chen You
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Ning Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shuai-Jie Wei
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shu-Fen Li
- 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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7
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Charlesworth D, Harkess A. Why should we study plant sex chromosomes? THE PLANT CELL 2024; 36:1242-1256. [PMID: 38163640 PMCID: PMC11062472 DOI: 10.1093/plcell/koad278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/10/2023] [Indexed: 01/03/2024]
Abstract
Understanding plant sex chromosomes involves studying interactions between developmental and physiological genetics, genome evolution, and evolutionary ecology. We focus on areas of overlap between these. Ideas about how species with separate sexes (dioecious species, in plant terminology) can evolve are even more relevant to plants than to most animal taxa because dioecy has evolved many times from ancestral functionally hermaphroditic populations, often recently. One aim of studying plant sex chromosomes is to discover how separate males and females evolved from ancestors with no such genetic sex-determining polymorphism, and the diversity in the genetic control of maleness vs femaleness. Different systems share some interesting features, and their differences help to understand why completely sex-linked regions may evolve. In some dioecious plants, the sex-determining genome regions are physically small. In others, regions without crossing over have evolved sometimes extensive regions with properties very similar to those of the familiar animal sex chromosomes. The differences also affect the evolutionary changes possible when the environment (or pollination environment, for angiosperms) changes, as dioecy is an ecologically risky strategy for sessile organisms. Dioecious plants have repeatedly reverted to cosexuality, and hermaphroditic strains of fruit crops such as papaya and grapes are desired by plant breeders. Sex-linked regions are predicted to become enriched in genes with sex differences in expression, especially when higher expression benefits one sex function but harms the other. Such trade-offs may be important for understanding other plant developmental and physiological processes and have direct applications in plant breeding.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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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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9
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Zhang Z, Liu Z, Wu H, Xu Z, Zhang H, Qian W, Gao W, She H. Genome-Wide Identification and Characterization of MYB Gene Family and Analysis of Its Sex-Biased Expression Pattern in Spinacia oleracea L. Int J Mol Sci 2024; 25:795. [PMID: 38255867 PMCID: PMC10815031 DOI: 10.3390/ijms25020795] [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: 11/27/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
The members of the myeloblastosis (MYB) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, such as circadian rhythm, metabolism, and flower development. However, the characterization of MYB genes across the genomes of spinach Spinacia oleracea L. has not been reported. Here, we identified 140 MYB genes in spinach and described their characteristics using bioinformatics approaches. Among the MYB genes, 54 were 1R-MYB, 80 were 2R-MYB, 5 were 3R-MYB, and 1 was 4R-MYB. Almost all MYB genes were located in the 0-30 Mb region of autosomes; however, the 20 MYB genes were enriched at both ends of the sex chromosome (chromosome 4). Based on phylogeny, conserved motifs, and the structure of genes, 2R-MYB exhibited higher conservation relative to 1R-MYB genes. Tandem duplication and collinearity of spinach MYB genes drive their evolution, enabling the functional diversification of spinach genes. Subcellular localization prediction indicated that spinach MYB genes were mainly located in the nucleus. Cis-acting element analysis confirmed that MYB genes were involved in various processes of spinach growth and development, such as circadian rhythm, cell differentiation, and reproduction through hormone synthesis. Furthermore, through the transcriptome data analysis of male and female flower organs at five different periods, ten candidate genes showed biased expression in spinach males, suggesting that these genes might be related to the development of spinach anthers. Collectively, this study provides useful information for further investigating the function of MYB TFs and novel insights into the regulation of sex determination in spinach.
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Affiliation(s)
- Zhilong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
| | - Hao Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China (W.Q.)
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10
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Ma X, Ju S, Lin H, Huang H, Huang J, Peng D, Ming R, Lan S, Liu ZJ. Sex-Related Gene Network Revealed by Transcriptome Differentiation of Bisexual and Unisexual Flowers of Orchid Cymbidium tortisepalum. Int J Mol Sci 2023; 24:16627. [PMID: 38068950 PMCID: PMC10706266 DOI: 10.3390/ijms242316627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Despite extensive research on orchid reproductive strategies, the genetic studies of sex differentiation in the orchid family are still lacking. In this study, we compared three sexual phenotypes of Cymbidium tortisepalum bisexual flowers as well as female and male unisexual mutants. Through comparative transcriptomes, we analyzed the sex-biased differentially expressed genes (DEGs) and gene co-expression networks of sex organs (gynostemium and ovary) among them, identified the candidate genes of sex differentiation, and validated their expression by qRT-PCR. The C. tortisepalum unisexual mutants with degenerated phenotypes were compared to the bisexual plants with respect to both the flower organs and plant morphologies. Totally, 12,145, 10,789, and 14,447 genes were uniquely expressed in the female, male, and hermaphrodite sex organs, respectively. A total of 4291 sex-biased DEGs were detected among them, with 871, 2867, and 1937 DEGs in the comparisons of bisexual vs. female, bisexual vs. male, and male vs. female flowers, respectively. Two co-expressed network modules, with 81 and 419 genes were tightly correlated with female sexual traits, while two others with 265 and 135 genes were highly correlated with male sexual traits. Two female-biased hub genes (CtSDR3b and CtSDR3b-like) nested in the female modules, the homologs of maize sex determinant tasselseed2, may control the feminization of C. tortisepalum. At the same time, two male-biased hub genes (CtYAB2 and CtYAB5) nested in the male modules, the homologs of grape sex determinant VviYABBY3, may control the androphany of C. tortisepalum. This study discovered the molecular regulation networks and proposed a model for orchid sex differentiation, therefore providing for the first time the genetic basis for the sex separation in the orchid family.
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Affiliation(s)
- Xiaokai Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Song Ju
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Han Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huaxing Huang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Donghui Peng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3707, USA
| | - Siren Lan
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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11
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Li N, Zhou J, Zhang W, Liu W, Wang B, She H, Mirbahar AA, Li S, Zhang Y, Gao W, Qian W, Deng C. A rapid method for assembly of single chromosome and identification of sex determination region based on single-chromosome sequencing. THE NEW PHYTOLOGIST 2023; 240:892-903. [PMID: 37533136 DOI: 10.1111/nph.19176] [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: 04/18/2023] [Accepted: 07/08/2023] [Indexed: 08/04/2023]
Abstract
The sex-determining-region (SDR) may offer the best prospects for studying sex-determining gene, recombination suppression, and chromosome heteromorphism. However, current progress of SDR identification and cloning showed following shortcomings: large near-isogenic lines need to be constructed, and a relatively large population is needed; the cost of whole-genome sequencing and assembly is high. Herein, the X/Y chromosomes of Spinacia oleracea L. subsp. turkestanica were successfully microdissected and assembled using single-chromosome sequencing. The assembly length of X and Y chromosome is c. 192.1 and 195.2 Mb, respectively. Three large inversions existed between X and Y chromosome. The SDR size of X and Y chromosome is c. 13.2 and 24.1 Mb, respectively. MSY region and six male-biased genes were identified. A Y-chromosome-specific marker in SDR was constructed and used to verify the chromosome assembly quality at cytological level via fluorescence in situ hybridization. Meanwhile, it was observed that the SDR located on long arm of Y chromosome and near the centromere. Overall, a technical system was successfully established for rapid cloning the SDR and it is also applicable to rapid assembly of specific chromosome in other plants. Furthermore, this study laid a foundation for studying the molecular mechanism of sex chromosome evolution in spinach.
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Affiliation(s)
- Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Jian Zhou
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wanqing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wenjia Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Bingxin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ameer Ahmed Mirbahar
- Date Palm Research Institute, Shah Abdul Latif University, Khairpur, Sindh, 66020, Pakistan
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yulan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
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12
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She H, Liu Z, Li S, Xu Z, Zhang H, Cheng F, Wu J, Wang X, Deng C, Charlesworth D, Gao W, Qian W. Evolution of the spinach sex-linked region within a rarely recombining pericentromeric region. PLANT PHYSIOLOGY 2023; 193:1263-1280. [PMID: 37403642 DOI: 10.1093/plphys/kiad389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a "Y duplication region" or "YDR" whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Kafkas S, Ma X, Zhang X, Topçu H, Navajas-Pérez R, Wai CM, Tang H, Xu X, Khodaeiaminjan M, Güney M, Paizila A, Karcı H, Zhang X, Lin J, Lin H, Herrán RDL, Rejón CR, García-Zea JA, Robles F, Muñoz CDV, Hotz-Wagenblatt A, Min XJ, Özkan H, Motalebipour EZ, Gozel H, Çoban N, Kafkas NE, Kilian A, Huang H, Lv X, Liu K, Hu Q, Jacygrad E, Palmer W, Michelmore R, Ming R. Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution. PLANT COMMUNICATIONS 2023; 4:100497. [PMID: 36435969 DOI: 10.1016/j.xplc.2022.100497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 10/01/2022] [Accepted: 11/23/2022] [Indexed: 05/11/2023]
Abstract
Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.
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Affiliation(s)
- Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hayat Topçu
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuming Xu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Mortaza Khodaeiaminjan
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Murat Güney
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Aibibula Paizila
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Harun Karcı
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Xiaodan Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jing Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Han Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | | | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Coral Del Val Muñoz
- Department of Computer Science, University of Granada, Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain
| | - Agnes Hotz-Wagenblatt
- German Cancer Research Center, Omics IT and Data Management Core Facility, Heidelberg, Germany
| | - Xiangjia Jack Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | | | - Hatice Gozel
- Pistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey
| | - Nergiz Çoban
- Pistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey
| | - Nesibe Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Andrej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, ACT, Australia
| | - HuaXing Huang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanrui Lv
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kunpeng Liu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qilin Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ewelina Jacygrad
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - William Palmer
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Richard Michelmore
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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14
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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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15
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Raiyemo DA, Bobadilla LK, Tranel PJ. Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes. BMC Biol 2023; 21:37. [PMID: 36804015 PMCID: PMC9940365 DOI: 10.1186/s12915-023-01539-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions. RESULTS We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination. CONCLUSIONS The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.
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Affiliation(s)
- Damilola A Raiyemo
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
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16
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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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17
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Li N, Wang Y, Wang J, Zhang W, Meng Z, Wang Y, Zhang Y, Li S, Gao W, Deng C. Identification of Sex Differentiation-Related microRNAs in Spinach Female and Male Flower. Int J Mol Sci 2022; 23:4090. [PMID: 35456907 PMCID: PMC9029227 DOI: 10.3390/ijms23084090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Sex determination and differentiation is an important biological process for unisexual flower development. Spinach is a model plant to study the mechanism of sex determination and differentiation of dioecious plant. Till now, little is known about spinach sex determination and differentiation mechanism. MicroRNAs are key factors in flower development. Herein, small RNA sequencing was performed to explore the roles of microRNAs in spinach sex determination and differentiation. As a result, 92 known and 3402 novel microRNAs were identified in 18 spinach female and male flower samples. 74 differentially expressed microRNAs were identified between female and male flowers, including 20 female-biased and 48 male-biased expression microRNAs. Target prediction identified 22 sex-biased microRNA-target pairs, which may be involved in spinach sex determination or differentiation. Among the differentially expressed microRNAs between FNS and M03, 55 microRNAs were found to reside in sex chromosome; one of them, sol-miR2550n, was functionally studied via genetic transformation. Silencing of sol-miR2550n resulted in abnormal anther while overexpression of sol-miR2550n induced early flowering, indicating sol-miR2550n was a male-promoting factor and validating the reliability of our small RNA sequencing data. Conclusively, this work can supply valuable information for exploring spinach sex determination and differentiation and provide a new insight in studying unisexual flower development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (N.L.); (Y.W.); (J.W.); (W.Z.); (Z.M.); (Y.W.); (Y.Z.); (S.L.); (W.G.)
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