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Basit A, Lim KB. Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112236. [PMID: 39186951 DOI: 10.1016/j.plantsci.2024.112236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 08/15/2024] [Accepted: 08/18/2024] [Indexed: 08/28/2024]
Abstract
Polyploidy is thought to be an evolutionary and systematic mechanism for gene flow and phenotypic advancement in flowering plants. It is a natural phenomenon that promotes diversity by creating new permutations enhancing the prime potentials as compared to progenitors. Two different pathways have been recognized in studying polyploidy in nature; mitotic or somatic chromosome doubling and cytogenetics variation. Secondly, the vital influence of being polyploid is its heritable property (unreduced reproductive cells) formed during first and second-division restitution (FDR & SDR). Different approaches either chemical (Colchicine, Oryzalin, Caffeine, Trifuralin, or phosphoric amides) or gaseous i.e. Nitrous oxide have been deliberated as strong polyploidy causing agents. A wide range of cytogenetic practices like chromosomes study, ploidy, genome analysis, and plant morphology and anatomy have been studied in different plant species. Flow cytometry for ploidy and chromosome analysis through fluorescence and genomic in situ hybridization (FISH & GISH) are the basic methods to evaluate heredity substances sampled from leaves and roots. Many horticultural crops have been developed successfully and released commercially for consumption. Moreover, some deep detailed studies are needed to check the strong relationship between unique morphological features and genetic makeup concerning genes and hormonal expression in a strong approach.
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Affiliation(s)
- Abdul Basit
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea.
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, South Korea.
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2
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Bray SM, Hämälä T, Zhou M, Busoms S, Fischer S, Desjardins SD, Mandáková T, Moore C, Mathers TC, Cowan L, Monnahan P, Koch J, Wolf EM, Lysak MA, Kolar F, Higgins JD, Koch MA, Yant L. Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids. Cell Rep 2024; 43:114576. [PMID: 39116207 DOI: 10.1016/j.celrep.2024.114576] [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: 11/08/2023] [Revised: 05/17/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024] Open
Abstract
Whole-genome duplication (WGD) occurs in all kingdoms and impacts speciation, domestication, and cancer outcome. However, doubled DNA management can be challenging for nascent polyploids. The study of within-species polyploidy (autopolyploidy) permits focus on this DNA management aspect, decoupling it from the confounding effects of hybridization (in allopolyploid hybrids). How is autopolyploidy tolerated, and how do young polyploids stabilize? Here, we introduce a powerful model to address this: the genus Cochlearia, which has experienced many polyploidization events. We assess meiosis and other polyploid-relevant phenotypes, generate a chromosome-scale genome, and sequence 113 individuals from 33 ploidy-contrasting populations. We detect an obvious autopolyploidy-associated selection signal at kinetochore components and ion transporters. Modeling the selected alleles, we detail evidence of the kinetochore complex mediating adaptation to polyploidy. We compare candidates in independent autopolyploids across three genera separated by 40 million years, highlighting a common function at the process and gene levels, indicating evolutionary flexibility in response to polyploidy.
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Affiliation(s)
- Sian M Bray
- The University of Nottingham, Nottingham NG7 2RD, UK; The John Innes Centre, Norwich NR4 7UH, UK
| | - Tuomas Hämälä
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Min Zhou
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Silvia Busoms
- The John Innes Centre, Norwich NR4 7UH, UK; Department of Plant Physiology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Sina Fischer
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Stuart D Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Chris Moore
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laura Cowan
- The University of Nottingham, Nottingham NG7 2RD, UK
| | | | | | - Eva M Wolf
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Filip Kolar
- Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic; The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Levi Yant
- The University of Nottingham, Nottingham NG7 2RD, UK; Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic.
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3
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Wang T, van Dijk ADJ, Zhao R, Bonnema G, Wang X. Contribution of homoeologous exchange to domestication of polyploid Brassica. Genome Biol 2024; 25:231. [PMID: 39192349 DOI: 10.1186/s13059-024-03370-z] [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: 12/10/2023] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoeologous exchange (HE) events between the subgenomes, causing changes in genomic composition, gene expression, and phenotypic variations. However, the role of HE in plant adaptation and domestication remains unclear. RESULTS Here we analyze the whole-genome resequencing data from Brassica napus accessions representing the different morphotypes and ecotypes, to investigate the role of HE in domestication. Our findings demonstrate frequent occurrence of HEs in Brassica napus, with substantial HE patterns shared across populations, indicating their potential role in promoting crop domestication. HE events are asymmetric, with the A genome more frequently replacing C genome segments. These events show a preference for specific genomic regions and vary among populations. We also identify candidate genes in HE regions specific to certain populations, which likely contribute to flowering-time diversification across diverse morphotypes and ecotypes. In addition, we assemble a new genome of a swede accession, confirming the HE signals on the genome and their potential involvement in root tuber development. By analyzing HE in another allopolyploid species, Brassica juncea, we characterize a potential broader role of HE in allopolyploid crop domestication. CONCLUSIONS Our results provide novel insights into the domestication of polyploid Brassica species and highlight homoeologous exchange as a crucial mechanism for generating variations that are selected for crop improvement in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Ranze Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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Wang J, Wang R, Luo F, Du W, Hou J, Chen G, Tang X, Wu J, Wang W, Huang B, Wang C, Yuan L. Comparative Morphological, Physiological, and Transcriptomic Analyses of Diploid and Tetraploid Wucai ( Brassica campestris L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2341. [PMID: 39204777 PMCID: PMC11359193 DOI: 10.3390/plants13162341] [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: 06/24/2024] [Revised: 08/10/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Polyploid plants often exhibit superior yield, stress resistance, and quality. In this study, homologous tetraploid wucai (Brassica campestris L.) was successfully obtained by spraying seedling growth points with colchicine. The morphological, cytological, and physiological characteristics of diploid and tetraploid wucai were analyzed, and transcriptomic sequencing was performed at three stages of development. Tetraploid seedings grew slowly but exhibited darker leaves, enlarged organs and cells, increased stomatal volume, decreased stomatal density, improved nutritional content, and enhanced photosynthesis. Differentially expressed genes (DEGs) identified in diploid and tetraploid plants at three stages of development were enriched in different pathways. Notably, DEGs identified in the tetraploid plants were specifically enriched in starch and sucrose metabolism, pentose and glucuronate interconversions, and ascorbate and aldarate metabolism. In addition, we found that the light green module was most relevant to ploidy, and DEGs in this module were significantly enriched in the glycolysis/gluconeogenesis and TCA cycle pathways. The differential expression of key glycolysis-associated genes at different developmental stages may be the driver of the observed differences between diploid and tetraploid wucai. This study lays a technical foundation for the development of polyploid wucai germplasm resources as well as the breeding of new varieties with improved quality, yield, and stress resistance. It also provides a good empirical reference for the genetic breeding of closely related Brassica species.
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Affiliation(s)
- Jian Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Ruxi Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Fan Luo
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Wenjing Du
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jianqiang Wu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Wenjie Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Bin Huang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
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Lv Z, Addo Nyarko C, Ramtekey V, Behn H, Mason AS. Defining autopolyploidy: Cytology, genetics, and taxonomy. AMERICAN JOURNAL OF BOTANY 2024; 111:e16292. [PMID: 38439575 DOI: 10.1002/ajb2.16292] [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: 09/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 03/06/2024]
Abstract
Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, "genetic" or "cytological" autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker-segregation-based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types.
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Affiliation(s)
- Zhenling Lv
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Charles Addo Nyarko
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Vinita Ramtekey
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- ICAR-Indian Institute of Seed Science, 275103, Mau, India
| | - Helen Behn
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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6
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Barker MS, Jiao Y, Glennon KL. Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy. AMERICAN JOURNAL OF BOTANY 2024; 111:e16395. [PMID: 39164922 DOI: 10.1002/ajb2.16395] [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: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024]
Abstract
All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.
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Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, 85721, AZ, USA
| | - Yuannian Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kelsey L Glennon
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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7
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Conover JL, Grover CE, Sharbrough J, Sloan DB, Peterson DG, Wendel JF. Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids. AMERICAN JOURNAL OF BOTANY 2024; 111:e16386. [PMID: 39107998 DOI: 10.1002/ajb2.16386] [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: 05/27/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 08/24/2024]
Abstract
PREMISE A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. METHODS Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange. RESULTS We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species. CONCLUSIONS Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0-0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.
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Affiliation(s)
- Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50010, IA, USA
- Ecology and Evolutionary Biology Department, University of Arizona, Tucson, 85718, AZ, USA
- Molecular and Cellular Biology Department, University of Arizona, Tucson, 85718, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50010, IA, USA
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, 87801, NM, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, 80521, CO, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, 39762, MS, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50010, IA, USA
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8
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Wu J, Zhang L, Ma X, Fu X, Chen F, Jiao Y, Liu J, Wu S. The evolutionary significance of whole genome duplications in oil biosynthesis of oil crops. HORTICULTURE RESEARCH 2024; 11:uhae156. [PMID: 39006001 PMCID: PMC11246240 DOI: 10.1093/hr/uhae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/30/2024] [Indexed: 07/16/2024]
Affiliation(s)
- Jingjing Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Linjing Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Xiaohui Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Xinxing Fu
- College of Life Sciences, Northwest Normal University, Lanzhou 730070, China
| | - Fei Chen
- National Key Laboratory for Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yuannian Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shengdan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
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9
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Choi SS, Mc Cartney A, Park D, Roberts H, Brav-Cubitt T, Mitchell C, Buckley TR. Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects. Mol Ecol 2024:e17422. [PMID: 38842022 DOI: 10.1111/mec.17422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 04/17/2024] [Indexed: 06/07/2024]
Abstract
During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyploid invertebrate genomes. If HEB is constrained by features of the parental genomes, then we predict repeated evolution of similar HEB patterns among hybrid genomes formed from the same parental lineages. To address this, we reconstructed the history of hybridization between the New Zealand stick insect genera Acanthoxyla and Clitarchus using a high-quality genome assembly from Clitarchus hookeri to call variants and phase alleles. These analyses revealed the formation of three independent diploid and triploid hybrid lineages between these genera. RNA sequencing revealed a similar magnitude and direction of HEB among these hybrid lineages, and we observed that many enriched functions and pathways were also shared among lineages, consistent with repeated evolution due to parental genome constraints. In most hybrid lineages, a slight majority of the genes involved in mitochondrial function showed HEB towards the maternal homoeologues, consistent with only weak effects of mitonuclear incompatibility. We also observed a proteasome functional enrichment in most lineages and hypothesize this may result from the need to maintain proteostasis in hybrid genomes. Reference bias was a pervasive problem, and we caution against relying on HEB estimates from a single parental reference genome.
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Affiliation(s)
- Seung-Sub Choi
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Ann Mc Cartney
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Duckchul Park
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Hester Roberts
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
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10
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Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, Bass HW, Wendel JF. Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton. Mol Biol Evol 2024; 41:msae095. [PMID: 38758089 PMCID: PMC11140268 DOI: 10.1093/molbev/msae095] [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: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
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Affiliation(s)
- Guanjing Hu
- State Key Laboratory of Cotton Bio-breeding and Integrated, Chinese Academy of Agricultural Sciences, Institute of Cotton Research, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | | | - Emma R Miller
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Justin L Conover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shujun Ou
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - De Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Dongming Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Joseph P Gallagher
- Forage Seed and Cereal Research Unit, USDA/Agricultural Research Service, Corvallis, OR 97331, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, College Station, TX 77845, USA
| | - Xin Sui
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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11
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Shahbazi M, Majka J, Kubíková D, Zwierzykowski Z, Glombik M, Wendel JF, Sharbrough J, Hartmann S, Szecówka M, Doležel J, Bartoš J, Kopecký D, Kneřová J. Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1102-1118. [PMID: 38323852 DOI: 10.1111/tpj.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/15/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.
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Affiliation(s)
- Mehrdad Shahbazi
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Joanna Majka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Denisa Kubíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Marek Glombik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, Iowa, USA
| | - Joel Sharbrough
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, 87801, USA
| | - Stephan Hartmann
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 4, 85354, Freising, Germany
| | - Marek Szecówka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Kneřová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
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12
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Shan S, Gitzendanner MA, Boatwright JL, Spoelhof JP, Ethridge CL, Ji L, Liu X, Soltis PS, Schmitz RJ, Soltis DE. Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid Tragopogon miscellus (Asteraceae). THE NEW PHYTOLOGIST 2024; 242:1363-1376. [PMID: 38450804 DOI: 10.1111/nph.19655] [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: 09/18/2023] [Accepted: 01/15/2024] [Indexed: 03/08/2024]
Abstract
Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.
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Affiliation(s)
- Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - J Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
| | - Jonathan P Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Xiaoxian Liu
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Bioinformatics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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13
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [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: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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14
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Ou Y, Li H, Li J, Dai X, He J, Wang S, Liu Q, Yang C, Wang J, Zhao R, Yin Z, Shu Y, Liu S. Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based on cntd1 Knockout in Zebrafish. Mol Biol Evol 2024; 41:msae047. [PMID: 38421617 PMCID: PMC10939445 DOI: 10.1093/molbev/msae047] [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: 08/11/2023] [Revised: 02/02/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024] Open
Abstract
Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the cyclin N-terminal domain containing 1 (cntd1) using CRISPR/Cas9 technology. This resulted in impaired formation of meiotic crossovers, leading to cell-cycle arrest during meiotic metaphase and triggering apoptosis of spermatocytes in the testes. Despite these defects, the mutant (cntd1-/-) males were still able to produce a limited amount of sperm with normal ploidy and function. Interestingly, in the mutant females, it was the ploidy not the capacity of egg production that was altered. This resulted in the production of haploid, aneuploid, and unreduced gametes. This alteration enabled us to successfully obtain triploid and tetraploid zebrafish from cntd1-/- and cntd1-/-/- females, respectively. Furthermore, the tetraploid-heterozygous zebrafish produced reduced-diploid gametes and yielded all-triploid or all-tetraploid offspring when crossed with wild-type (WT) or tetraploid zebrafish, respectively. Collectively, our findings provide direct evidence supporting the crucial role of meiotic crossover defects in the process of polyploidization. This is particularly evident in the generation of unreduced eggs in fish and, potentially, other vertebrate species.
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Affiliation(s)
- Yuan Ou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Huilin Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Juan Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xiangyan Dai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiaxin He
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha 410078, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Yuqin Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
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15
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Li X, Zhang L, Wei X, Datta T, Wei F, Xie Z. Polyploidization: A Biological Force That Enhances Stress Resistance. Int J Mol Sci 2024; 25:1957. [PMID: 38396636 PMCID: PMC10888447 DOI: 10.3390/ijms25041957] [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: 12/24/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.
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Affiliation(s)
- Xiaoying Li
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Luyue Zhang
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Tanusree Datta
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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16
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Olofsson JK, Tyler T, Dunning LT, Hjertson M, Rühling Å, Hansen AJ. Morphological and genetic evidence suggest gene flow among native and naturalized mint species. AMERICAN JOURNAL OF BOTANY 2024; 111:e16280. [PMID: 38334273 DOI: 10.1002/ajb2.16280] [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: 08/09/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 02/10/2024]
Abstract
PREMISE Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens. METHODS We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments. RESULTS The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate. CONCLUSIONS Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.
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Affiliation(s)
- Jill K Olofsson
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark
| | - Torbjörn Tyler
- Department of Biology, The Biological Museum, Lund University, Box 117, SE-221 00, Lund, Sweden
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, Western Bank, UK
| | - Mats Hjertson
- Museum of Evolution, Botany, Uppsala University, Norbyvägen 16, SE-752 36, Uppsala, Sweden
| | - Åke Rühling
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, Western Bank, UK
- Biological Museum, Gyllings väg 9, SE-572 36 Oskarshamn, Sverige
| | - Anders J Hansen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K, 1353, Denmark
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17
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Yoo MJ, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, Chen S. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1191-1205. [PMID: 37997015 DOI: 10.1111/tpj.16553] [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: 08/10/2023] [Revised: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, 13699, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, USA
| | - J Lucas Boatwright
- Plant and Environmental Science Department, Clemson University, Clemson, South Carolina, 29634, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, Mississippi, 38677, USA
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18
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Wang M, Li X, Wang C, Zou M, Yang J, Li XD, Guo B. Asymmetric and parallel subgenome selection co-shape common carp domestication. BMC Biol 2024; 22:4. [PMID: 38166816 PMCID: PMC10762839 DOI: 10.1186/s12915-023-01806-9] [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: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally. RESULTS We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement. CONCLUSIONS In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.
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Affiliation(s)
- Min Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yang
- Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, 443100, Hubei, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, 443100, Hubei, China
| | - Xiang-Dong Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810008, China.
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19
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Simko I, Zhao R. Phenotypic characterization, plant growth and development, genome methylation, and mineral elements composition of neotetraploid lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1296660. [PMID: 38143587 PMCID: PMC10739468 DOI: 10.3389/fpls.2023.1296660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023]
Abstract
Stable neotetraploid lines of lettuce (Lactuca sativa L.) were produced from three phenotypically distinct cultivars (Annapolis, Eruption, Merlot) and an advanced breeding line (SM13-L2) using colchicine treatment of seeds or young seedlings. When tested under the greenhouse and field conditions, neotetraploids initially grew more rapidly than their diploid progenitors, however they reached their reproductive stage (bolting, flower bud formation, and flowering) substantially later. Seeds production on neotetraploids was delayed by more than 30 days compared to diploids. Tetraploid plants had fewer, but larger stomata and leaves, less chlorophyll per area, higher photosystem II photochemical efficiency, generally lighter root system, and produced less than 1% of seeds in comparison with diploids. Field-grown neotetraploids of all lines displayed a significant reduction in tipburn (1.8% vs. 22.2%, respectively), a highly undesirable physiological disorder. Changes in leaf and root mineral composition were detected in neotetraploids. Several elements were found in lower abundance than in diploids, most notably iron, calcium, and silicon. Whole genome bisulfite sequencing (WGBS) revealed 498 differentially methylated regions (DMR), with 106 of these regions having at least 50% difference in the level of methylation between neotetraploids and their diploid progenitors. At least 18 of the most prominent DMR were detected in proximity to genes predicted to be involved in plant development or reaction to biotic and abiotic stressors. Because neotetraploid lines have low seed production, they are not suitable for commercial cultivation. They can be used, however, in research to study the factors contributing to tipburn, traits affected by stomata size or density, and the effect of ploidy on resistance to environmental stressors.
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Affiliation(s)
- Ivan Simko
- Sam Farr United States Crop Improvement and Protection Research Center, Agricultural Research Service, U.S. Department of Agriculture, Salinas, CA, United States
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20
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Kileeg Z, Haldar A, Khan H, Qamar A, Mott GA. Differential expansion and retention patterns of LRR-RLK genes across plant evolution. PLANT DIRECT 2023; 7:e556. [PMID: 38145254 PMCID: PMC10739070 DOI: 10.1002/pld3.556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/03/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
Abstract
To maximize overall fitness, plants must accurately respond to a host of growth, developmental, and environmental signals throughout their life. Many of these internal and external signals are perceived by the leucine-rich repeat receptor-like kinases, which play roles in regulating growth, development, and immunity. This largest family of receptor kinases in plants can be divided into subfamilies based on the conservation of the kinase domain, which demonstrates that shared evolutionary history often indicates shared molecular function. Here we investigate the evolutionary history of this family across the evolution of 112 plant species. We identify lineage-specific expansions of the malectin-domain containing subfamily LRR subfamily I primarily in the Brassicales and bryophytes. Most other plant lineages instead show a large expansion in LRR subfamily XII, which in Arabidopsis is known to contain key receptors in pathogen perception. This striking asymmetric expansion may reveal a dichotomy in the evolutionary history and adaptation strategies employed by plants. A greater understanding of the evolutionary pressures and adaptation strategies acting on members of this receptor family offers a way to improve functional predictions for orphan receptors and simplify the identification of novel stress-related receptors.
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Affiliation(s)
- Zachary Kileeg
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Aparna Haldar
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Hasna Khan
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Arooj Qamar
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
| | - G. Adam Mott
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
- Centre for the Analysis of Genome Evolution & FunctionUniversity of TorontoTorontoCanada
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21
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Zhang Z, Huo W, Wang X, Ren Z, Zhao J, Liu Y, He K, Zhang F, Li W, Jin S, Yang D. Origin, evolution, and diversification of the wall-associated kinase gene family in plants. PLANT CELL REPORTS 2023; 42:1891-1906. [PMID: 37743376 DOI: 10.1007/s00299-023-03068-9] [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: 06/13/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023]
Abstract
KEY MESSAGE The study of the origin, evolution, and diversification of the wall-associated kinase gene family in plants facilitates their functional investigations in the future. Wall-associated kinases (WAKs) make up one subfamily of receptor-like kinases (RLKs), and function directly in plant cell elongation and responses to biotic and abiotic stresses. The biological functions of WAKs have been extensively characterized in angiosperms; however, the origin and evolutionary history of the WAK family in green plants remain unclear. Here, we performed a comprehensive analysis of the WAK family to reveal its origin, evolution, and diversification in green plants. In total, 1061 WAK genes were identified in 37 species from unicellular algae to multicellular plants, and the results showed that WAK genes probably originated before bryophyte differentiation and were widely distributed in land plants, especially angiosperms. The phylogeny indicated that the land plant WAKs gave rise to five clades and underwent lineage-specific expansion after species differentiation. Cis-acting elements and expression patterns analyses of WAK genes in Arabidopsis and rice demonstrated the functional diversity of WAK genes in these two species. Many gene gains and losses have occurred in angiosperms, leading to an increase in the number of gene copies. The evolutionary trajectory of the WAK family during polyploidization was uncovered using Gossypium species. Our results provide insights into the evolution of WAK genes in green plants, facilitating their functional investigations in the future.
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Affiliation(s)
- Zhiqiang Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqi Huo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xingxing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhongying Ren
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Junjie Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yangai Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kunlun He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fei Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Daigang Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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22
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Lin J, Zhang B, Zou J, Luo Z, Yang H, Zhou P, Chen X, Zhou W. Induction of tetraploids in Paper Mulberry (Broussonetia papyrifera (L.) L'Hér. ex Vent.) by colchicine. BMC PLANT BIOLOGY 2023; 23:574. [PMID: 37978431 PMCID: PMC10655367 DOI: 10.1186/s12870-023-04487-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/25/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Broussonetia papyrifera (L.) L'Hér. ex Vent. has the characteristics of strong stress resistance, high crude protein content, and pruning tolerance. It is an ecological, economic, and medicinal plant. Polyploid plants usually perform better than their corresponding diploid plants in terms of nutrients, active substances, and stress resistance. RESULTS In this study, the leaves, calli, and seeds of diploid B. papyrifera were used for tetraploid induction by colchicine. The induction effect of colchicine on B. papyrifera was summarized through the early morphology, chromosome count and flow cytometry. It was concluded that the best induction effect (18.6%) was obtained when the leaves of B. papyrifera were treated in liquid MS (Murashige and Skoog) medium containing 450 mg·L-1 colchicine for 3 d. The comparative analysis of the growth characteristics of diploid and tetraploid B. papyrifera showed that tetraploid B. papyrifera has larger ground diameter, larger stomata, thicker palisade tissue and thicker sponge tissue than diploid B. papyrifera. In addition, the measurement of photosynthetic features also showed that tetraploids had higher chlorophyll content and higher photosynthetic rates. CONCLUSION This study showed that tetraploid B. papyrifera could be obtained by treating leaves, callus and seeds with liquid and solid colchicine, but the induction efficiency was different. Moreover, there were differences in stomata, leaf cell structure and photosynthetic features between tetraploid B. papyrifera and its corresponding diploid. The induced tetraploid B. papyrifera can provide a technical basis and breeding material for the creation of B. papyrifera germplasm resources in the future.
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Affiliation(s)
- Jiana Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, 510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Bingnan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, 510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jintuo Zou
- Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, South China Agricultural University, Guangzhou, 510642, China
| | - Zhen Luo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Yang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Peng Zhou
- Guangdong Eco-Engineering Polytechnic, Guangzhou, 510642, China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangzhou, 510642, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China.
| | - Wei Zhou
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, 510642, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
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23
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Zhou W, Zhang L, He J, Chen W, Zhao F, Fu C, Li M. Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid. Int J Mol Sci 2023; 24:16238. [PMID: 38003428 PMCID: PMC10671433 DOI: 10.3390/ijms242216238] [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: 10/13/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.
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Affiliation(s)
- Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Wang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Feifan Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
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24
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You J, Liu Z, Qi Z, Ma Y, Sun M, Su L, Niu H, Peng Y, Luo X, Zhu M, Huang Y, Chang X, Hu X, Zhang Y, Pi R, Liu Y, Meng Q, Li J, Zhang Q, Zhu L, Lin Z, Min L, Yuan D, Grover CE, Fang DD, Lindsey K, Wendel JF, Tu L, Zhang X, Wang M. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nat Genet 2023; 55:1987-1997. [PMID: 37845354 PMCID: PMC10632151 DOI: 10.1038/s41588-023-01530-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 09/14/2023] [Indexed: 10/18/2023]
Abstract
Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.
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Affiliation(s)
- Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengling Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hao Niu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yabing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuanxuan Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengmeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xing Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiubao Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruizhen Pi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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Yan X, Chen X, Li Y, Li Y, Wang F, Zhang J, Ning G, Bao M. The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane ( Platanus × acerifolia). Int J Mol Sci 2023; 24:14486. [PMID: 37833935 PMCID: PMC10572260 DOI: 10.3390/ijms241914486] [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: 08/24/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Transcription and alternative splicing (AS) are now appreciated in plants, but few studies have examined the effects of changing ploidy on transcription and AS. In this study, we showed that artificially autododecaploid plants of London plane (Platanus × acerifolia (Aiton) Willd) had few flowers relative to their hexaploid progenitors. Transcriptome analysis based on full-length Oxford Nanopore Technologies (ONTs) and next-generation sequencing (NGS) revealed that the increased ploidy level in P. × acerifolia led to more transcribed isoforms, accompanied by an increase in the number of isoforms per gene. The functional enrichment of genes indicated that novel genes transcribed specifically in the dodecaploids may have been highly correlated with the ability to maintain genome stability. The dodecaploids showed a higher number of genes with upregulated differentially expressed genes (DEGs) compared with the hexaploid counterpart. The genome duplication of P. × acerifolia resulted mainly in the DEGs involved in basic biological pathways. It was noted that there was a greater abundance of alternative splicing (AS) events and AS genes in the dodecaploids compared with the hexaploids in P. × acerifolia. In addition, a significant difference between the structure and expression of AS events between the hexaploids and dodecaploids of Platanus was found. Of note, some DEGs and differentially spliced genes (DSGs) related to floral transition and flower development were consistent with the few flower traits in the dodecaploids of P. × acerifolia. Collectively, our findings explored the difference in transcription and AS regulation between the hexaploids and dodecaploids of P. × acerifolia and gained new insight into the molecular mechanisms underlying the few-flower phenotype of P. × acerifolia. These results contribute to uncovering the regulatory role of transcription and AS in polyploids and breeding few-flower germplasms.
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Affiliation(s)
| | | | | | | | | | | | | | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (X.Y.); (J.Z.)
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26
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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [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: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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27
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Yu RM, Zhang N, Zhang BW, Liang Y, Pang XX, Cao L, Chen YD, Zhang WP, Yang Y, Zhang DY, Pang EL, Bai WN. Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus. BMC Biol 2023; 21:168. [PMID: 37553642 PMCID: PMC10408227 DOI: 10.1186/s12915-023-01668-1] [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: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual. RESULTS Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture. CONCLUSIONS Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
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Affiliation(s)
- Rui-Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ning Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Xu Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Dan Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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28
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Du L, Ma Z, Mao H. Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2465. [PMID: 37447026 DOI: 10.3390/plants12132465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.
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Affiliation(s)
- Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Zhenbing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
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29
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Lu M, Zhang QC, Zhu ZY, Peng F, Li Z, Wang Y, Li XY, Wang ZW, Zhang XJ, Zhou L, Gui JF. An efficient approach to synthesize sterile allopolyploids through the combined reproduction mode of ameiotic oogenesis and sperm-egg fusion in the polyploid Carassius complex. Sci Bull (Beijing) 2023; 68:1038-1050. [PMID: 37173259 DOI: 10.1016/j.scib.2023.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
The association between polyploidy and reproduction transition, which is an intriguing issue in evolutionary genetics, can also be exploited as an approach for genetic improvement in agriculture. Recently, we generated novel amphitriploids (NA3n) by integrating the genomes of the gynogenetic Carassius gibelio and sexual C. auratus, and found gynogenesis was recovered in most NA3n females (NA3n♀I). Here, we discovered a unique reproduction mode, termed ameio-fusiongenesis, which combines the abilities of both ameiotic oogenesis and sperm-egg fusion, in a few NA3n females (NA3n♀II). These females inherited ameiotic oogenesis to produce unreduced eggs from gynogenetic C. gibelio and sperm-egg fusion from sexual C. auratus. Subsequently, we utilized this unique reproduction mode to generate a group of synthetic alloheptaploids by crossing NA3n♀II with Megalobrama amblycephala. They contained all chromosomes of maternal NA3n♀II and a chromosomal set of paternal M. amblycephala. Intergenomic chromosome translocations between NA3n♀II and M. amblycephala were also observed in a few somatic cells. Primary oocytes of the alloheptaploid underwent severe apoptosis owing to incomplete double-strand break repair at prophase I. Although spermatocytes displayed similar chromosome behavior at prophase I, they underwent apoptosis due to chromosome separation failure at metaphase I. Therefore, the alloheptaploid females and males were all sterile. Finally, we established a sustainable clone for the large-scale production of NA3n♀II and developed an efficient approach to synthesize diverse allopolyploids containing genomes of different cyprinid species. These findings not only broaden our understanding of reproduction transition but also offer a practical strategy for polyploidy breeding and heterosis fixing.
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Affiliation(s)
- Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin-Can Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Yu Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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30
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Chen K, Yang H, Peng Y, Liu D, Zhang J, Zhao Z, Wu L, Lin T, Bai L, Wang L. Genomic analyses provide insights into the polyploidization-driven herbicide adaptation in Leptochloa weeds. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37154437 PMCID: PMC10363762 DOI: 10.1111/pbi.14065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/21/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
Polyploidy confers a selective advantage under stress conditions; however, whether polyploidization mediates enhanced herbicide adaptation remains largely unknown. Tetraploid Leptochloa chinensis is a notorious weed in the rice ecosystem, causing severe yield loss in rice. In China, L. chinensis has only one sister species, the diploid L. panicea, whose damage is rarely reported. To gain insights into the effects of polyploidization on herbicide adaptation, we first assembled a high-quality genome of L. panicea and identified genome structure variations with L. chinensis. Moreover, we identified herbicide-resistance genes specifically expanded in L. chinensis, which may confer a greater herbicide adaptability in L. chinensis. Analysis of gene retention and loss showed that five herbicide target-site genes and several herbicide nontarget-site resistance gene families were retained during polyploidization. Notably, we identified three pairs of polyploidization-retained genes including LcABCC8, LcCYP76C1 and LcCYP76C4 that may enhance herbicide resistance. More importantly, we found that both copies of LcCYP76C4 were under herbicide selection during the spread of L. chinensis in China. Furthermore, we identified another gene potentially involved in herbicide resistance, LcCYP709B2, which is also retained during polyploidization and under selection. This study provides insights into the genomic basis of the enhanced herbicide adaptability of Leptochloa weeds during polyploidization and provides guidance for the precise and efficient control of polyploidy weeds.
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Affiliation(s)
- Ke Chen
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ducai Liu
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | | | - Zhenghong Zhao
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Lamei Wu
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Tao Lin
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Lianyang Bai
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Lifeng Wang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
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31
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Zhao Y, Yang Z, Zhang Z, Yin M, Chu S, Tong Z, Qin Y, Zha L, Fang Q, Yuan Y, Huang L, Peng H. The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad047. [PMID: 37213683 PMCID: PMC10194901 DOI: 10.1093/hr/uhad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/07/2023] [Indexed: 05/23/2023]
Abstract
Fallopia multiflora (Thunb.) Harald, a vine belonging to the Polygonaceae family, is used in traditional medicine. The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging. This study describes the assembly of the F. multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data (with a contig N50 of 1.97 megabases), 1.44 gigabases of which was assigned to 11 pseudochromosomes. Comparative genomics confirmed that F. multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation. Combining genomics, transcriptomics, and metabolomics data to map a network of associated genes and metabolites, we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F. multiflora. These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes. Moreover, the reference genome of F. multiflora is a useful addition to the genomes of the Polygonaceae family.
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Affiliation(s)
| | | | | | | | - Shanshan Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, China
| | - Zhenzhen Tong
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Yuejian Qin
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Liangping Zha
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, China
| | - Qingying Fang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, China
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32
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Bellec A, Sow MD, Pont C, Civan P, Mardoc E, Duchemin W, Armisen D, Huneau C, Thévenin J, Vernoud V, Depège-Fargeix N, Maunas L, Escale B, Dubreucq B, Rogowsky P, Bergès H, Salse J. Tracing 100 million years of grass genome evolutionary plasticity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36919199 DOI: 10.1111/tpj.16185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/29/2023] [Accepted: 02/24/2023] [Indexed: 05/17/2023]
Abstract
Grasses derive from a family of monocotyledonous plants that includes crops of major economic importance such as wheat, rice, sorghum and barley, sharing a common ancestor some 100 million years ago. The genomic attributes of plant adaptation remain obscure and the consequences of recurrent whole genome duplications (WGD) or polyploidization events, a major force in plant evolution, remain largely speculative. We conducted a comparative analysis of omics data from ten grass species to unveil structural (inversions, fusions, fissions, duplications, substitutions) and regulatory (expression and methylation) basis of genome plasticity, as possible attributes of plant long lasting evolution and adaptation. The present study demonstrates that diverged polyploid lineages sharing a common WGD event often present the same patterns of structural changes and evolutionary dynamics, but these patterns are difficult to generalize across independent WGD events as a result of non-WGD factors such as selection and domestication of crops. Polyploidy is unequivocally linked to the evolutionary success of grasses during the past 100 million years, although it remains difficult to attribute this success to particular genomic consequences of polyploidization, suggesting that polyploids harness the potential of genome duplication, at least partially, in lineage-specific ways. Overall, the present study clearly demonstrates that post-polyploidization reprogramming is more complex than traditionally reported in investigating single species and calls for a critical and comprehensive comparison across independently polyploidized lineages.
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Affiliation(s)
- Arnaud Bellec
- INRAE/CNRGV US 1258, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Mamadou Dia Sow
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Caroline Pont
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Peter Civan
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Emile Mardoc
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | | | - David Armisen
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Cécile Huneau
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Johanne Thévenin
- INRAE/AgroParisTech-UMR 1318. Bat 2. Centre INRA de Versailles, route de Saint Cyr, 78026, Versailles CEDEX, France
| | - Vanessa Vernoud
- INRAE/CNRS/ENS/Univ. Lyon-UMR 879, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | | | - Laurent Maunas
- Arvalis-Institut du végétal, 21 chemin de Pau, 64121 Montardon, France
| | - Brigitte Escale
- Arvalis-Institut du végétal, 21 chemin de Pau, 64121 Montardon, France
- Direction de l'agriculture de Polynésie française, Route de l'Hippodrome, 98713, Papeete, France
| | - Bertrand Dubreucq
- INRAE/AgroParisTech-UMR 1318. Bat 2. Centre INRA de Versailles, route de Saint Cyr, 78026, Versailles CEDEX, France
| | - Peter Rogowsky
- INRAE/CNRS/ENS/Univ. Lyon-UMR 879, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | - Hélène Bergès
- INRAE/CNRGV US 1258, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Jerome Salse
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
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Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M, Sun L, Dong X. A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. PLANT COMMUNICATIONS 2023; 4:100469. [PMID: 36307985 PMCID: PMC10030368 DOI: 10.1016/j.xplc.2022.100469] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
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Affiliation(s)
- Yi Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - He Su
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510120, China
| | - Sifei Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ping Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenbin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qichen Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Bomblies K. Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis. PLANT REPRODUCTION 2023; 36:107-124. [PMID: 36149479 PMCID: PMC9957869 DOI: 10.1007/s00497-022-00448-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/10/2022] [Indexed: 05/29/2023]
Abstract
Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.
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Affiliation(s)
- Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Plant Molecular Biology, Department of Biology, ETH Zürich, Zurich, Switzerland.
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35
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Pašakinskienė I. Festuca pratensis-like Subgenome Reassembly from a "Chromosomal Cocktail" in the Intergeneric Festulolium (Poaceae) Hybrid: A Rare Chromoanagenesis Event in Grasses. PLANTS (BASEL, SWITZERLAND) 2023; 12:984. [PMID: 36903845 PMCID: PMC10005718 DOI: 10.3390/plants12050984] [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: 01/26/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Festuca and Lolium grass species are used for Festulolium hybrid variety production where they display trait complementarities. However, at the genome level, they show antagonisms and a broad scale of rearrangements. A rare case of an unstable hybrid, a donor plant manifesting pronounced variability of its clonal parts, was discovered in the F2 group of 682 plants of Lolium multiflorum × Festuca arundinacea (2n = 6x = 42). Five phenotypically distinct clonal plants were determined to be diploids, having only 14 chromosomes out of the 42 in the donor. GISH defined the diploids as having the basic genome from F. pratensis (2n = 2x = 14), one of the progenitors of F. arundinacea (2n = 6x = 42), with minor components from L. multiflorum and another subgenome, F. glaucescens. The 45S rDNA position on two chromosomes also corresponded to the variant of F. pratensis in the F. arundinacea parent. In the highly unbalanced donor genome, F. pratensis was the least represented, but the most involved in numerous recombinant chromosomes. Specifically, FISH highlighted 45S rDNA-containing clusters involved in the formation of unusual chromosomal associations in the donor plant, suggesting their active role in karyotype realignment. The results of this study show that F. pratensis chromosomes have a particular fundamental drive for restructuring, which prompts the disassembly/reassembly processes. The finding of F. pratensis "escaping" and rebuilding itself from the chaotic "chromosomal cocktail" of the donor plant points to a rare chromoanagenesis event and extends the view of plant genome plasticity.
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Affiliation(s)
- Izolda Pašakinskienė
- Life Sciences Centre, Vilnius University, Saulėtekio 7, 10221 Vilnius, Lithuania;
- Botanical Garden of Vilnius University, Kairėnų 43, 10239 Vilnius, Lithuania
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36
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Chen S, Yu Y, Wang X, Wang S, Zhang T, Zhou Y, He R, Meng N, Wang Y, Liu W, Liu Z, Liu J, Guo Q, Huang H, Sederoff RR, Wang G, Qu G, Chen S. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour 2023. [PMID: 36789493 DOI: 10.1111/1755-0998.13770] [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: 11/29/2021] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Many recent studies have provided significant insights into polyploid breeding, but limited research has been carried out on trees. The genomic information needed to understand growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to forests imposed by climate change. Populus alba 'Berolinensis,' also known "Yinzhong poplar," is a triploid poplar from northeast China. This hybrid triploid poplar is widely used as a landscape ornamental and in urban forestry owing to its adaptation to adverse environments and faster growth than its parental diploid. It is an artificially synthesized male allotriploid hybrid, with three haploid genomes of P. alba 'Berolinensis' originating from different poplar species, so it is attractive for studying polyploidy genomic mechanisms in heterosis. In this study, we focused on the allelic genomic interactions in P. alba 'Berolinensis,' and generated a high-quality chromosome-level genome assembly consisting of 19 allelic chromosomes. Its three haploid chromosome sets are polymorphic with an average of 25.73 nucleotide polymorphism sites per kilobase. We found that some stress-related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. The genome assembly has been deposited in our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genome-related resources will provide a critical foundation for the molecular breeding of P. alba 'Berolinensis' and help us uncover the allopolyploidization effects of heterosis and abiotic stress resistance and traits of polyploidy species in the future.
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Affiliation(s)
- Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruihan He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenxuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jinwen Liu
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
| | - Qiwen Guo
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R Sederoff
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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37
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Mattingly KZ, Hovick SM. Autopolyploids of Arabidopsis thaliana are more phenotypically plastic than their diploid progenitors. ANNALS OF BOTANY 2023; 131:45-58. [PMID: 34175922 PMCID: PMC9904351 DOI: 10.1093/aob/mcab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/25/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Polyploids are often hypothesized to have increased phenotypic plasticity compared with their diploid progenitors, but recent work suggests that the relationship between whole-genome duplication (WGD) and plasticity is not so straightforward. Impacts of WGD on plasticity are moderated by other evolutionary processes in nature, which has impeded generalizations regarding the effects of WGD alone. We assessed shifts in phenotypic plasticity and mean trait values accompanying WGD, as well as the adaptive consequences of these shifts. METHODS To isolate WGD effects, we compared two diploid lineages of Arabidopsis thaliana wiht corresponding autotetraploids grown across different salt and nutrient conditions in a growth chamber. KEY RESULTS For the few cases in which diploids and polyploids differed in plasticity, polyploids were more plastic, consistent with hypotheses that WGD increases plasticity. Under stress, increased plasticity was often adaptive (associated with higher total seed mass), but in other cases plasticity was unrelated to fitness. Mean trait values and plasticity were equally likely to be affected by WGD, but the adaptive consequences of these shifts were often context dependent or lineage specific. For example, polyploids had extended life spans, a shift that was adaptive in one polyploid lineage under amenable conditions but was maladaptive in the other lineage under stress. CONCLUSIONS Our work shows that increased phenotypic plasticity can result from WGD alone, independent of other evolutionary processes. We find that the effects of WGD can differ depending on the genotype of the progenitor and the environmental context. Though our experiment was limited to two genotypes of a single species, these findings support the idea that WGD can indeed increase plasticity.
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Affiliation(s)
| | - Stephen M Hovick
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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38
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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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39
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Ma Y, Yu H, Lu Y, Gao S, Fatima M, Ming R, Yue J. Transcriptome analysis of sugarcane reveals rapid defense response of SES208 to Xanthomonas albilineans in early infection. BMC PLANT BIOLOGY 2023; 23:52. [PMID: 36694139 PMCID: PMC9872421 DOI: 10.1186/s12870-023-04073-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Diseases are the major factor affecting the quality and yield of sugarcane during its growth and development. However, our knowledge about the factors regulating disease responses remain limited. The present study focuses on identifying genes regulating transcriptional mechanisms responsible for resistance to leaf scald caused by Xanthomonas albilineans in S. spontaneum and S. officinarum. RESULTS After inoculation of the two sugarcane varieties SES208 (S. spontaneum) and LA Purple (S. officinarum) with Xanthomonas albilineans, SES208 exhibited significantly greater resistance to leaf scald caused by X. albilineans than did LA Purple. Using transcriptome analysis, we identified a total of 4323 and 1755 differentially expressed genes (DEGs) in inoculated samples of SES208 and LA Purple, respectively. Significantly, 262 DEGs were specifically identified in SES208 that were enriched for KEGG pathway terms such as plant-pathogen interaction, MAPK signaling pathway, and plant hormone signal transduction. Furthermore, we built a transcriptional regulatory co-expression network that specifically identified 16 and 25 hub genes in SES208 that were enriched for putative functions in plant-pathogen interactions, MAPK signaling, and plant hormone signal transduction. All of these essential genes might be significantly involved in resistance-regulating responses in SES208 after X. albilineans inoculation. In addition, we found allele-specific expression in SES208 that was associated with the resistance phenotype of SES208 when infected by X. albilineans. After infection with X. albilineans, a great number of DEGs associated with the KEGG pathways 'phenylpropanoid biosynthesis' and 'flavonoid biosynthesis' exhibited significant expression changes in SES208 compared to LA Purple that might contribute to superior leaf scald resistance in SES208. CONCLUSIONS We provided the first systematical transcriptome map that the higher resistance of SES208 is associated with and elicited by the rapid activation of multiple clusters of defense response genes after infection by X. albilineans and not merely due to changes in the expression of genes generically associated with stress resistance. These results will serve as the foundation for further understanding of the molecular mechanisms of resistance against X. albilineans in S. spontaneum.
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Affiliation(s)
- Yaying Ma
- Center 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, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hongying Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yijing Lu
- Center 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, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sanji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jingjing Yue
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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40
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Lukjanová E, Hanulíková A, Řepková J. Investigating the Origin and Evolution of Polyploid Trifolium medium L. Karyotype by Comparative Cytogenomic Methods. PLANTS (BASEL, SWITZERLAND) 2023; 12:235. [PMID: 36678948 PMCID: PMC9866396 DOI: 10.3390/plants12020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though allopolyploid origin has previously been suggested, little has in fact been known about the T. medium karyotype and its origin. We researched T. medium and related karyotypes using comparative cytogenomic methods, such as fluorescent in situ hybridization (FISH) and RepeatExplorer cluster analysis. The results indicate an exceptional karyotype diversity regarding numbers and mutual positions of 5S and 26S rDNA loci and centromeric repeats in populations of T. medium ecotypes and varieties. The observed variability among T. medium ecotypes and varieties suggests current karyotype instability that can be attributed to ever-ongoing battle between satellite DNA together with genomic changes and rearrangements enhanced by post-hybridization events. Comparative cytogenomic analyses of a T. medium hexaploid variety and diploid relatives revealed stable karyotypes with a possible case of chromosomal rearrangement. Moreover, the results provided evidence of T. medium having autopolyploid origin.
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41
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [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: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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42
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Wang N, Wang S, Qi F, Wang Y, Lin Y, Zhou Y, Meng W, Zhang C, Wang Y, Ma J. Autotetraploidization Gives Rise to Differential Gene Expression in Response to Saline Stress in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:3114. [PMID: 36432844 PMCID: PMC9698567 DOI: 10.3390/plants11223114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Plant polyploidization represents an effective means for plants to perpetuate their adaptive advantage in the face of environmental variation. Numerous studies have identified differential responsiveness to environmental cues between polyploids and their related diploids, and polyploids might better adapt to changing environments. However, the mechanism that underlies polyploidization contribution during abiotic stress remains hitherto obscure and needs more comprehensive assessment. In this study, we profile morphological and physiological characteristics, and genome-wide gene expression between an autotetraploid rice and its diploid donor plant following saline stress. The results show that the autotetraploid rice is more tolerant to saline stress than its diploid precursor. The physiological characteristics were rapidly responsive to saline stress in the first 24 h, during which the elevations in sodium ion, superoxide dismutase, peroxidase, and 1-aminocyclopropane-1-carboxylic acid were all significantly higher in the autotetraploid than in the diploid rice. Meanwhile, the genome-wide gene expression analysis revealed that the genes related to ionic transport, peroxidase activity, and phytohormone metabolism were differentially expressed in a significant manner between the autotetraploid and the diploid rice in response to saline stress. These findings support the hypothesis that diverse mechanisms exist between the autotetraploid rice and its diploid donor plant in response to saline stress, providing vital information for improving our understanding on the enhanced performance of polyploid plants in response to salt stress.
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Affiliation(s)
- Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Shiyan Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yingkai Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yiming Zhou
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Weilong Meng
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Chunying Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yunpeng Wang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jian Ma
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
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43
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Tan Z, Peng Y, Xiong Y, Xiong F, Zhang Y, Guo N, Tu Z, Zong Z, Wu X, Ye J, Xia C, Zhu T, Liu Y, Lou H, Liu D, Lu S, Yao X, Liu K, Snowdon RJ, Golicz AA, Xie W, Guo L, Zhao H. Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus. Genome Biol 2022; 23:233. [PMID: 36345039 PMCID: PMC9639296 DOI: 10.1186/s13059-022-02801-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) is an important source for the vegetable oil in the world, and the seed oil content is an important trait of B. napus. RESULTS We perform a comprehensive analysis of the transcriptional variability in the seeds of B. napus at two developmental stages, 20 and 40 days after flowering (DAF). We detect 53,759 and 53,550 independent expression quantitative trait loci (eQTLs) for 79,605 and 76,713 expressed genes at 20 and 40 DAF, respectively. Among them, the local eQTLs are mapped to the adjacent genes more frequently. The adjacent gene pairs are regulated by local eQTLs with the same open chromatin state and show a stronger mode of expression piggybacking. Inter-subgenomic analysis indicates that there is a feedback regulation for the homoeologous gene pairs to maintain partial expression dosage. We also identify 141 eQTL hotspots and find that hotspot87-88 co-localizes with a QTL for the seed oil content. To further resolve the regulatory network of this eQTL hotspot, we construct the XGBoost model using 856 RNA-seq datasets and the Basenji model using 59 ATAC-seq datasets. Using these two models, we predict the mechanisms affecting the seed oil content regulated by hotspot87-88 and experimentally validate that the transcription factors, NAC13 and SCL31, positively regulate the seed oil content. CONCLUSIONS We comprehensively characterize the gene regulatory features in the seeds of B. napus and reveal the gene networks regulating the seed oil content of B. napus.
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Affiliation(s)
- Zengdong Tan
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Yan Peng
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Yao Xiong
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Feng Xiong
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Yuting Zhang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Ning Guo
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Zhuo Tu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Zhanxiang Zong
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaokun Wu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Jiang Ye
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Chunjiao Xia
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Tao Zhu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Yinmeng Liu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Hongxiang Lou
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Dongxu Liu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Shaoping Lu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
| | - Kede Liu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Rod J. Snowdon
- grid.8664.c0000 0001 2165 8627Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Agnieszka A. Golicz
- grid.8664.c0000 0001 2165 8627Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Weibo Xie
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Liang Guo
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China ,grid.35155.370000 0004 1790 4137Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China ,grid.488316.00000 0004 4912 1102Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hu Zhao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China ,Hubei Hongshan Laboratory, Wuhan, China
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44
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Preston R, Blomster J, Schagerström E, Seppä P. Clonality, polyploidy and spatial population structure in Baltic Sea Fucus vesiculosus. Ecol Evol 2022; 12:e9336. [PMID: 36188503 PMCID: PMC9486819 DOI: 10.1002/ece3.9336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 01/16/2023] Open
Abstract
Genetic characteristics of populations can have substantial impacts on the adaptive potential of a species. Species are heterogeneous, often defined by variability at a range of scales including at the genetic, individual and population level. Using microsatellite genotyping, we characterize patterns underlying the genetic heterogeneity in marine macroalga Fucus vesiculosus, with a particular focus on two forms: attached and free-living. Here we demonstrate that sympatric populations representing the two forms display marked differences in characteristics of reproduction and genetic diversity. Asexual reproduction was ubiquitous in the free-living form despite being almost entirely absent in the attached form, while signals of polyploidy were common in both forms despite the distinct reproductive modes. Gene flow within and between the forms differed, with barriers to gene flow occurring between forms at various spatial scales due to the reproductive modes employed by individuals of each form. The divergent genetic characteristics of F. vesiculosus demonstrate that intraspecific differences can influence the properties of populations with consequential effects on the whole ecosystem. The differing genetic patterns and habitat requirements of the two forms define separate but closely associated ecological entities that will likely display divergent responses to future changes in environmental conditions.
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Affiliation(s)
- Roxana Preston
- Ecosystems and Environment Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
| | - Jaanika Blomster
- Ecosystems and Environment Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Ellen Schagerström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Stockholm University Baltic Sea CentreStockholm UniversityStockholmSweden
| | - Perttu Seppä
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
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45
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of "foreign" recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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Affiliation(s)
| | | | - Huw D. Jones
- IBERS, Aberystwyth University, Aberystwyth, United Kingdom
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46
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Wang N, Yin Z, Zhao Y, Li Z, Dou D, Wei L. Two divergent immune receptors of the allopolyploid Nicotiana benthamiana reinforce the recognition of a fungal microbe-associated molecular pattern VdEIX3. FRONTIERS IN PLANT SCIENCE 2022; 13:968562. [PMID: 36046591 PMCID: PMC9421165 DOI: 10.3389/fpls.2022.968562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The allotetraploid Solanaceae plant Nicotiana benthamiana contains two closely related receptor-like proteins (RLPs), NbEIX2 and NbRXEG1, which regulate the recognition of VdEIX3 and PsXEG1, respectively. VdEIX3, PsXEG1, and their homologs represent two types of microbe-associated molecular patterns (MAMPs) that are widespread in diverse pathogens. Here, we report that NbRXEG1 also participates in VdEIX3 recognition. Both eix2 and rxeg1 single mutants exhibited significantly impaired but not abolished ability to mediate VdEIX3-triggered immune responses, which are nearly abolished in eix2 rxeg1 double mutants. Moreover, a dominant negative mutant of eix2 that contains a 60 bp deletion failed to respond to VdEIX3 and could suppress VdEIX3-induced cell death in the wild-type N. benthamiana. Further phylogenetic analyses showed that NbEIX2 and NbRXEG1 are obtained from different diploid ancestors by hybridization. These results demonstrate that the allotetraploid N. benthamiana recognizes two types of MAMPs by two homologous but diverged RLPs, which provides a model in which an allopolyploid plant probably exhibits defense hybrid vigor by acquiring divergent immune receptors from different ancestors.
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Affiliation(s)
- Nan Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhiyuan Yin
- College of Plant Protection, China Agricultural University, Beijing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yaning Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhengpeng Li
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huaian, China
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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47
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Dong Y, Hu G, Grover CE, Miller ER, Zhu S, Wendel JF. Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:872-887. [PMID: 35686631 PMCID: PMC9540634 DOI: 10.1111/tpj.15863] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.
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Affiliation(s)
- Yating Dong
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang455 000China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen518 120China
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Shuijin Zhu
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
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48
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Cardoso-Silva CB, Aono AH, Mancini MC, Sforça DA, da Silva CC, Pinto LR, Adams KL, de Souza AP. Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2022; 13:923069. [PMID: 35845637 PMCID: PMC9280035 DOI: 10.3389/fpls.2022.923069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological functions difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements and whole-genome duplication occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis revealed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.
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Affiliation(s)
- Cláudio Benício Cardoso-Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre Hild Aono
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Melina Cristina Mancini
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Agronomy Department, Federal University of Viçosa (UFV), Viçosa, Brazil
| | - Luciana Rossini Pinto
- Sugarcane Research Advanced Centre, Agronomic Institute of Campinas (IAC/APTA), Ribeirão Preto, Brazil
| | - Keith L. Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Anete Pereira de Souza
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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49
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Wang H, Umer MJ, Liu F, Cai X, Zheng J, Xu Y, Hou Y, Zhou Z. Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development. Front Genet 2022; 13:921096. [PMID: 35754813 PMCID: PMC9213653 DOI: 10.3389/fgene.2022.921096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.
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Affiliation(s)
- Heng Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Jie Zheng
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
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50
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Wu P, Zhang L, Zhang K, Yin Y, Liu A, Zhu Y, Fu Y, Sun F, Zhao S, Feng K, Xu X, Chen X, Cheng F, Li L. The adaptive evolution of Euryale ferox to the aquatic environment through paleo-hexaploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:627-645. [PMID: 35218099 PMCID: PMC9314984 DOI: 10.1111/tpj.15717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/24/2022] [Accepted: 02/20/2022] [Indexed: 05/25/2023]
Abstract
Occupation of living space is one of the main driving forces of adaptive evolution, especially for aquatic plants whose leaves float on the water surface and thus have limited living space. Euryale ferox, from the angiosperm basal family Nymphaeaceae, develops large, rapidly expanding leaves to compete for space on the water surface. Microscopic observation found that the cell proliferation of leaves is almost completed underwater, while the cell expansion occurs rapidly after they grow above water. To explore the mechanism underlying the specific development of leaves, we performed sequences assembly and analyzed the genome and transcriptome dynamics of E. ferox. Through reconstruction of the three sub-genomes generated from the paleo-hexaploidization event in E. ferox, we revealed that one sub-genome was phylogenetically closer to Victoria cruziana, which also exhibits gigantic floating leaves. Further analysis revealed that while all three sub-genomes promoted the evolution of the specific leaf development in E. ferox, the genes from the sub-genome closer to V. cruziana contributed more to this adaptive evolution. Moreover, we found that genes involved in cell proliferation and expansion, photosynthesis, and energy transportation were over-retained and showed strong expression association with the leaf development stages, such as the expression divergence of SWEET orthologs as energy uploaders and unloaders in the sink and source leaf organs of E. ferox. These findings provide novel insights into the genome evolution through polyploidization, as well as the adaptive evolution regarding the leaf development accomplished through biased gene retention and expression sub-functionalization of multi-copy genes in E. ferox.
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Affiliation(s)
- Peng Wu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Yulai Yin
- Suzhou Academy of Agricultural ScienceSuzhou215000China
| | - Ailian Liu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Yue Zhu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Yu Fu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Fangfang Sun
- Suzhou Academy of Agricultural ScienceSuzhou215000China
| | - Shuping Zhao
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Kai Feng
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Xuewen Xu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Xuehao Chen
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Liangjun Li
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhou225000China
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