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Sun R, Wu Y, Zhang X, Lv M, Yu D, Sun Y. Chromosome-level genome assembly and annotation of a potential model organism Gossypium arboreum ZB-1. Sci Data 2024; 11:620. [PMID: 38866802 PMCID: PMC11169495 DOI: 10.1038/s41597-024-03481-z] [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: 12/15/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Recent advancements in plant regeneration and synthetic polyploid creation have been documented in Gossypium arboreum ZB-1. These developments make ZB-1 a potential model within the Gossypium genus for investigating gene function and polyploidy. This work generated the sequence and annotation of the ZB-1 genome. The contig-level genome was constructed using the PacBio high-fidelity reads, encompassing 81 contigs with an N50 length of 112.12 Mb. The Hi-C data assisted the construction of the chromosome-level genome, which consists of 13 pseudo-chromosomes and 39 un-anchored contigs, with a total length of about 1.67 Gb. Repetitive sequences accounted for about 69.7% of the genome in length. Based on ab initio and evidence-based prediction, we have identified 48,021 protein-coding genes in the ZB-1 genome. Comparative genomics analysis revealed conserved gene content and arrangement between ZB-1 and G. arboreum SXY1. The single nucleotide polymorphism occurrence rate between ZB-1 and SXY1 was about 0.54 per 1,000 nucleotides. This study enriched the genomic resources for further exploration into cotton regeneration and polyploidy mechanisms.
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Affiliation(s)
- Rongnan Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Yuqing Wu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Xinyu Zhang
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Minghua Lv
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Dongliang Yu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
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2
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Khidirov MT, Ernazarova DK, Rafieva FU, Ernazarova ZA, Toshpulatov AK, Umarov RF, Kholova MD, Oripova BB, Kudratova MK, Gapparov BM, Khidirova MM, Komilov DJ, Turaev OS, Udall JA, Yu JZ, Kushanov FN. Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton ( Gossypium) Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:4184. [PMID: 38140511 PMCID: PMC10748080 DOI: 10.3390/plants12244184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A1-genome) and G. mustelinum Miers ex Watt (AD4-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C22H25NO6) treatment. The fertile F1C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F1C and F2C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8-92.2%, the fertility of seeds in hybrid bolls from 9.7-16.3%, and the pollen viability rates from 36.6-63.8%. Two transgressive plants with long fiber of 35.1-37.0 mm and one plant with extra-long fiber of 39.1-41.0 mm were identified in the F2C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.
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Affiliation(s)
- Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ziraatkhan A. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Abdulqahhor Kh. Toshpulatov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ramziddin F. Umarov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | | | - Doniyor J. Komilov
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Joshua A. Udall
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
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3
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Zhang Y, Zhang Y, Gao C, Zhang Z, Yuan Y, Zeng X, Hu W, Yang L, Li F, Yang Z. Uncovering genomic and transcriptional variations facilitates utilization of wild resources in cotton disease resistance improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:204. [PMID: 37668681 DOI: 10.1007/s00122-023-04451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Upland cotton wild/landraces represent a valuable resource for disease resistance alleles. Genetic differentiation between genotypes, as well as variation in Verticillium wilt (VW) resistance, has been poorly characterized for upland cotton accessions on the domestication spectrum (from wild/landraces to elite lines). RESULTS To illustrate the effects of modern breeding on VW resistance in upland cotton, 37 wild/landraces were resequenced and phenotyped for VW resistance. Genomic patterns of differentiation were identified between wild/landraces and improved upland cotton, and a significant decline in VW resistance was observed in association with improvement. Four genotypes representing different degrees of improvement were used in a full-length transcriptome analysis to study the genetic basis of VW resistance. ROS signaling was highly conserved at the transcriptional level, likely providing the basis for VW resistance in upland cotton. ASN biosynthesis and HSP90-mediated resistance moderated the response to VW in wild/landraces, and loss of induction activity of these genes resulted in VW susceptibility. The observed genomic differentiation contributed to the loss of induction of some important VW resistance genes such as HSP90.4 and PR16. CONCLUSIONS Besides providing new insights into the evolution of upland cotton VW resistance, this study also identifies important resistance pathways and genes for both fundamental research and cotton breeding.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yaning Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Zhibin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaolin Zeng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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4
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Zhang Y, Zhang Y, Ge X, Yuan Y, Jin Y, Wang Y, Zhao L, Han X, Hu W, Yang L, Gao C, Wei X, Li F, Yang Z. Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton. Genome Biol 2023; 24:111. [PMID: 37165460 PMCID: PMC10170703 DOI: 10.1186/s13059-023-02950-9] [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: 10/20/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown. RESULTS By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae. CONCLUSIONS We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yaning Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiaoyang Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuying Jin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao Han
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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5
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Molecular mapping of CLCuD resistance introgressed from synthetic cotton polyploid in upland cotton. J Genet 2022. [DOI: 10.1007/s12041-022-01365-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Tao X, Li M, Zhao T, Feng S, Zhang H, Wang L, Han J, Gao M, Lu K, Chen Q, Zhou B, Guan X. Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation. PLANT PHYSIOLOGY 2021; 186:2152-2168. [PMID: 33871645 PMCID: PMC8331171 DOI: 10.1093/plphys/kiab179] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/31/2021] [Indexed: 05/26/2023]
Abstract
The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.
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Affiliation(s)
- Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Menglin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shouli Feng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hailin Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luyao Wang
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Center of Ministry of Cotton Education, Urumqi 830052, China
| | - Jin Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Center of Ministry of Cotton Education, Urumqi 830052, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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7
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Feng L, Chen Y, Xu M, Yang Y, Yue H, Su Q, Zhou C, Feng G, Ai N, Wang N, Zhou B. Genome-Wide Introgression and Quantitative Trait Locus Mapping Reveals the Potential of Asian Cotton ( Gossypium arboreum) in Improving Upland Cotton ( Gossypium hirsutum). FRONTIERS IN PLANT SCIENCE 2021; 12:719371. [PMID: 34408767 PMCID: PMC8365338 DOI: 10.3389/fpls.2021.719371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Gossypium arboreum (2n=2x=26, A2), the putative progenitor of the At-subgenome of Gossypium hirsutum (2n=4x=52, AD), is a repository of genes of interesting that have been eliminated during evolution/domestication of G. hirsutum. However, its valuable genes remain untapped so far due to species isolation. Here, using a synthetic amphiploid (AADDA2A2) previously reported, we developed a set of 289 G. arboreum chromosome segment introgression lines (ILs) in G. hirsutum by expanding the backcrossing population and through precise marker-assisted selection (MAS) although complex chromosomal structural variations existed between parents which severely hindered introgression. Our results showed the total coverage length of introgressed segments was 1,116.29 Mb, representing 78.48% of the At-subgenome in the G. hirsutum background, with an average segment-length of 8.69 Mb. A total of 81 co- quantitative trait loci (QTLs) for yield and fiber quality were identified by both the RSTEP-ADD-based QTL mapping and the genome-wide association study (GWAS) analysis, with 1.01-24.78% of the phenotypic variance explained. Most QTLs for boll traits showed negative additive effects, but G. arboreum still has the potential to improve boll-number traits in G. hirsutum. Most QTLs for fiber quality showed negative additive effects, implying these QTLs were domesticated in G. hirsutum compared with G. arboreum and, a small quantity of fiber quality QTLs showing positive additive effects, conversely; however, indicates that G. arboreum has the underlying genes of enhancing fiber quality of G. hirsutum. This study provides new insights into the breeding genetic potential of G. arboreum, lays the foundation for further mining favorable genes of interest, and provides guidance for inter-ploidy gene transference from relatives into cultivated crops.
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Affiliation(s)
- Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Ying Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Haoran Yue
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Qiao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Guoli Feng
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Ningshan Wang
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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Yin X, Zhan R, He Y, Song S, Wang L, Ge Y, Chen D. Morphological description of a novel synthetic allotetraploid(A1A1G3G3) of Gossypium herbaceum L.and G.nelsonii Fryx. suitable for disease-resistant breeding applications. PLoS One 2020; 15:e0242620. [PMID: 33270669 PMCID: PMC7714114 DOI: 10.1371/journal.pone.0242620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 11/05/2020] [Indexed: 11/19/2022] Open
Abstract
Wild species of Gossypium ssp. are an important source of traits for improving commercial cotton cultivars. Previous reports show that Gossypium herbaceum L. and Gossypium nelsonii Fryx. have better disease resistance characteristics than commercial cotton varieties. However, chromosome ploidy and biological isolation make it difficult to hybridize diploid species with the tetraploid Gossypium hirsutum L. We developed a new allotetraploid cotton genotype (A1A1G3G3) using a process of distant hybridization within wild cotton species to create new germplasms. First of all, G. herbaceum and G. nelsonii were used for interspecific hybridization to obtain F1 generation. Afterwards, apical meristems of the F1 diploid cotton plants were treated with colchicine to induce chromosome doubling. The new interspecific F1 hybrid and S1 cotton plants originated from chromosome duplication, were tested via morphological and molecular markers and confirmed their tetraploidy through flowrometric and cytological identification. The S1 tetraploid cotton plants was crossed with a TM-1 line and fertile hybrid offspring were obtained. These S2 offsprings were tested for resistance to Verticillium wilt and demonstrated adequate tolerance to this fungi. The results shows that the new S1 cotton line could be used as parental material for hybridization with G. hirsutum to produce pathogen-resistant cotton hybrids. This new S1 allotetraploid genotype will contributes to the enrichment of Gossypium germplasm resources and is expected to be valuable in polyploidy evolutionary studies.
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Affiliation(s)
- Xiaomin Yin
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Rulin Zhan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yingdui He
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shun Song
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lixia Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Di Chen
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail:
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9
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Kumar K, Neelam K, Singh G, Mathan J, Ranjan A, Brar DS, Singh K. Production and cytological characterization of a synthetic amphiploid derived from a cross between Oryza sativa and Oryza punctata. Genome 2019; 62:705-714. [PMID: 31330117 DOI: 10.1139/gen-2019-0062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Oryza punctata Kotschy ex Steud. (BB, 2n = 24) is a wild species of rice that has many useful agronomic traits. An interspecific hybrid (AB, 2n = 24) was produced by crossing O. punctata and Oryza sativa variety Punjab Rice 122 (PR122, AA, 2n = 24) to broaden the narrow genetic base of cultivated rice. Cytological analysis of the pollen mother cells (PMCs) of the interspecific hybrids confirmed that they have 24 chromosomes. The F1 hybrids showed the presence of 19-20 univalents and 1-3 bivalents. The interspecific hybrid was treated with colchicine to produce a synthetic amphiploid (AABB, 2n = 48). Pollen fertility of the synthetic amphiploid was found to be greater than 50% and partial seed set was observed. Chromosome numbers in the PMCs of the synthetic amphiploid were 24II, showing normal pairing. Flow cytometric analysis also confirmed doubled genomic content in the synthetic amphiploid. Leaf morphological and anatomical studies of the synthetic amphiploid showed higher chlorophyll content and enlarged bundle sheath cells as compared with both of its parents. The synthetic amphiploid was backcrossed with PR122 to develop a series of addition and substitution lines for the transfer of useful genes from O. punctata with least linkage drag.
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Affiliation(s)
- Kishor Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.,Faculty Centre on Integrated Rural Development and Management, Ramakrishna Mission Vivekanada Educational and Research Institute, Narendrapur, Kolkata, 700103, India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gurpreet Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jyotirmaya Mathan
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Aashish Ranjan
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Darshan Singh Brar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.,ICAR-National Bureau of Plant Genetic Resources, PUSA, New Delhi, 110012, India
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Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet 2018; 50:796-802. [PMID: 29736014 DOI: 10.1038/s41588-018-0116-x] [Citation(s) in RCA: 298] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/15/2018] [Indexed: 01/17/2023]
Abstract
The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243 G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.
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11
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Wang Y, Feng S, Li S, Tang D, Chen Y, Chen Y, Zhou B. Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum. BMC Genomics 2018; 19:15. [PMID: 29301494 PMCID: PMC5755069 DOI: 10.1186/s12864-017-4398-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 12/19/2017] [Indexed: 11/23/2022] Open
Abstract
Background We previously reported the development of a set of Gossypium hirsutum-G. australe alien chromosome addition lines. Naturally, however, G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G2G2 genome) into the most cultivated cotton, G. hirsutum (AADD). Results In the present report, the pollen from a pentaploid (2n = AADDG2) of G. hirsutum-G. australe was irradiated with seven different doses ranging from 10 to 40 Grays and used to pollinate emasculated flowers of G. hirsutum over three consecutive years. Irradiation greatly increased the genetic recombination rates of the G. hirsutum and G. australe chromosomes and a total of 107 chromosome introgression individuals in 192 GISH-negative (with no GISH signal on chromosome) survived individuals, 11 chromosome translocation individuals (containing 12 chromosome translocation events) and 67 chromosome addition individuals were obtained in 70 GISH-positive (with GISH signal(s) on chromosome(s)) survived individuals, which are invaluable for mining desirable genes from G. australe. Multicolor genomic in situ hybridization results showed that there were three types of translocation, whole arm translocation, large alien segment translocation and small alien segment translocation, and that all translocations occurred between the G2-genome and the A-subgenome chromosomes in G. hirsutum. We also found that higher doses induced much higher rates of chromosome variation but also greatly lowered the seed viability and seedling survivability. Conclusions Irradiation has been successfully employed to induce chromosome introgressions and chromosome translocations and promote chromosome exchanges between cultivated and wild species. In addition, by balancing the rates of chromosome introgression and translocation to those of seed set, seed germination, and seedling rates in the M1 generation, we conclude that the dosage of 20 Grays is the most suitable. The established methodology may guide the utilization of the tertiary gene pool of Gossypium species such as G. australe in cotton breeding in the future. Electronic supplementary material The online version of this article (10.1186/s12864-017-4398-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shouli Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Sai Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dong Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.,Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, People's Republic of China
| | - Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.,Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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12
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Zhao G, Song Y, Wang C, Butt HI, Wang Q, Zhang C, Yang Z, Liu Z, Chen E, Zhang X, Li F. Genome-wide identification and functional analysis of the TIFY gene family in response to drought in cotton. Mol Genet Genomics 2016; 291:2173-2187. [PMID: 27640194 PMCID: PMC5080297 DOI: 10.1007/s00438-016-1248-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 09/02/2016] [Indexed: 11/26/2022]
Abstract
Jasmonates control many aspects of plant biological processes. They are important for regulating plant responses to various biotic and abiotic stresses, including drought, which is one of the most serious threats to sustainable agricultural production. However, little is known regarding how jasmonate ZIM-domain (JAZ) proteins mediate jasmonic acid signals to improve stress tolerance in cotton. This represents the first comprehensive comparative study of TIFY transcription factors in both diploid A, D and tetraploid AD cotton species. In this study, we identified 21 TIFY family members in the genome of Gossypium arboretum, 28 members from Gossypium raimondii and 50 TIFY genes in Gossypium hirsutum. The phylogenetic analyses indicated the TIFY gene family could be divided into the following four subfamilies: TIFY, PPD, ZML, and JAZ subfamilies. The cotton TIFY genes have expanded through tandem duplications and segmental duplications compared with other plant species. Gene expression profile revealed temporal and tissue specificities for TIFY genes under simulated drought conditions in Gossypium arboretum. The JAZ subfamily members were the most highly expressed genes, suggesting that they have a vital role in responses to drought stress. Over-expression of GaJAZ5 gene decreased water loss, stomatal openings, and the accumulation of H2O2 in Arabidopsis thaliana. Additionally, the results of drought tolerance assays suggested that this subfamily might be involved in increasing drought tolerance. Our study provides new data regarding the genome-wide analysis of TIFY gene families and their important roles in drought tolerance in cotton species. These data may form the basis of future studies regarding the relationship between drought and jasmonic acid.
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Affiliation(s)
- Ge Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yun Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Caixiang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hamama Islam Butt
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qianhua Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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13
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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