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Li L, Zhang C, Huang J, Liu Q, Wei H, Wang H, Liu G, Gu L, Yu S. Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:109-123. [PMID: 32652678 PMCID: PMC7769233 DOI: 10.1111/pbi.13446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 05/05/2023]
Abstract
Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole-genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome-wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.
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Affiliation(s)
- Libei Li
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Chi Zhang
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Jianqin Huang
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
| | - Qibao Liu
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Hengling Wei
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Hantao Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Guoyuan Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Lijiao Gu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Shuxun Yu
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
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Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z. LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Res 2020; 48:D1069-D1075. [PMID: 31599330 PMCID: PMC6943054 DOI: 10.1093/nar/gkz898] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 12/02/2022] Open
Abstract
The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.
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Affiliation(s)
- Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yang Zhang
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhao
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.,College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Jingchu Luo
- College of Life Sciences, Peking University, Beijing 100871, China.,Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.,Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Lin L, Cai W, Du Z, Zhang W, Xu Q, Sun W, Chen M. Establishing a System for Functional Characterization of Full-Length cDNAs of Camellia sinensis. Int J Mol Sci 2019; 20:ijms20235929. [PMID: 31775391 PMCID: PMC6929147 DOI: 10.3390/ijms20235929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis) is enriched with bioactive secondary metabolites, and is one of the most popular nonalcoholic beverages globally. Two tea reference genomes have been reported; however, the functional analysis of tea genes has lagged, mainly due to tea’s recalcitrance to genetic transformation and the absence of alternative high throughput heterologous expression systems. A full-length cDNA collection with a streamlined cloning system is needed in this economically important woody crop species. RNAs were isolated from nine different vegetative tea tissues, pooled, then used to construct a normalized full-length cDNA library. The titer of unamplified and amplified cDNA library was 6.89 × 106 and 1.8 × 1010 cfu/mL, respectively; the library recombinant rate was 87.2%. Preliminary characterization demonstrated that this collection can complement existing tea reference genomes and facilitate rare gene discovery. In addition, to streamline tea cDNA cloning and functional analysis, a binary vector (pBIG2113SF) was reengineered, seven tea cDNAs isolated from this library were successfully cloned into this vector, then transformed into Arabidopsis. One FL-cDNA, which encodes a putative P1B-type ATPase 5 (CsHMA5), was characterized further as a proof of concept. We demonstrated that overexpression of CsHMA5 in Arabidopsis resulted in copper hyposensitivity. Thus, our data demonstrated that this represents an efficient system for rare gene discovery and functional characterization of tea genes. The integration of a tea FL-cDNA collection with efficient cloning and a heterologous expression system would facilitate functional annotation and characterization of tea genes.
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Affiliation(s)
- Lin Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weiwei Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Zhenghua Du
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Wenjing Zhang
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quanming Xu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weijiang Sun
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
| | - Mingjie Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
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Dou L, Jia X, Wei H, Fan S, Wang H, Guo Y, Duan S, Pang C, Yu S. Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq. PLoS One 2017; 12:e0179141. [PMID: 28715427 PMCID: PMC5513416 DOI: 10.1371/journal.pone.0179141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.
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Affiliation(s)
- Lingling Dou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- Weinan Institute of Agricultural Sciences, Weinan, Shaanxi, P. R. China
| | - Xiaoyun Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Yaning Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Shan Duan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- * E-mail: (CP); (SY)
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- * E-mail: (CP); (SY)
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Shi G, Guo X, Guo J, Liu L, Hua J. Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.). PLANT CELL REPORTS 2015; 34:1005-23. [PMID: 25700980 DOI: 10.1007/s00299-015-1761-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/22/2023]
Abstract
By comparing series full-length cDNA libraries stressed and control, the dynamic process of salt stress response in Upland cotton was studied, and reactive oxygen species and gibberellins signaling pathways were proposed. The Upland cotton is the most important fiber plant with highly salt tolerance. However, the molecular mechanism underlying salt tolerance in domesticated cotton was unclear. Here, seven full-length cDNA libraries were constructed for seedling roots of Upland cotton 'Zhong G 5' at 0, 3, 12 and 48 h after the treatment of control or 150 mM NaCl stress. About 3300 colonies in each library were selected robotically for 5'-end pyrosequencing, resulting in 20,358 expressed sequence tags (ESTs) totally. And 8516 uniESTs were then assembled, including 2914 contigs and 5602 singletons, and explored for Gene Ontology (GO) function. GO comparison between serial stress libraries and control reflected the growth regulation, stimulus response, signal transduction and biology regulation processes were conducted dynamically in response to salt stress. MYB, MYB-related, WRKY, bHLH, GRAS and ERF families of transcription factors were significantly enriched in the early response. 65 differentially expressed genes (DEGs), mainly associated with reactive oxygen species (ROS) scavenging, gibberellins (GAs) metabolism, signal transduction, transcription regulation, stress response and transmembrane transport, were identified and confirmed by quantitative real-time PCR. Overexpression of selected DEGs increased tolerance against salt stress in transgenic yeast. Results in this study supported that a ROS-GAs interacting signaling pathway of salt stress response was activated in Upland cotton. Our results provided valuable gene resources for further investigation of the molecular mechanism of salinity tolerance.
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Affiliation(s)
- Gongyao Shi
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China,
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Lin M, Pang C, Fan S, Song M, Wei H, Yu S. Global analysis of the Gossypium hirsutum L. Transcriptome during leaf senescence by RNA-Seq. BMC PLANT BIOLOGY 2015; 15:43. [PMID: 25849479 PMCID: PMC4342795 DOI: 10.1186/s12870-015-0433-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/20/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Leaf senescence is an important developmental programmed degeneration process that dramatically affects crop quality and yield. The regulation of senescence is highly complex. Although senescence regulatory genes have been well characterized in model species such as Arabidopsis and rice, there is little information on the control of this process in cotton. Here, the senescence process in cotton (Gossypium hirsutum L.) leaves was investigated over a time course including young leaf, mature leaf and leaf samples from different senescence stages using RNA-Seq. RESULTS Of 24,846 genes detected by mapping the tags to Gossypium genomes, 3,624 genes were identified as differentially expressed during leaf senescence. There was some overlap between the genes identified here and senescence-associated genes previously identified in other species. Most of the genes related to photosynthesis, chlorophyll metabolism and carbon fixation were downregulated; whereas those for plant hormone signal transduction were upregulated. Quantitative real-time PCR was used to evaluate the results of RNA-Seq for gene expression profiles. Furthermore, 519 differentially expressed transcription factors were identified, notably WRKY, bHLH and C3H. In addition, 960 genes involved in the metabolism and regulation of eight hormones were identified, of which many genes involved in the abscisic acid, brassinosteroid, jasmonic acid, salicylic acid and ethylene pathways were upregulated, indicating that these hormone-related genes might play crucial roles in cotton leaf development and senescence. However, most auxin, cytokinin and gibberellin pathway-related genes were downregulated, suggesting that these three hormones may act as negative regulators of senescence. CONCLUSIONS This is the first high-resolution, multiple time-course, genome-wide comprehensive analysis of gene expression in cotton. These data are the most comprehensive dataset currently available for cotton leaf senescence, and will serve as a useful resource for unraveling the functions of many specific genes involved in cotton leaf development and senescence.
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Affiliation(s)
- Min Lin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455112 China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455112 China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455112 China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455112 China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455112 China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455112 China
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Genomic organization, differential expression, and functional analysis of the SPL gene family in Gossypium hirsutum. Mol Genet Genomics 2014; 290:115-26. [PMID: 25159110 DOI: 10.1007/s00438-014-0901-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/19/2014] [Indexed: 10/24/2022]
Abstract
SQUAMOSA promoter binding protein-like (SPL) genes encode plant-specific transcription factors that are involved in many fundamental developmental processes. Certain SPL genes contain sequences complementary to miR156, a microRNA (miRNA) that plays a role in modulating plant gene expression. In this study, 30 SPL genes were identified in the reference genome of Gossypium raimondii and 24 GhSPLs were cloned from Gossypium hirsutum. G. raimondii is regarded as the putative contributor of the D-subgenome of G. hirsutum. Comparative analysis demonstrated sequence conservation between GhSPLs and other plant species. GhSPL genes could be classified into seven subclades based on phylogenetic analysis, diverse intron-exon structure, and motif prediction. Within each subclade, genes shared a similar structure. Sequence and experimental analysis predicted that 18 GhSPL genes are putative targets of GhmiR156. Additionally, tissue-specific expression analysis of GhSPL genes showed that their spatiotemporal expression patterns during development progressed differently, with most genes having high transcript levels in leaves, stems, and flowers. Finally, overexpression of GhSPL3 and GhSPL18 in Arabidopsis plants demonstrated that these two genes are involved in the development of leaves and second shoots and play an integral role in promoting flowering. The flowering integrator GhSOC1 may bind to the promoter of GhSPL3 but not GhSPL18 to regulate flowering. In conclusion, our analysis of GhSPL genes will provide some gene resources and a further understanding of GhSPL3 and GhSPL18 function in flowering promotion. Furthermore, the comparative genomics and functional analysis deepened our understanding of GhSPL genes during upland cotton vegetative and reproductive growth.
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