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Wang L, Kartika D, Ruan YL. Looking into 'hair tonics' for cotton fiber initiation. THE NEW PHYTOLOGIST 2021; 229:1844-1851. [PMID: 32858773 DOI: 10.1111/nph.16898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Cotton fiber is the most important source of cellulose for the global textile industry. These hair-like single-celled trichomes develop from ovule epidermis. They are classified into long spinnable lint and short fuzz. A key objective in the cotton industry is to breed elite cultivars with fuzzless seeds carrying high lint yield. Molecular basis underlying lint and fuzz initiation remains obscure. Recent studies indicate fiber initiation is under the control of MYB-bHLH-WDR (MBW) transcription factor complex. Based on molecular genetic studies and gene expression patterns linking fiber phenotypes, we propose that specific but different sets of MBW genes are required to precisely regulate the initiation of the lint and fuzz fibers. Emerging evidence further points to sugar signaling as a 'hair-tonic' to boost fiber initiation through interaction with MBW complex and auxin signaling. An integrative model is provided as a conceptual framework for future studies to dissect the molecular network responsible for cotton fiber initiation.
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Affiliation(s)
- Lu Wang
- School of Environmental and Life Sciences and Australia-China Research Center for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Dewi Kartika
- School of Environmental and Life Sciences and Australia-China Research Center for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Yong-Ling Ruan
- School of Environmental and Life Sciences and Australia-China Research Center for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
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Tian Y, Zhang T. MIXTAs and phytohormones orchestrate cotton fiber development. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101975. [PMID: 33296746 DOI: 10.1016/j.pbi.2020.10.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 05/24/2023]
Abstract
Cotton is the largest source of natural fiber for textile industry in the world. Cotton fibers are seed trichomes that make cotton unique among plants. Cotton fibers originate from ovule epidermal cells and serve as an excellent model to study the process of cell differentiation in plants. Characterization of factors contributing to fiber development will help to reveal general mechanisms of cell differentiation in plants. Transcription factors (TFs), especially MYB-MIXTA-like (MML) factors, appear to have evolved unique roles in fiber development. In addition, phytohormones including brassinosteroids, jasmonic acid, GA and auxin also play an important role in regulating fiber development. Here, we summarize the mechanisms of MIXTAs and phytohormones orchestrating cotton fiber development. The progress in understanding molecular basis of fiber development will facilitate future genetic engineering and breeding to improve cotton fiber quality and yield.
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Affiliation(s)
- Yue Tian
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, 310029 Zhejiang, PR China; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, 310029 Zhejiang, PR China.
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Wu H, Zheng L, Qanmber G, Guo M, Wang Z, Yang Z. Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.). BMC PLANT BIOLOGY 2021; 21:13. [PMID: 33407131 PMCID: PMC7788912 DOI: 10.1186/s12870-020-02787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/08/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. RESULTS In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. CONCLUSION This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.
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Affiliation(s)
- Huanhuan Wu
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Lei Zheng
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Chen W, Li Y, Zhu S, Fang S, Zhao L, Guo Y, Wang J, Yuan L, Lu Y, Liu F, Yao J, Zhang Y. A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li3 of Tetraploid Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:593679. [PMID: 33324436 PMCID: PMC7725795 DOI: 10.3389/fpls.2020.593679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/09/2020] [Indexed: 05/31/2023]
Abstract
Cotton (Gossypium) seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene Li3 was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 (GhMML3_D12). Sequence analysis revealed that li3 is a loss-of-function allele containing a retrotransposon insertion in the second exon that completely blocks the gene’s expression. The genetic loci n2 and n3 underlying the recessive fuzzless phenotype in Gossypium hirsutum were also mapped. The genomic location of n3 overlapped with that of the dominant fuzzless locus N1, and n3 appeared to be a loss-of-function allele caused by a single nucleotide polymorphism (SNP) mutation in the coding region of GhMML3_A12. The n2 allele was found to be co-located with li3 and originated from G. babardense. n2 and li3 are possibly the multiple alleles of the GhMML3_D12 gene. Genetic analysis showed that Li3 and N3 are a pair of homologs with additive effects for the initiation of fibers (fuzz or lint). In addition, the presence of another locus was speculated, and it appeared to show an inhibitory effect on the expression of GhMML3. These findings provide new information about the genetic factors affecting the initiation of fibers in cotton.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junyi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youjun Lu
- School of Biological Science and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Mol Genet Genomics 2020; 296:193-206. [PMID: 33141290 DOI: 10.1007/s00438-020-01736-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
Most commercially produced cotton cultivars have two types of fibers on the seed coat, short fuzz and long lint. Lint fiber is used in the textile industry, while fuzz is considered an undesirable trait. Both types of fibers are believed to be controlled by the same regulators; however, their mechanisms of actions are still obscure. Cotton fiber mutants provide an excellent system to study the genes that regulate fiber development. Here we described four uncharacterized and three previously reported cotton mutants with fuzzless seed phenotypes. To evaluate whether or not the genes previously associated with fuzzless seed phenotypes have mutations we sequenced whole genomic DNA of seven mutants and wild type varieties. We identified multiple polymorphic changes among the tested genes. Non-synonymous SNPs in the coding region of the MML3-A gene was common in the six mutant lines tested in this study, showing both dominant and recessive fuzzless phenotypes. We have mapped the locus of the causative mutation for one of the uncharacterized fuzzless lines using an F2 population that originated from a cross between the dominant fuzzless mutant and a wild type. Further, we have clarified the current knowledge about the causative n2 mutations by analyzing the sequence data and previously reported mapping data. The key genes and possible mechanisms of fiber differentiation are discussed in this study.
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56
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Cheng G, Zhang L, Wei H, Wang H, Lu J, Yu S. Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense. Genes (Basel) 2020; 11:genes11091066. [PMID: 32927688 PMCID: PMC7565297 DOI: 10.3390/genes11091066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022] Open
Abstract
Gossypium barbadense is an important source of natural textile fibers, as is Gossypium hirsutum. Cotton fiber development is often affected by various environmental factors, such as abnormal temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation. In this study, we reveal that high temperatures (HT) accelerate fiber development, improve fiber quality, and induced fuzz initiation of a thermo-sensitive G. barbadense variety L7009. It was proved that fuzz initiation was inhibited by low temperature (LT), and 4 dpa was the stage most susceptible to temperature stress during the fuzz initiation period. A total of 43,826 differentially expressed genes (DEGs) were identified through comparative transcriptome analysis. Of these, 9667 were involved in fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were potentially involved in fuzz initiation induced by high temperature. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in the asparagine biosynthetic process, cell wall biosynthesis, and stress response. The expression trends of sixteen genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR. Our study revealed several potential candidate genes and pathways related to fuzz initiation induced by high temperature. This provides a new view of temperature-induced tissue and organ development in Gossypium barbadense.
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Affiliation(s)
- Gongmin Cheng
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling 712100, China;
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (L.Z.); (H.W.); (H.W.); (J.L.)
| | - Longyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (L.Z.); (H.W.); (H.W.); (J.L.)
- College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (L.Z.); (H.W.); (H.W.); (J.L.)
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (L.Z.); (H.W.); (H.W.); (J.L.)
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (L.Z.); (H.W.); (H.W.); (J.L.)
| | - Shuxun Yu
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling 712100, China;
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (L.Z.); (H.W.); (H.W.); (J.L.)
- Correspondence: ; Tel.: +86-188-0372-9718
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Tan J, Walford SA, Dennis ES, Llewellyn DJ. Trichomes at the Base of the Petal Are Regulated by the Same Transcription Factors as Cotton Seed Fibers. PLANT & CELL PHYSIOLOGY 2020; 61:1590-1599. [PMID: 32579215 DOI: 10.1093/pcp/pcaa082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Many polypetalous plants have a constriction at the base of the petal that leaves a small gap that can provide entry into the young flower bud before the reproductive organs are fully developed. In cotton (Gossypium hirsutum L.), this gap is occluded by tufts of short unicellular trichomes superficially resembling the fibers found on cotton seeds. We are just beginning to understand the developmental regulation of the seed fibers and have previously characterized several MIXTA-like MYB transcription factors (TFs) that are critical for correct seed fiber development but know little about the molecular regulation of other types of cotton trichomes. Here, using RNAi or dominant suppression transgenic cotton lines and natural fiber mutants, we investigated the development and regulation of the petal base trichomes. Petal base trichomes and seed trichomes were also examined across several different species within and outside of the Malvoideae. We found that the petal base trichomes are regulated by the same MYB TFs as cotton seed fibers and, since they are more widely distributed across different taxa than the seed fibers, could have preceded them in the evolution of these important textile fibers produced by some cotton species.
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Affiliation(s)
- Jiafu Tan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- University of Technology Sydney, Ultimo, NSW 2007, Australia
| | | | - Elizabeth S Dennis
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- University of Technology Sydney, Ultimo, NSW 2007, Australia
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Liu W, Song C, Ren Z, Zhang Z, Pei X, Liu Y, He K, Zhang F, Zhao J, Zhang J, Wang X, Yang D, Li W. Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2020; 20:395. [PMID: 32854609 PMCID: PMC7450593 DOI: 10.1186/s12870-020-02611-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/18/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Fiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding. To better understand the genetic mechanisms responsible for fiber quality traits, we conducted a genome-wide association study to identify and mine fiber-quality-related quantitative trait loci (QTLs) and genes. RESULTS In total, 42 single nucleotide polymorphisms (SNPs) and 31 QTLs were identified as being significantly associated with five fiber quality traits. Twenty-five QTLs were identified in previous studies, and six novel QTLs were firstly identified in this study. In the QTL regions, 822 genes were identified and divided into four clusters based on their expression profiles. We also identified two pleiotropic SNPs. The SNP locus i52359Gb was associated with fiber elongation, strength, length and uniformity, while i11316Gh was associated with fiber strength and length. Moreover, these two SNPs were nonsynonymous and located in genes Gh_D09G2376 and Gh_D06G1908, respectively. RT-qPCR analysis revealed that these two genes were preferentially expressed at one or more stages of cotton fiber development, which was consistent with the RNA-seq data. Thus, Gh_D09G2376 and Gh_D06G1908 may be involved in fiber developmental processes. CONCLUSIONS The findings of this study provide insights into the genetic bases of fiber quality traits, and the identified QTLs or genes may be applicable in cotton breeding to improve fiber quality.
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Affiliation(s)
- Wei Liu
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chengxiang Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhiqiang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Junjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Wei Li
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Ali F, Qanmber G, Wei Z, Yu D, Li YH, Gan L, Li F, Wang Z. Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses. BMC Genomics 2020; 21:561. [PMID: 32799801 PMCID: PMC7430837 DOI: 10.1186/s12864-020-06970-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/03/2020] [Indexed: 11/12/2022] Open
Abstract
Background GGPP (geranylgeranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has not been performed in any plant species except Arabidopsis thaliana. Here, we performed a complete computational and bioinformatics analysis of GGPPS and detected their transcription expression pattern in Gossypium hirsutum for the first time so that to explore their evolutionary relationship and potential functions. Finally, we unravelled evolutionary relationship, conserved sequence logos, gene duplication and potential involvement in plant development and abiotic stresses tolerance of GGPPS genes in G. hirsutum and other plant species. Results A total of 159 GGPPS genes from 18 plant species were identified and evolutionary analysis divided these GGPPS genes into five groups to indicate their divergence from a common ancestor. Further, GGPPS family genes were conserved during evolution and underwent segmental duplication. The identified 25 GhGGPPS genes showed diverse expression pattern particularly in ovule and fiber development indicating their vital and divers roles in the fiber development. Additionally, GhGGPPS genes exhibited wide range of responses when subjected to abiotic (heat, cold, NaCl and PEG) stresses and hormonal (BL, GA, IAA, SA and MeJA) treatments, indicating their potential roles in various biotic and abiotic stresses tolerance. Conclusions The GGPPS genes are evolutionary conserved and might be involve in different developmental stages and stress response. Some potential key genes (e.g. GhGGPP4, GhGGPP9, and GhGGPP15) were suggested for further study and provided valuable source for cotton breeding to improve fiber quality and resistant to various stresses.
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Affiliation(s)
- Faiza Ali
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhenzhen Wei
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Daoqian Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yong Hui Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lei Gan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Wang L, Wang G, Long L, Altunok S, Feng Z, Wang D, Khawar KM, Mujtaba M. Understanding the role of phytohormones in cotton fiber development through omic approaches; recent advances and future directions. Int J Biol Macromol 2020; 163:1301-1313. [PMID: 32679330 DOI: 10.1016/j.ijbiomac.2020.07.104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/27/2020] [Accepted: 07/09/2020] [Indexed: 01/13/2023]
Abstract
Cotton is among the most important fiber crops for the textile-based industry, thanks to its cellulose-rich mature fibers. The fiber initiation and elongation are one of the best models for deciphering mechanisms of single-cell differentiation and growth, that also target of fiber development programs. During the last couple of decades, high yielding omics approaches (genomics, transcriptomics, and proteomics), have helped in the identification of several genes and gene products involved in fiber development along with functional relationship to phytohormones. For example, MYB transcription factor family and Sus gene family have been evidenced by controlling cotton fiber initiation. Most importantly, the biosynthesis, responses, and transporting of phytohormones is documented to participate in the initiation of cotton fibers. Herein, in this review, the reliable genetic evidence by manipulating the above genes in cotton have been summarized to describe the relationships among key phytohormones, transcription factors, proteins, and downstream fiber growth-related genes such as Sus. The effect of other important factors such as ROS, fatty acid metabolism, and actin (globular multi-functional proteins) over fiber development has also been discussed. The challenges and deficiencies in the research of cotton fiber development have been mentioned along with a future perspective to discover new crucial genes using multiple omics analysis.
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Affiliation(s)
- Lichen Wang
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Guifeng Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei 430070, China; Shandong Cotton Production Technical Guidance Station, Jinan, Shandong 250100, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan 475004, China
| | - Sumeyye Altunok
- Institute of Biotechnology, Ankara University, 06110 Ankara, Turkey
| | - Zongqin Feng
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Depeng Wang
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, 06100 Ankara, Turkey
| | - Muhammad Mujtaba
- Institute of Biotechnology, Ankara University, 06110 Ankara, Turkey.
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Ding M, Cao Y, He S, Sun J, Dai H, Zhang H, Sun C, Jiang Y, Paterson AH, Rong J. GaHD1, a candidate gene for the Gossypium arboreum SMA-4 mutant, promotes trichome and fiber initiation by cellular H 2O 2 and Ca 2+ signals. PLANT MOLECULAR BIOLOGY 2020; 103:409-423. [PMID: 32189187 DOI: 10.1007/s11103-020-01000-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
Cotton fibers are initiated from the epidermal cells of the ovule before or on the day of anthesis. Gossypium arboreum SMA-4 mutant contains recessive mutation (sma-4(ha)) and has the phenotypes of fibreless seeds and glabrous stems. In this study, fine mapping and alternative splicing analysis indicated a nucleotide substitution (AG → AC) at splicing site in a homeodomain-leucine zipper IV family gene (GaHD1) might cause gene A3S (Alternative 3' splicing) mistake, suggested that GaHD1 was the candidate gene of sma-4(ha). Many genes related to the fiber initiation are identified to be differentially expressed in the mutant which could result in the blocked fiber initiation signals such as H2O2, or Ca in the mutant. Further comparative physiological analysis of H2O2 production and Ca2+ flux in the SMA-4 and wide type cotton confirmed that H2O2 and Ca were important fiber initiation signals and regulated by GaHD1. The in vitro ovule culture of the mutant with hormones recovered the fibered phenotype coupled with the restoration of these signals. Overexpressing of GaHD1 in Arabidopsis increased trichome densities on the sepal, leaf, and stem tissues while transient silencing of the GaHD1 gene in G. arboreum reduced the trichome densities. These phenotypes indicated that GaHD1 is the candidate gene of SMA-4 with a crucial role in acting upstream molecular switch of signal transductions for cotton trichome and fiber initiations.
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Affiliation(s)
- Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yuefen Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Shae He
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jian Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Huaqin Dai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Chendong Sun
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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Zhu D, Li X, Wang Z, You C, Nie X, Sun J, Zhang X, Zhang D, Lin Z. Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton. BMC Genomics 2020; 21:431. [PMID: 32586283 PMCID: PMC7318736 DOI: 10.1186/s12864-020-06800-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 01/07/2023] Open
Abstract
Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.
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Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Key Laboratory of Dryland Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhiwei Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Peanut Research Institute, Qingdao, 266109, Shangdong, China
| | - Chunyuan You
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, 832003, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dawei Zhang
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Tian Y, Du J, Wu H, Guan X, Chen W, Hu Y, Fang L, Ding L, Li M, Yang D, Yang Q, Zhang T. The transcription factor MML4_D12 regulates fiber development through interplay with the WD40-repeat protein WDR in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3499-3511. [PMID: 32149350 PMCID: PMC7475258 DOI: 10.1093/jxb/eraa104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 02/28/2020] [Indexed: 05/24/2023]
Abstract
In planta, a vital regulatory complex, MYB-basic helix-loop-helix (bHLH)-WD40 (MBW), is involved in trichome development and synthesis of anthocyanin and proanthocyanin in Arabidopsis. Usually, WD40 proteins provide a scaffold for protein-protein interaction between MYB and bHLH proteins. Members of subgroup 9 of the R2R3 MYB transcription factors, which includes MYBMIXTA-Like (MML) genes important for plant cell differentiation, are unable to interact with bHLH. In this study, we report that a cotton (Gossypium hirsutum) seed trichome or lint fiber-related GhMML factor, GhMML4_D12, interacts with a diverged WD40 protein (GhWDR) in a process similar to but different from that of the MBW ternary complex involved in Arabidopsis trichome development. Amino acids 250-267 of GhMML4_D12 and the first and third WD40 repeat domains of GhWDR determine their interaction. GhWDR could rescue Arabidopsis ttg1 to its wild type, confirming its orthologous function in trichome development. Our findings shed more light towards understanding the key role of the MML and WD40 families in plants and in the improvement of cotton fiber production.
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Affiliation(s)
- Yue Tian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Jingjing Du
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Huaitong Wu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xueying Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Weihang Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yan Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Lei Fang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Linyun Ding
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Menglin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Duofeng Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Qinli Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
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Zhao T, Tao X, Li M, Gao M, Chen J, Zhou N, Mei G, Fang L, Ding L, Zhou B, Zhang T, Guan X. Role of phasiRNAs from two distinct phasing frames of GhMYB2 loci in cis- gene regulation in the cotton genome. BMC PLANT BIOLOGY 2020; 20:219. [PMID: 32414380 PMCID: PMC7227086 DOI: 10.1186/s12870-020-02430-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/05/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Phased small interfering RNA (phasiRNA) is primarily derived from the 22-nt miRNA targeting loci. GhMYB2, a gene with potential roles in cotton fiber cell fate determination, is a target gene of miR828 and miR858 in the generation of phasiRNAs. RESULTS In the presented work, through the evaluation of phasing scores and phasiRNA distribution pattern, we found that phasiRNAs from GhMYB2 were derived from the 3' cleavage fragments of 22-nt miR828 and 21-nt miR858 respectively. These two miRNA targeting sites initiated two phasing frames on transcripts of one locus. By means of RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we further demonstrated that phasiRNAs derived from the two phasing frames played a role in cis-regulation of GhMYB2. The phasiRNAs derived from GhMYB2 were expressed in the somatic tissues, especially in anther and hypocotyl. We further employed our previous small RNA sequencing data as well as the degradome data of cotton fiber bearing ovules, anthers, hypocotyls and embryogenic calli tissues published in public databases, to validate the expression, phasing pattern and functions of phasiRNAs. CONCLUSIONS The presenting research provide insights of the molecular mechanism of phasiRNAs in regulation of GhMYB2 loci.
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Affiliation(s)
- Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 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, Jiangsu 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, Jiangsu China
| | - Jiedan Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Na 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, Jiangsu China
| | - Gaofu Mei
- 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, Jiangsu China
| | - Lei Fang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Linyun Ding
- 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, Jiangsu 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, Jiangsu China
| | - Tianzhen Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
- 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, Jiangsu China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
- 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, Jiangsu China
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Yang Z, Qanmber G, Wang Z, Yang Z, Li F. Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement. TRENDS IN PLANT SCIENCE 2020; 25:488-500. [PMID: 31980282 DOI: 10.1016/j.tplants.2019.12.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/19/2019] [Accepted: 12/09/2019] [Indexed: 05/23/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.
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Affiliation(s)
- Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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66
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Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L. Int J Mol Sci 2020; 21:ijms21051675. [PMID: 32121400 PMCID: PMC7084617 DOI: 10.3390/ijms21051675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 11/17/2022] Open
Abstract
Cotton fibres, as single cells arising from the seed coat, can be classified as lint and fuzz according to their final length. Gossypium arboreum is a cultivated diploid cotton species and a potential donor of the A subgenome of the more widely grown tetraploid cottons. In this study, we performed genetic studies on one lintless and seven fuzzless G. arboreum accessions. Through association and genetic linkage analyses, a recessive locus on Chr06 containing GaHD-1 was found to be the likely gene underlying the lintless trait. GaHD-1 carried a mutation at a splicing acceptor site that resulted in alternative splicing and a deletion of 247 amino acid from the protein. The regions containing GaGIR1 and GaMYB25-like were found to be associated with fuzz development in G. arboreum, with the former being the major contributor. Comparative transcriptome analyses using 0-5 days post-anthesis (dpa) ovules from lintless, fuzzless, and normal fuzzy seed G. arboreum accessions revealed gene modules and hub genes potentially important for lint and fuzz initiation and development. Three significant modules and 26 hub genes associated with lint fibre initiation were detected by weighted gene co-expression network analysis. Similar analyses identified three vital modules and 10 hub genes to be associated with fuzz development. The findings in this study contribute to understanding the complex molecular mechanism(s) regulating fibre initiation and development and indicate that G. arboreum may have fibre developmental pathways different from tetraploid cotton. It also provides candidate genes for further investigation into modifying fibre development in G. arboreum.
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Chen W, Yao J, Li Y, Zhu S, Guo Y, Fang S, Zhao L, Wang J, Yuan L, Lu Y, Zhang Y. Open-Bud Duplicate Loci Are Identified as MML10s, Orthologs of MIXTA-Like Genes on Homologous Chromosomes of Allotetraploid Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:81. [PMID: 32133019 PMCID: PMC7040098 DOI: 10.3389/fpls.2020.00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The open-bud (ob) mutants in cotton display abnormal flower buds with the stigma and upper anthers exposed before blooming. This characteristic is potentially useful for the efficient production of hybrid seeds. The recessive inheritance pattern of the ob phenotype in allotetraploid cotton is determined by duplicated recessive loci (ob1ob1ob2ob2). In this study, ob1, which is a MIXTA-like MYB gene on chromosome D13 (MML10_Dt), was identified by map-based cloning. In Gossypium barbadense (Gb) acc. 3-79, a single nucleotide polymorphism (SNP) (G/A) at the splice site of the first intron and an 8-bp deletion in the third exon of MML10_Dt were found, which are the causative mutations at the ob1 loci. A 1783-bp deletion that leads to the loss of the third exon and accounts for the causal variation at the ob2 loci was found in MML10_At of Gossypium hirsutum (Gh) acc. TM-1. The ob phenotype results from the combination of these two loss-of-function loci. Genotyping assays showed that the ob1 and ob2 loci appeared after the formation of allotetraploid cotton and were specific for Gb and Gh, respectively. All Gb lines and most Gh cultivars carry the single corresponding mutant alleles. Genome-wide transcriptome analysis showed that some of the MYB genes and genes related to cell wall biogenesis, trichome differentiation, cytokinin signal transduction, and cell division were repressed in the ob mutants, which may lead to suppression of petal growth. These findings should be of value for breeding superior ob lines in cotton.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junyi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youjun Lu
- School of Biological Science and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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68
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Fang DD, Naoumkina M, Thyssen GN, Bechere E, Li P, Florane CB. An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the li y short fiber phenotype in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:271-282. [PMID: 31624873 DOI: 10.1007/s00122-019-03456-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/09/2019] [Indexed: 05/15/2023]
Abstract
The EMS-induced threonine/isoleucine substitution in a tetratricopeptide repeat-like superfamily protein encoded by gene Ghir_A12G008870 is responsible for the Ligon-lintless-y (liy) short fiber phenotype in cotton. A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate. Genetic analysis indicated that the short fiber phenotype is controlled by a single recessive locus designated liy. From F2 populations derived from crosses between the mutant and its wild type (WT), we selected 132 short fiber progeny (liy/liy) and made two DNA bulks. We sequenced these DNA bulks along with the two parents of the population. The liy locus was located on chromosome A12. Using multiple F2 populations and F3 progeny plants, we mapped the liy locus within a genomic region of 1.18 Mb. In this region, there is only one gene, i.e., Ghir_A12G008870 encoding a tetratricopeptide repeat-like superfamily protein that has a non-synonymous mutation between the liy mutant and its WT. Analysis of a SNP marker representing this gene in the F2 and F3 progeny plants demonstrated its complete linkage with the liy short fiber phenotype. We further analyzed this SNP marker in a panel of 384 cotton varieties. The mutant allele is absent in all varieties analyzed. RNAseq and RT-qPCR analysis of the gene Ghir_A12G008870 during fiber development showed a significant expression difference between the liy mutant and its WT in developing fiber cells beginning at 12 days post-anthesis. Virus-induced gene silencing of the gene Ghir_A12G008870 significantly reduced the fiber length of the WT cotton line MD15. Taken together, our results suggest that the gene Ghir_A12G008870 is involved in the cotton fiber cell elongation process and is a promising candidate gene responsible for the liy short fiber phenotype.
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Affiliation(s)
- David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA.
| | - Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
- Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - Efrem Bechere
- Crop Genetics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ping Li
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
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Ayubov MS, Mirzakhmedov MH, Sripathi VR, Buriev ZT, Ubaydullaeva KA, Usmonov DE, Norboboyeva RB, Emani C, Kumpatla SP, Abdurakhmonov IY. Role of MicroRNAs and small RNAs in regulation of developmental processes and agronomic traits in Gossypium species. Genomics 2019; 111:1018-1025. [PMID: 30026106 DOI: 10.1016/j.ygeno.2018.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 02/08/2023]
Abstract
Small RNAs (sRNAs) are short, non-coding, 17-24 nucleotides long RNA molecules that play vital roles in regulating gene expression in every known organism investigated to date including cotton (Gossypium ssp.). These tiny RNA molecules target diverse categories of genes from different bioliogical and metabolic processes and have been reported in the three domains of life. Small RNAs, including miRNAs, are involved in ovule and fiber development, biotic and abiotic stresses, fertility, and other biochemical processes in cotton species. Also, sRNAs are the critical components in RNA interference pathway. In this article, we have reviewed the research efforts related to the isolation and characterization of miRNAs using molecular and genomic approaches. The progress made in understanding the functional roles of miRNAs in regulation, alteration, and inactivation of fundamental plant processes and traits of importance in cotton are presented here.
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Affiliation(s)
- Mirzakamol S Ayubov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Mukhammad H Mirzakhmedov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan; Faculty of Agricultural Science, University of Hohenheim, Germany
| | - Venkateswara R Sripathi
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama A and M University, AL, USA
| | - Zabardast T Buriev
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | | | - Dilshod E Usmonov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Risolat B Norboboyeva
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
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Wang Z, Yang Z, Li F. Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1706-1722. [PMID: 31111642 PMCID: PMC6686129 DOI: 10.1111/pbi.13167] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 05/11/2023]
Abstract
Trichomes are specialized epidermal cells and a vital plant organ that protect plants from various harms and provide valuable resources for plant development and use. Some key genes related to trichomes have been identified in the model plant Arabidopsis thaliana through glabrous mutants and gene cloning, and the hub MYB-bHLH-WD40, consisting of several factors including GLABRA1 (GL1), GL3, TRANSPARENT TESTA GLABRA1 (TTG1), and ENHANCER OF GLABRA3 (EGL3), has been established. Subsequently, some upstream transcription factors, phytohormones and epigenetic modification factors have also been studied in depth. In cotton, a very important fibre and oil crop globally, in addition to the key MYB-like factors, more important regulators and potential molecular mechanisms (e.g. epigenetic modifiers, distinct metabolic pathways) are being exploited during different fibre developmental stages. This occurs due to increased cotton research, resulting in the discovery of more complex regulation mechanisms from the allotetraploid genome of cotton. In addition, some conservative as well as specific mediators are involved in trichome development in other species. This study summarizes molecular mechanisms in trichome development and provides a detailed comparison of the similarities and differences between Arabidopsis and cotton, analyses the possible reasons for the discrepancy in identification of regulators, and raises future questions and foci for understanding trichome development in more detail.
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Affiliation(s)
- Zhi Wang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zuoren Yang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Fuguang Li
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
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71
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Wang N, Ma Q, Ma J, Pei W, Liu G, Cui Y, Wu M, Zang X, Zhang J, Yu S, Ma L, Yu J. A Comparative Genome-Wide Analysis of the R2R3-MYB Gene Family Among Four Gossypium Species and Their Sequence Variation and Association With Fiber Quality Traits in an Interspecific G. hirsutum × G. barbadense Population. Front Genet 2019; 10:741. [PMID: 31475040 PMCID: PMC6704801 DOI: 10.3389/fgene.2019.00741] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 07/15/2019] [Indexed: 11/17/2022] Open
Abstract
Cotton (Gossypium spp.) is the most important natural fiber crop in the world. The R2R3-MYB gene family is a large gene family involved in many plant functions including cotton fiber development. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in tetraploid G. hirsutum and diploid G. raimondii, little is known about the sequence variation of the members between G. hirsutum and G. barbadense and their involvement in the natural quantitative variation in fiber quality and yield. In this study, a comprehensive genome-wide comparative analysis was performed among the four Gossypium species using whole genome sequences, i.e., tetraploid G. hirsutum (AD1) and G. barbadense (AD2) as well as their likely ancestral diploid extants G. raimondii (D5) and G. arboreum (A2), leading to the identification of 406, 393, 216, and 213 R2R3-MYB genes, respectively. To elucidate whether the R2R3-MYB genes are genetically associated with fiber quality traits, 86 R2R3-MYB genes were co-localized with quantitative trait loci (QTL) hotspots for fiber quality and yield, including 42 genes localized within the fiber length QTL hotspots, in interspecific G. hirsutum × G. barbadense populations. There were 20 interspecific nonsynonymous single-nucleotide polymorphism (SNP) sites between the two tetraploid cultivated species, of which 16 developed from 11 R2R3-MYB genes were significantly correlated with fiber quality and yield in a backcross inbred population (BIL) of G. hirsutum × G. barbadense in at least one of the four field tests. Taken together, these results indicate that the sequence variation in these 11 R2R3-MYB genes is associated with the natural variation (i.e., QTL) in fiber quality and yield. Moreover, the functional SNPs of five R2R3-MYB allele pairs from the AD1 and AD2 genomes were significantly correlated with the gene expression related to fiber quality in fiber development. The results will be useful in further elucidating the role of the R2R3-MYB genes during fiber development.
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Affiliation(s)
- Nuohan Wang
- College of Agronomy, Northwest A&F University, Yangling, China.,State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Qiang Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Jianjiang Ma
- College of Agronomy, Northwest A&F University, Yangling, China.,State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Yupeng Cui
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Xinshan Zang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, China.,State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
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72
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Qin Y, Sun H, Hao P, Wang H, Wang C, Ma L, Wei H, Yu S. Transcriptome analysis reveals differences in the mechanisms of fiber initiation and elongation between long- and short-fiber cotton (Gossypium hirsutum L.) lines. BMC Genomics 2019; 20:633. [PMID: 31382896 PMCID: PMC6683361 DOI: 10.1186/s12864-019-5986-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
Background Improving the yield and fiber quality of upland cotton is a goal of plant breeders. However, increasing the yield and quality of cotton fibers is becoming more urgent. While the growing human population needs more cotton fiber, climate change is reducing the amount of land on which cotton can be planted, or making it difficult to ensure that water and other resources will be available in optimal quantities. The most logical means of improving yield and quality is understanding and manipulating the genes involved. Here, we used comparative transcriptomics to explore differences in gene expression between long- and short-fiber cotton lines to identify candidate genes useful for cotton improvement. Results Light and electron microscopy revealed that the initial fiber density was significantly greater in our short-fiber group (SFG) than in our long-fiber group (LFG). Compared with the SFG fibers, the LFG fibers were longer at all developmental stages. Comparison of the LFG and SFG transcriptomes revealed a total of 3538 differentially expressed genes (DEGs). Notably, at all three developmental stages examined, two expression patterns, consistently downregulated (profile 0) and consistently upregulated (profile 7), were identified, and both were significantly enriched in the SFG and LFG. Twenty-two DEGs known to be involved in fiber initiation were detected in profile 0, while 31 DEGs involved in fiber elongation were detected in profile 7. Functional annotation suggested that these DEGs, which included ERF1, TUA2, TUB1, and PER64, affect fiber elongation by participating in the ethylene response, microtubule synthesis, and/or the peroxidase (POD) catalytic pathway. qRT-PCR was used to confirm the RNA sequencing results for select genes. Conclusions A comparison of SFG and LFG transcription profiles revealed modest but important differences in gene expression between the groups. Notably, our results confirm those of previous studies suggesting that genes involved in ethylene, tubulin, and POD pathways play important roles in fiber development. The 22 consistently downregulated DEGs involved in fiber initiation and the 31 consistently upregulated genes involved in fiber elongation are seemingly good candidate genes for improving fiber initiation and elongation in cotton. Electronic supplementary material The online version of this article (10.1186/s12864-019-5986-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan Qin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Congcong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, China.
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Feng X, Cheng H, Zuo D, Zhang Y, Wang Q, Liu K, Ashraf J, Yang Q, Li S, Chen X, Song G. Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2169-2179. [PMID: 30941465 PMCID: PMC6647196 DOI: 10.1007/s00122-019-03330-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/14/2018] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE The fuzzless gene GaFzl was fine mapped to a 70-kb region containing a GIR1 gene, Cotton_A_11941, responsible for the fuzzless trait in Gossypium arboreum DPL972. Cotton fiber is the most important natural textile resource. The fuzzless mutant DPL972 (Gossypium arboreum) provides a useful germplasm resource to explore the molecular mechanism underlying fiber and fuzz initiation and development. In our previous research, the fuzzless gene in DPL972 was identified as a single dominant gene and named GaFzl. In the present study, we fine mapped this gene using F2 and BC1 populations. By combining traditional map-based cloning and next-generation sequencing, we mapped GaFzl to a 70-kb region containing seven annotated genes. RNA-Sequencing and re-sequencing analysis narrowed these candidates to two differentially expressed genes, Cotton_A_11941 and Cotton_A_11942. Sequence alignment uncovered no variation in coding or promoter regions of Cotton_A_11942 between DPL971 and DPL972, whereas two single-base mutations in the promoter region and a TTG insertion in the coding region were detected in Cotton_A_11941 in DPL972. Cotton_A_11941 encoding a homologous gene of GIR1 (GLABRA2-interacting repressor) in Arabidopsis thaliana is thus the candidate gene most likely responsible for the fuzzless trait in DPL972. Our findings should lead to a better understanding of cotton fuzz formation, thereby accelerating marker-assisted selection during cotton breeding.
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Affiliation(s)
- Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Plant Genetics, Gembloux Agro Bio Tech, University of Liège, Gembloux, Belgium
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ke Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Javaria Ashraf
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiuhong Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Simin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoqin Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Guo JC, Fang SS, Wu Y, Zhang JH, Chen Y, Liu J, Wu B, Wu JR, Li EM, Xu LY, Sun L, Zhao Y. CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition. Nucleic Acids Res 2019; 47:W516-W522. [PMID: 31147700 PMCID: PMC6602462 DOI: 10.1093/nar/gkz400] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/25/2019] [Accepted: 05/02/2019] [Indexed: 02/05/2023] Open
Abstract
As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-Non-Coding Identifying Tool), which provides faster and more accurate evaluation of the coding ability of RNA transcripts. CNIT runs ∼200 times faster than CNCI and exhibits more accuracy compared with CNCI (0.98 versus 0.94 for human, 0.95 versus 0.93 for mouse, 0.93 versus 0.92 for zebrafish, 0.93 versus 0.92 for fruit fly, 0.92 versus 0.88 for worm, and 0.98 versus 0.85 for Arabidopsis transcripts). Moreover, the AUC values of 11 animal species and 27 plant species showed that CNIT was capable of obtaining relatively accurate identification results for almost all eukaryotic transcripts. In addition, a mobile-friendly web server is now freely available at http://cnit.noncode.org/CNIT.
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Affiliation(s)
- Jin-Cheng Guo
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuang-Sang Fang
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wu
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Jian-Hua Zhang
- Department of Blood Transfusion, Peking University People's Hospital, Beijing 100000, China
| | - Yang Chen
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Jing Liu
- The College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Bo Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Jia-Rui Wu
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - En-Min Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
- Correspondence may also be addressed to Li-Yan Xu. Tel: +86 754 88900460; Fax: +86 754 88900847;
| | - Liang Sun
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- Correspondence may also be addressed to Liang Sun. Tel: +86 10 6260 0822; Fax: +86 10 6260 1356;
| | - Yi Zhao
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
- To whom correspondence should be addressed. Tel: +86 10 6260 0822; Fax: +86 10 6260 1356;
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Sun W, Gao Z, Wang J, Huang Y, Chen Y, Li J, Lv M, Wang J, Luo M, Zuo K. Cotton fiber elongation requires the transcription factor GhMYB212 to regulate sucrose transportation into expanding fibers. THE NEW PHYTOLOGIST 2019; 222:864-881. [PMID: 30506685 DOI: 10.1111/nph.15620] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/24/2018] [Indexed: 05/18/2023]
Abstract
Cotton is white gold across the globe and composed of fiber cells derived from the outer integument of cotton ovules. Fiber elongation uses sucrose as a direct carbon source. The molecular mechanism transcriptionally controlling sucrose transport from ovules into the elongating fibers remains elusive. In this study the involvement of GhMYB212 in the regulation of sucrose transportion into expanding fibers was investigated. GhMYB212 RNAi plants (GhMYB212i) accumulated less sucrose and glucose in developing fibers, and had shorter fibers and a lower lint index. RNA-seq and protein-DNA binding assays revealed that GhMYB212 was closely linked to the pathways of sucrose and starch transportation and metabolism, directly controling the expression of a sucrose transporter gene GhSWEET12. GhSWEET12 RNAi plants (GhSWEET12i) possessed similar fiber phenotypes to those of GhMYB212i. Exogenous sucrose supplementation in ovule cultures did not rescue the shorter fiber phenotype of GhMYB212i and GhSWEET12i. This finding supported the idea that the attenuated rate of sucrose transport from the outer seed coat into the fibers is responsible for the retardation of fiber elongation. Current investigations support the idea that GhMYB212 functions as the main regulator of fiber elongation by controlling the expression of GhSWEET12, and therefore it is important to study cell expansion and sugar transportation during seed development.
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Affiliation(s)
- Wenjie Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiqun Huang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianfu Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mengli Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ming Luo
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, 400715, China
| | - Kaijing Zuo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Zhao T, Tao X, Feng S, Wang L, Hong H, Ma W, Shang G, Guo S, He Y, Zhou B, Guan X. LncRNAs in polyploid cotton interspecific hybrids are derived from transposon neofunctionalization. Genome Biol 2018; 19:195. [PMID: 30419941 PMCID: PMC6233382 DOI: 10.1186/s13059-018-1574-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Interspecific hybridization and whole genome duplication are driving forces of genomic and organism diversification. But the effect of interspecific hybridization and whole genome duplication on the non-coding portion of the genome in particular remains largely unknown. In this study, we examine the profile of long non-coding RNAs (lncRNAs), comparing them with that of coding genes in allotetraploid cotton (Gossypium hirsutum), its putative diploid ancestors (G. arboreum; G. raimondii), and an F1 hybrid (G. arboreum × G. raimondii, AD). RESULTS We find that most lncRNAs (80%) that were allelic expressed in the allotetraploid genome. Moreover, the genome shock of hybridization reprograms the non-coding transcriptome in the F1 hybrid. Interestingly, the activated lncRNAs are predominantly transcribed from demethylated TE regions, especially from long interspersed nuclear elements (LINEs). The DNA methylation dynamics in the interspecies hybridization are predominantly associated with the drastic expression variation of lncRNAs. Similar trends of lncRNA bursting are also observed in the progress of polyploidization. Additionally, we find that a representative novel lncRNA XLOC_409583 activated after polyploidization from a LINE in the A subgenome of allotetraploid cotton was involved in control of cotton seedling height. CONCLUSION Our results reveal that the processes of hybridization and polyploidization enable the neofunctionalization of lncRNA transcripts, acting as important sources of increased plasticity for plants.
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Affiliation(s)
- Ting Zhao
- 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, Jiangsu, China
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Shouli Feng
- 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, Jiangsu, China
| | - Luyao Wang
- 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, Jiangsu, China
| | - Hui Hong
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Ma
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Guandong Shang
- 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, Jiangsu, China
| | - Shisong Guo
- 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, Jiangsu, China
| | - Yuxin He
- 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, Jiangsu, 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, Jiangsu, China.
| | - Xueying Guan
- 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, Jiangsu, China.
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China.
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Kumar V, Singh B, Singh SK, Rai KM, Singh SP, Sable A, Pant P, Saxena G, Sawant SV. Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1069-1083. [PMID: 29952050 DOI: 10.1111/tpj.14011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/28/2023]
Abstract
Cotton fibers are single-celled trichomes that initiate from the epidermal cells of the ovules at or before anthesis. Here, we identified that the histone deacetylase (HDAC) activity is essential for proper cotton fiber initiation. We further identified 15 HDACs homoeologs in each of the A- and D-subgenomes of Gossypium hirsutum. Few of these HDAC homoeologs expressed preferentially during the early stages of fiber development [-1, 0 and 6 days post-anthesis (DPA)]. Among them, GhHDA5 expressed significantly at the time of fiber initiation (-1 and 0 DPA). The in vitro assay for HDAC activity indicated that GhHDA5 primarily deacetylates H3K9 acetylation marks. Moreover, the reduced expression of GhHDA5 also suppresses fiber initiation and lint yield in the RNA interference (RNAi) lines. The 0 DPA ovules of GhHDA5RNAi lines also showed alterations in reactive oxygen species homeostasis and elevated autophagic cell death in the developing fibers. The differentially expressed genes (DEGs) identified through RNA-seq of RNAi line (DEP12) and their pathway analysis showed that GhHDA5 modulates expression of many stress and development-related genes involved in fiber development. The reduced expression of GhHDA5 in the RNAi lines also resulted in H3K9 hyper-acetylation on the promoter region of few DEGs assessed by chromatin immunoprecipitation assay. The positively co-expressed genes with GhHDA5 showed cumulative higher expression during fiber initiation, and gene ontology annotation suggests their involvement in fiber development. Furthermore, the predicted protein interaction network in the positively co-expressed genes indicates HDA5 modulates fiber initiation-specific gene expression through a complex involving reported repressors.
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Affiliation(s)
- Verandra Kumar
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Babita Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
| | - Sunil K Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Krishan M Rai
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Surendra P Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Anshulika Sable
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Poonam Pant
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
| | - Gauri Saxena
- Department of Botany, University of Lucknow, Lucknow, India
| | - Samir V Sawant
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
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78
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Zhao B, Cao J, Hu G, Chen Z, Wang L, Shangguan X, Wang L, Mao Y, Zhang T, Wendel JF, Chen X. Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. THE NEW PHYTOLOGIST 2018; 218:1061-1075. [PMID: 29465754 PMCID: PMC6079642 DOI: 10.1111/nph.15063] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 01/17/2018] [Indexed: 05/18/2023]
Abstract
Cotton cultivars have evolved to produce extensive, long, seed-born fibers important for the textile industry, but we know little about the molecular mechanism underlying spinnable fiber formation. Here, we report how PACLOBUTRAZOL RESISTANCE 1 (PRE1) in cotton, which encodes a basic helix-loop-helix (bHLH) transcription factor, is a target gene of spinnable fiber evolution. Differential expression of homoeologous genes in polyploids is thought to be important to plant adaptation and novel phenotypes. PRE1 expression is specific to cotton fiber cells, upregulated during their rapid elongation stage and A-homoeologous biased in allotetraploid cultivars. Transgenic studies demonstrated that PRE1 is a positive regulator of fiber elongation. We determined that the natural variation of the canonical TATA-box, a regulatory element commonly found in many eukaryotic core promoters, is necessary for subgenome-biased PRE1 expression, representing a mechanism underlying the selection of homoeologous genes. Thus, variations in the promoter of the cell elongation regulator gene PRE1 have contributed to spinnable fiber formation in cotton. Overexpression of GhPRE1 in transgenic cotton yields longer fibers with improved quality parameters, indicating that this bHLH gene is useful for improving cotton fiber quality.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Jun‐Feng Cao
- Plant Stress Biology CenterInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
- Plant Science Research CenterShanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai201602China
| | - Guan‐Jing Hu
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Zhi‐Wen Chen
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Lu‐Yao Wang
- Nanjing Agricultural UniversityNanjingJiangsu210095China
| | - Xiao‐Xia Shangguan
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Ling‐Jian Wang
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Ying‐Bo Mao
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Tian‐Zhen Zhang
- Nanjing Agricultural UniversityNanjingJiangsu210095China
- Zhejiang UniversityHangzhouZhejiang310058China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Xiao‐Ya Chen
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
- Plant Science Research CenterShanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai201602China
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79
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Hu H, Wang M, Ding Y, Zhu S, Zhao G, Tu L, Zhang X. Transcriptomic repertoires depict the initiation of lint and fuzz fibres in cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1002-1012. [PMID: 28944536 PMCID: PMC5902776 DOI: 10.1111/pbi.12844] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/25/2017] [Accepted: 09/20/2017] [Indexed: 05/22/2023]
Abstract
Cotton fibre is an important natural fibre for the textile industry. The number of fibre initials determines the lint percentage, which is an important factor for cotton fibre yield. Although fibre development has been described by transcriptomic analysis, the mechanism by which the long noncoding RNA manipulates the initiation of lint and fuzz fibres remains unknown. In this study, three lines with different lint percentages were developed by crossing Xu142 with its fibreless mutant Xu142 fl. We collected the epidermal cells from the ovules with attached fibres at 0 and 5 days post anthesis (DPA) from Xu142, the fibreless mutant Xu142 fl and the three lint percent diversified lines for deep transcriptome sequencing. A total of 2641 novel genes, 35 802 long noncoding RNAs (lncRNAs) and 2262 circular RNAs (circRNAs) were identified, of which 645 lncRNAs were preferentially expressed in the fibreless mutant Xu142 fl and 651 lncRNAs were preferentially expressed in the fibre-attached lines. We demonstrated the functional roles of the three lncRNAs in fibre development via a virus-induced gene silencing (VIGS) system. Our results showed that silencing XLOC_545639 and XLOC_039050 in Xu142 fl increased the number of fibre initials on the ovules, but silencing XLOC_079089 in Xu142 resulted in a short fibre phenotype. This study established the transcriptomic repertoires in cotton fibre initiation and provided evidence for the potential functions of lncRNAs in fibre development.
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Affiliation(s)
- Haiyan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yuanhao Ding
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Sitao Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Guannan Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lili Tu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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80
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He P, Xiao G, Liu H, Zhang L, Zhao L, Tang M, Huang S, An Y, Yu J. Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation. THE NEW PHYTOLOGIST 2018; 218:167-182. [PMID: 29417579 DOI: 10.1111/nph.14999] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/14/2017] [Indexed: 06/08/2023]
Abstract
RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule. Biochemical and genetic analyses revealed that the two vital editing sites were important for the interaction between the α and β subunits of ATP synthase, which resulted in ATP accumulation and promoted cell growth in yeast. Ectopic expression of C1292, C1415, or doubly edited Ghatp1 in Arabidopsis caused a significant increase in the number of trichomes in leaves and root length. Our results indicate that editing at C1292 and C1415 sites in Ghatp1 is crucial for ATP synthase to produce sufficient ATP for cotton fiber cell elongation. This work extends our understanding of RNA editing in atp1 and ATP synthesis, and provides insights into the function of mitochondrial edited Atp1 protein in higher plants.
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Affiliation(s)
- Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hao Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Lihua Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Li Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Meiju Tang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Sheng Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yingjie An
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
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81
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Zhu QH, Yuan Y, Stiller W, Jia Y, Wang P, Pan Z, Du X, Llewellyn D, Wilson I. Genetic dissection of the fuzzless seed trait in Gossypium barbadense. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:997-1009. [PMID: 29351643 PMCID: PMC6018843 DOI: 10.1093/jxb/erx459] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/29/2017] [Indexed: 05/21/2023]
Abstract
Cotton fibres are single-celled trichomes arising from the epidermal cells of the seed coat and may be either long (lint) or very short (fuzz). The dominant fuzzless N1 of Gossypium hirsutum is a defective allele of the At-subgenome homoeolog of MYB25-like, but the genetic components underlying the recessive fuzzless trait from G. barbadense (Gb) are unknown. We have identified five genetic loci, including a major contributing locus containing MYB25-like_Dt, associated with Gb fuzzless seeds based on genotyping of fuzzy and fuzzless near isogenic lines (NILs) from an interspecies cross (G. barbadense × G. hirsutum). At 3 d post-anthesis when fuzz fibres are initiating, expression of MYB25-like_Dt was significantly lower in fuzzless NILs than in fuzzy seeded NILs, while higher MYB25-like_Dt expression was associated with more seed fuzz across different cotton genotypes. Phenotypic and genotypic analysis of MYB25-like homoeoalleles in cottons showing different fibre phenotypes and their crossing progeny indicated that both MYB25-like_At and MYB25-like_Dt are associated with lint development, and that fuzz development is mainly determined by the expression level of MYB25-like_Dt at ~3 d post-anthesis. Expression of Gb fuzzless seeds depends on genetic background and interactions amongst the multiple loci identified. MYB25-like_Dt is one of the best candidates for N2.
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Affiliation(s)
- Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Correspondence: and
| | - Yuman Yuan
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Warwick Stiller
- CSIRO Agriculture and Food, Locked, Narrabri, NSW, Australia
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Pengpeng Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | | | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Correspondence: and
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82
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Zhang Z, Ge X, Luo X, Wang P, Fan Q, Hu G, Xiao J, Li F, Wu J. Simultaneous Editing of Two Copies of Gh14-3-3d Confers Enhanced Transgene-Clean Plant Defense Against Verticillium dahliae in Allotetraploid Upland Cotton. FRONTIERS IN PLANT SCIENCE 2018; 9:842. [PMID: 30013582 PMCID: PMC6036271 DOI: 10.3389/fpls.2018.00842] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/30/2018] [Indexed: 05/02/2023]
Abstract
Gossypium hirsutum is an allotetraploid species, meaning that mutants that are difficult to be generated by classical approaches due to gene redundancy. The CRISPR/Cas9 genome editing system is a robust and highly efficient tool for generating target gene mutants, by which the genes of interest may be functionally dissected and applied through genotype-to-phenotype approaches. In this study, the CRISPR/Cas9 genome editing system was developed in G. hirsutum through editing the Gh14-3-3d gene. In T0 transgenic plants, lots of insertions and deletions (indels) in Gh14-3-3d at the expected target site were detected in the allotetraploid cotton At or Dt subgenomes. The results of the PCR, T7EI digestion and sequencing analyses showed that the indels in Gh14-3-3d gene can be stably transmitted to the next generation. Additionally, the indels in the At and Dt subgenomes were segregated in the T1 transgenic plants following Mendelian law, independing on the T-DNA segregation. Two homozygous Gh14-3-3d-edited plants free of T-DNA were chosen by PCR and sequencing assays in the T1 plants, which were called transgene-clean editing plants and were designated ce1 and ce2 in the T2 lines showed higher resistance to Verticillium dahliae infestation compared to the wild-type plants. Thus, the two transgene-clean edited lines can be used as a germplasm to breed disease-resistant cotton cultivars, possibly avoiding complex and expensive safety assessments of the transgenic plants.
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Affiliation(s)
- Zhennan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoli Luo
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Peng Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiang Fan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guang Hu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juanli Xiao
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Fuguang Li, Jiahe Wu,
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Fuguang Li, Jiahe Wu,
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83
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Wu H, Tian Y, Wan Q, Fang L, Guan X, Chen J, Hu Y, Ye W, Zhang H, Guo W, Chen X, Zhang T. Genetics and evolution of MIXTA genes regulating cotton lint fiber development. THE NEW PHYTOLOGIST 2018; 217:883-895. [PMID: 29034968 DOI: 10.1111/nph.14844] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 05/24/2023]
Abstract
Cotton, with cellulose-enriched mature fibers, is the largest source of natural textiles. Through a map-based cloning strategy, we isolated an industrially important lint fiber development gene (Li3 ) that encodes an MYB-MIXTA-like transcription factor (MML) on chromosome D12 (GhMML4_D12). Virus-induced gene silencing or decreasing the expression of the GhMML4_D12 gene in n2 NSM plants resulted in a significant reduction in epidermal cell prominence and lint fiber production. GhMML4_D12 is arranged in tandem with GhMML3, another MIXTA gene responsible for fuzz fiber development. These two very closely related MIXTA genes direct fiber initiation production in two specialized cell forms: lint and fuzz fibers. They may control the same metabolic pathways in different cell types. The MIXTAs expanded in Malvaceae during their evolution and produced a Malvaceae-specific family that regulates epidermal cell differentiation, different from the gene family that regulates leaf hair trichome development. Cotton has developed a unique transcriptional regulatory network for fiber development. Characterization of target genes regulating fiber production has provided insights into the molecular mechanisms underlying cotton fiber development and has allowed the use of genetic engineering to increase lint yield by inducing more epidermal cells to develop into lint rather than fuzz fibers.
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Affiliation(s)
- Huaitong Wu
- 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
| | - Yue Tian
- 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
| | - Qun Wan
- 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
| | - Lei Fang
- 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
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China
| | - Xueying Guan
- 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
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China
| | - Jiedan Chen
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China
| | - Yan Hu
- 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
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China
| | - Wenxue Ye
- 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
| | - Hua Zhang
- 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
| | - Wangzhen Guo
- 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
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tianzhen Zhang
- 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
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China
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84
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Genome sequencing brought Gossypium biology research into a new era. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1463-1466. [PMID: 29285713 DOI: 10.1007/s11427-017-9233-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 10/18/2022]
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85
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Zhu J, Chen J, Gao F, Xu C, Wu H, Chen K, Si Z, Yan H, Zhang T. Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis-next generation sequencing and virus-induced gene silencing strategies. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4125-4135. [PMID: 28922761 PMCID: PMC5853531 DOI: 10.1093/jxb/erx240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method. The v1 locus was further fine-mapped. Only one gene, GhCHLI, which encodes one of the subunits of Mg chelatase, was differentially down-regulated in T582 compared with TM-1. A point mutation occurred in the AAA+ conserved region of GhCHLI and led to an amino acid substitution. Suppression of its expression by VIGS in TM-1 resulted in a yellow blade phenotype that was similar to T582. This integrated approach provides a paradigm for the rapid mapping and identification of the candidate genes underlying the genetic traits in plants with large and complex genomes in the future.
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Affiliation(s)
- Jiankun Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Jiedan Chen
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang 310029, China
| | - Fengkai Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Chenyu Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Huaitong Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Zhanfeng Si
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Hu Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang 310029, China
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86
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Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (li y) in cotton (Gossypium hirsutum L.). Genomics 2017; 109:320-329. [PMID: 28577792 DOI: 10.1016/j.ygeno.2017.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022]
Abstract
In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (liy), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, 2629 and 3397 genes were significantly down-regulated, while 2700, 477 and 3260 were significantly up-regulated in liy at 3, 8 and 16 DPA. Gene set enrichment analysis revealed that many metabolic pathways, including carbohydrate, cell wall, hormone metabolism and transport were substantially altered in liy developing fibers. We discuss perturbed expression of genes involved in signal transduction and biosynthesis of phytohormones, such as auxin, abscisic acid, gibberellin and ethylene. The results of this study provide new insights into transcriptional regulation of cotton fiber development.
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87
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Streubel J, Baum H, Grau J, Stuttman J, Boch J. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017; 12:e0173580. [PMID: 28301511 PMCID: PMC5354296 DOI: 10.1371/journal.pone.0173580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.
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Affiliation(s)
- Jana Streubel
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Heidi Baum
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute of Computer Science, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Johannes Stuttman
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.). Sci Rep 2017; 7:43902. [PMID: 28256588 PMCID: PMC5335549 DOI: 10.1038/srep43902] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/30/2017] [Indexed: 12/26/2022] Open
Abstract
The complex allotetraploid genome is one of major challenges in cotton for repressing gene expression. Developing site-specific DNA mutation is the long-term dream for cotton breeding scientists. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system is emerging as a robust biotechnology for targeted-DNA mutation. In this study, two sgRNAs, GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2, were designed in the identical genomic regions of GhMYB25-like A and GhMYB25-like D, which were encoded by cotton A subgenome and the D subgenome, respectively, was assembled to direct Cas9-mediated allotetraploid cotton genome editing. High proportion (14.2–21.4%) CRISPR/Cas9-induced specific truncation events, either from GhMYB25-like A DNA site or from GhMYB25-like D DNA site, were detected in 50% examined transgenic cotton through PCR amplification assay and sequencing analyses. Sequencing results also demonstrated that 100% and 98.8% mutation frequency were occurred on GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2 target site respectively. The off-target effect was evaluated by sequencing two putative off-target sites, which have 3 and 1 mismatched nucleotides with GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2, respectively; all the examined samples were not detected any off-target-caused mutation events. Thus, these results demonstrated that CRISPR/Cas9 is qualified for generating DNA level mutations on allotetraploid cotton genome with high-efficiency and high-specificity.
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89
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Hinchliffe DJ, Condon BD, Thyssen G, Naoumkina M, Madison CA, Reynolds M, Delhom CD, Fang DD, Li P, McCarty J. The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton (Gossypium hirsutum L.) fibres. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5461-5471. [PMID: 27567364 PMCID: PMC5049394 DOI: 10.1093/jxb/erw312] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Some naturally coloured brown cotton fibres from accessions of Gossypium hirsutum L. can be used to make textiles with enhanced flame retardancy (FR). Several independent brown fibre loci have been identified and mapped to chromosomes, but the underlying genes have not yet been identified, and the mechanism of lint fibre FR is not yet fully understood. In this study, we show that both the brown colour and enhanced FR of the Lc1 lint colour locus are linked to a 1.4Mb inversion on chromosome A07 that is immediately upstream of a gene with similarity to Arabidopsis TRANSPARENT TESTA 2 (TT2). As a result of the alternative upstream sequence, the transcription factor GhTT2_A07 is highly up-regulated in developing fibres. In turn, genes in the phenylpropanoid metabolic pathway are activated, leading to biosynthesis of proanthocyanidins and accumulation of inorganic elements. We show that enhanced FR and anthocyanin precursors appear in developing brown fibres well before the brown colour is detectible, demonstrating for the first time that the polymerized proanthocyanidins that constitute the brown colour are not the source of enhanced FR. Identifying the particular colourless metabolite that provides Lc1 cotton with enhanced FR could help minimize the use of synthetic chemical flame retardant additives in textiles.
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Affiliation(s)
- Doug J Hinchliffe
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Brian D Condon
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Gregory Thyssen
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Crista A Madison
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Michael Reynolds
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Christopher D Delhom
- Cotton Structure and Quality Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Ping Li
- Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Jack McCarty
- Genetics and Sustainable Agriculture Research Unit, Agricultural Research Service, USDA, Mississippi State, MS 39762, USA
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90
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Wang J, Tang Y, Yang Y, Ma N, Ling X, Kan J, He Z, Zhang B. Cotton Leaf Curl Multan Virus-Derived Viral Small RNAs Can Target Cotton Genes to Promote Viral Infection. FRONTIERS IN PLANT SCIENCE 2016; 7:1162. [PMID: 27540385 PMCID: PMC4972823 DOI: 10.3389/fpls.2016.01162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/19/2016] [Indexed: 05/19/2023]
Abstract
RNA silencing is a conserved mechanism in plants that targets viruses. Viral small RNAs (vsiRNAs) can be generated from viral double-stranded RNA replicative intermediates within the infected host, or from host RNA-dependent RNA polymerases activity on viral templates. The abundance and profile of vsiRNAs in viral infections have been reported previously. However, the involvement of vsiRNAs during infection of the Geminiviridae family member cotton leaf curl virus (CLCuD), which causes significant economic losses in cotton growing regions, remains largely uncharacterized. Cotton leaf curl Multan virus (CLCuMuV) associated with a betasatellite called Cotton leaf curl Multan betasatellite (CLCuMuB) is a major constraint to cotton production in South Asia and is now established in Southern China. In this study, we obtained the profiles of vsiRNAs from CLCuMV and CLCuMB in infected upland cotton (Gossypium hirsutum) plants by deep sequencing. Our data showed that vsiRNA that were derived almost equally from sense and antisense CLCuD DNA strands accumulated preferentially as 21- and 22-nucleotide (nt) small RNA population and had a cytosine bias at the 5'-terminus. Polarity distribution revealed that vsiRNAs were almost continuously present along the CLCuD genome and hotspots of sense and antisense strands were mainly distributed in the Rep proteins region of CLCuMuV and in the C1 protein of CLCuMuB. In addition, hundreds of host transcripts targeted by vsiRNAs were predicted, many of which encode transcription factors associated with biotic and abiotic stresses. Quantitative real-time polymerase chain reaction analysis of selected potential vsiRNA targets showed that some targets were significantly down-regulated in CLCuD-infected cotton plants. We also verified the potential function of vsiRNA targets that may be involved in CLCuD infection by virus-induced gene silencing (VIGS) and 5'-rapid amplification of cDNA end (5'-RACE). Here, we provide the first report on vsiRNAs responses to CLCuD infection in cotton.
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Affiliation(s)
- Jinyan Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Yafei Tang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Yuwen Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Na Ma
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Xitie Ling
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Jialiang Kan
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Zifu He
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- *Correspondence: Baolong Zhang, Zifu He,
| | - Baolong Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
- *Correspondence: Baolong Zhang, Zifu He,
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