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Xu F, Li G, He S, Zeng Z, Wang Q, Zhang H, Yan X, Hu Y, Tian H, Luo M. Sphingolipid inhibitor response gene GhMYB86 controls fiber elongation by regulating microtubule arrangement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38995105 DOI: 10.1111/jipb.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024]
Abstract
Although the cell membrane and cytoskeleton play essential roles in cellular morphogenesis, the interaction between the membrane and cytoskeleton is poorly understood. Cotton fibers are extremely elongated single cells, which makes them an ideal model for studying cell development. Here, we used the sphingolipid biosynthesis inhibitor, fumonisin B1 (FB1), and found that it effectively suppressed the myeloblastosis (MYB) transcription factor GhMYB86, thereby negatively affecting fiber elongation. A direct target of GhMYB86 is GhTUB7, which encodes the tubulin protein, the major component of the microtubule cytoskeleton. Interestingly, both the overexpression of GhMYB86 and GhTUB7 caused an ectopic microtubule arrangement at the fiber tips, and then leading to shortened fibers. Moreover, we found that GhMBE2 interacted with GhMYB86 and that FB1 and reactive oxygen species induced its transport into the nucleus, thereby enhancing the promotion of GhTUB7 by GhMYB86. Overall, we established a GhMBE2-GhMYB86-GhTUB7 regulation module for fiber elongation and revealed that membrane sphingolipids affect fiber elongation by altering microtubule arrangement.
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Affiliation(s)
- Fan Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Guiming Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Shengyang He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Dianjiang No.1 Middle School of Chongqing, Chongqing, 408300, China
| | - Zhifeng Zeng
- Yushan No.1 Senior High School, Shangrao, 334700, China
| | - Qiaoling Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongju Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Xingying Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yulin Hu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Huidan Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Ming Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400715, China
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Song Z, Zhang C, Song G, Wei H, Xu W, Pan H, Ding C, Xu M, Zhen Y. Unraveling the lncRNA-miRNA-mRNA Regulatory Network Involved in Poplar Coma Development through High-Throughput Sequencing. Int J Mol Sci 2024; 25:7403. [PMID: 39000510 PMCID: PMC11242837 DOI: 10.3390/ijms25137403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Poplar coma, the fluff-like appendages of seeds originating from the differentiated surface cells of the placenta and funicle, aids in the long-distance dispersal of seeds in the spring. However, it also poses hazards to human safety and causes pollution in the surrounding environment. Unraveling the regulatory mechanisms governing the initiation and development of coma is essential for addressing this issue comprehensively. In this study, strand-specific RNA-seq was conducted at three distinct stages of coma development, revealing 1888 lncRNAs and 52,810 mRNAs. The expression profiles of lncRNAs and mRNAs during coma development were analyzed. Subsequently, potential target genes of lncRNAs were predicted through co-localization and co-expression analyses. Integrating various types of sequencing data, lncRNA-miRNA-TF regulatory networks related to the initiation of coma were constructed. Utilizing identified differentially expressed genes encoding kinesin and actin, lncRNA-miRNA-mRNA regulatory networks associated with the construction and arrangement of the coma cytoskeleton were established. Additionally, relying on differentially expressed genes encoding cellulose synthase, sucrose synthase, and expansin, lncRNA-miRNA-mRNA regulatory networks related to coma cell wall synthesis and remodeling were developed. This study not only enhances the comprehension of lncRNA but also provides novel insights into the molecular mechanisms governing the initiation and development of poplar coma.
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Affiliation(s)
- Zihe Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Chenghao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Guotao Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hang Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenlin Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Huixin Pan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Meng Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yan Zhen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Li X, Wang L, Cui Y, Liu C, Liu Y, Lu L, Luo M. The cotton protein GhIQD21 interacts with GhCaM7 and modulates organ morphogenesis in Arabidopsis by influencing microtubule stability. PLANT CELL REPORTS 2023; 42:1025-1038. [PMID: 37010557 DOI: 10.1007/s00299-023-03010-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE GhIQD21, a cotton IQ67-domain protein, interacts with GhCaM7 and alters organ shape in Arabidopsis by modulating microtubule stability. Calcium ion (Ca2+) and the calcium sensor calmodulin play crucial roles in the growth and development of plants. GhCaM7, a calmodulin in upland cotton (Gossypium hirsutum L.), is highly expressed in cotton fiber cells during the rapid elongation period and plays an important role in fiber cell development. In this study, we screened for GhCaM7-interacting proteins and identified GhIQD21, which contains a typical IQ67-domain. GhIQD21 was preferentially expressed at the fiber rapid elongation stage, and the protein localized to microtubules (MTs). Ectopic expression of GhIQD21 in Arabidopsis resulted in shorter leaves, petals, siliques, and plant height, thicker inflorescences, and more trichomes when compared with wild type (WT). Further investigation indicated that the morphogenesis of leaf epidermal cells and silique cells was altered. There was less consistency in the orientation of cortical microtubules in cotyledon and hypocotyl epidermal cells. Furthermore, compared with WT, transgenic seedling hypocotyls were more sensitive to oryzalin, a MT depolymerization drug. These results indicated that GhIQD21 is a GhCaM7-interacting protein located in MTs and that it plays a role in plant growth and potentially cotton fiber development. This study provides a foundation for further studies of the function and regulatory mechanism of GhIQD21 in fiber cell development.
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Affiliation(s)
- Xing Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yupeng Cui
- Anyang Institute of Technology, Anyang, 455000, China
| | - Chen Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yujie Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China.
| | - Ming Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, 400716, China.
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Zhang L, Wu Y, Yu Y, Zhang Y, Wei F, Zhu QH, Zhou J, Zhao L, Zhang Y, Feng Z, Feng H, Sun J. Acetylation of GhCaM7 enhances cotton resistance to Verticillium dahliae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1405-1424. [PMID: 36948889 DOI: 10.1111/tpj.16200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 06/17/2023]
Abstract
Protein lysine acetylation is an important post-translational modification mechanism involved in cellular regulation in eukaryotes. Calmodulin (CaM) is a ubiquitous Ca2+ sensor in eukaryotes and is crucial for plant immunity, but it is so far unclear whether acetylation is involved in CaM-mediated plant immunity. Here, we found that GhCaM7 is acetylated upon Verticillium dahliae (V. dahliae) infection and a positive regulator of V. dahliae resistance. Overexpressing GhCaM7 in cotton and Arabidopsis enhances V. dahliae resistance and knocking-down GhCaM7 makes cotton more susceptible to V. dahliae. Transgenic Arabidopsis plants overexpressing GhCaM7 with mutation at the acetylation site are more susceptible to V. dahliae than transgenics overexpressing the wild-type GhCaM7, implying the importance of the acetylated GhCaM7 in response to V. dahliae infection. Yeast two-hybrid, bimolecular fluorescent complementation, luciferase complementation imaging, and coimmunoprecipitation assays demonstrated interaction between GhCaM7 and an osmotin protein GhOSM34 that was shown to have a positive role in V. dahliae resistance. GhCaM7 and GhOSM34 are co-localized in the cell membrane. Upon V. dahliae infection, the Ca2+ content reduces almost instantly in plants with downregulated GhCaM7 or GhOSM34. Down regulating GhOSM34 enhances accumulation of Na+ and increases cell osmotic pressure. Comparative transcriptomic analyses between cotton plants with an increased or reduced expression level of GhCaM7 and wild-type plants indicate the involvement of jasmonic acid signaling pathways and reactive oxygen species in GhCaM7-enabled disease resistance. Together, these results demonstrate the involvement of CaM protein in the interaction between cotton and V. dahliae, and more importantly, the involvement of the acetylated CaM in the interaction.
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Affiliation(s)
- Lei Zhang
- College of Agriculture/The Key Laboratory of Oasis Eco-agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yajie Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Yongang Yu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yihao Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, Australia
| | - Jinglong Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Hongjie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jie Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
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Niu H, Kuang M, Huang L, Shang H, Yuan Y, Ge Q. Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60. BMC PLANT BIOLOGY 2023; 23:179. [PMID: 37020180 PMCID: PMC10074700 DOI: 10.1186/s12870-023-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. RESULTS Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. CONCLUSIONS A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Longyu Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Li S, Xing K, Qanmber G, Chen G, Liu L, Guo M, Hou Y, Lu L, Qu L, Liu Z, Yang Z. GhBES1 mediates brassinosteroid regulation of leaf size by activating expression of GhEXO2 in cotton (Gossypium hirsutum). PLANT MOLECULAR BIOLOGY 2023; 111:89-106. [PMID: 36271986 DOI: 10.1007/s11103-022-01313-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
We proposed a working model of BR to promote leaf size through cell expansion. In the BR signaling pathway, GhBES1 affects cotton leaf size by binding to and activating the expression of the E-box element in the GhEXO2 promoter region. Brassinosteroid (BR) is an essential phytohormone that controls plant growth. However, the mechanisms of BR regulation of leaf size remain to be determined. Here, we found that the BR deficient cotton mutant pagoda1 (pag1) had a smaller leaf size than wild-type CRI24. The expression of EXORDIUM (GhEXO2) gene, was significantly downregulated in pag1. Silencing of BRI1-EMS-SUPPRESSOR 1 (GhBES1), inhibited leaf cell expansion and reduced leaf size. Overexpression of GhBES1.4 promoted leaf cell expansion and enlarged leaf size. Expression analysis showed GhEXO2 expression positively correlated with GhBES1 expression. In plants, altered expression of GhEXO2 promoted leaf cell expansion affecting leaf size. Furthermore, GhBES1.4 specifically binds to the E-box elements in the GhEXO2 promoter, inducing its expression. RNA-seq data revealed many down-regulated genes related to cell expansion in GhEXO2 silenced plants. In summary, we discovered a novel mechanism of BR regulation of leaf size through GhBES1 directly activating the expression of GhEXO2.
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Affiliation(s)
- Shengdong Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Kun Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Biology (Hebei Base), Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoquan Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Yan Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lingbo Qu
- College of Chemistry, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China.
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Molecular Regulation of Cotton Fiber Development: A Review. Int J Mol Sci 2022; 23:ijms23095004. [PMID: 35563394 PMCID: PMC9101851 DOI: 10.3390/ijms23095004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Cotton (Gossypium spp.) is an economically important natural fiber crop. The quality of cotton fiber has a substantial effect on the quality of cotton textiles. The identification of cotton fiber development-related genes and exploration of their biological functions will not only enhance our understanding of the elongation and developmental mechanisms of cotton fibers but also provide insights that could aid the cultivation of new cotton varieties with improved fiber quality. Cotton fibers are single cells that have been differentiated from the ovule epidermis and serve as a model system for research on single-cell differentiation, growth, and fiber production. Genes and fiber formation mechanisms are examined in this review to shed new light on how important phytohormones, transcription factors, proteins, and genes linked to fiber development work together. Plant hormones, which occur in low quantities, play a critically important role in regulating cotton fiber development. Here, we review recent research that has greatly contributed to our understanding of the roles of different phytohormones in fiber development and regulation. We discuss the mechanisms by which phytohormones regulate the initiation and elongation of fiber cells in cotton, as well as the identification of genes involved in hormone biosynthetic and signaling pathways that regulate the initiation, elongation, and development of cotton fibers.
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Jan M, Liu Z, Guo C, Zhou Y, Sun X. An Overview of Cotton Gland Development and Its Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094892. [PMID: 35563290 PMCID: PMC9103798 DOI: 10.3390/ijms23094892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cotton refers to species in the genus Gossypium that bear spinnable seed coat fibers. A total of 50 species in the genus Gossypium have been described to date. Of these, only four species, viz. Gossypium, hirsutum, G. barbadense, G. arboretum, and G. herbaceum are cultivated; the rest are wild. The black dot-like structures on the surfaces of cotton organs or tissues, such as the leaves, stem, calyx, bracts, and boll surface, are called gossypol glands or pigment glands, which store terpenoid aldehydes, including gossypol. The cotton (Gossypium hirsutum) pigment gland is a distinctive structure that stores gossypol and its derivatives. It provides an ideal system for studying cell differentiation and organogenesis. However, only a few genes involved in the process of gland formation have been identified to date, and the molecular mechanisms underlying gland initiation remain unclear. The terpenoid aldehydes in the lysigenous glands of Gossypium species are important secondary phytoalexins (with gossypol being the most important) and one of the main defenses of plants against pests and diseases. Here, we review recent research on the development of gossypol glands in Gossypium species, the regulation of the terpenoid aldehyde biosynthesis pathway, discoveries from genetic engineering studies, and future research directions.
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Affiliation(s)
- Masood Jan
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Zhixin Liu
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yaping Zhou
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Correspondence:
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9
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Niu H, Ge Q, Shang H, Yuan Y. Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton. Front Genet 2022; 13:855574. [PMID: 35450216 PMCID: PMC9016478 DOI: 10.3389/fgene.2022.855574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
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10
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Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Abdul Hafeez
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | | | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Li Pengtao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Maozhi Ren
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Youlu Yuan
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
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11
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Zhao N, Wang W, Jiang K, Grover CE, Cheng C, Pan Z, Zhao C, Zhu J, Li D, Wang M, Xiao L, Yang J, Ning X, Li B, Xu H, Su Y, Aierxi A, Li P, Guo B, Wendel JF, Kong J, Hua J. A Calmodulin-Like Gene ( GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2022; 12:815648. [PMID: 35185964 PMCID: PMC8850914 DOI: 10.3389/fpls.2021.815648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/29/2021] [Indexed: 05/23/2023]
Abstract
Sea Island cotton (Gossypium barbadense) is world-renowned for its superior natural fiber. Although fiber strength is one of the most important fiber quality traits, genes contributing to fiber strength are poorly understood. Production of sea island cotton also is inextricably linked to improving its relatively low yield, thus enhancing the importance of joint improvement of both fiber quality and yield. We used genomic variation to uncover the genetic evidence of trait improvement resulting from pedigree breeding of Sea Island cotton. This pedigree was aimed at improving fiber strength and yielded an elite cultivar, XH35. Using a combination of genome-wide association study (GWAS) and selection screens, we detected 82 putative fiber-strength-related genes. Expression analysis confirmed a calmodulin-like gene, GbCML7, which enhanced fiber strength in a specific haplotype. This gene is a major-effect gene, which interacts with a minor-effect gene, GbTUA3, facilitating the enhancement of fiber strength in a synergistic fashion. Moreover, GbCML7 participates in the cooperative improvement of fiber strength, fiber length, and fiber uniformity, though a slight compromise exists between the first two of these traits and the latter. Importantly, GbCML7 is shown to boost yield in some backgrounds by increasing multiple yield components to varying degrees, especially boll number. Our work provides valuable genomic evidence and a key genetic factor for the joint improvement of fiber quality and yield in Sea Island cotton.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Weiran Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Cheng Cheng
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhuanxia Pan
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Cunpeng Zhao
- Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Jiahui Zhu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Dan Li
- Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Meng Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Li Xiao
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Jing Yang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Xinmin Ning
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haijiang Xu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Ying Su
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Alifu Aierxi
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Pengbo Li
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Baosheng Guo
- Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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12
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Li X, Liu W, Ren Z, Wang X, Liu J, Yang Z, Zhao J, Pei X, Liu Y, He K, Zhang F, Zhang Z, Yang D, Ma X, Li W. Glucose regulates cotton fiber elongation by interacting with brassinosteroid. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:711-726. [PMID: 34636403 DOI: 10.1093/jxb/erab451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/09/2021] [Indexed: 05/18/2023]
Abstract
In plants, glucose (Glc) plays important roles, as a nutrient and signal molecule, in the regulation of growth and development. However, the function of Glc in fiber development of upland cotton (Gossypium hirsutum) is unclear. Here, using gas chromatography-mass spectrometry (GC-MS), we found that the Glc content in fibers was higher than that in ovules during the fiber elongation stage. In vitro ovule culture revealed that lower Glc concentrations promoted cotton fiber elongation, while higher concentrations had inhibitory effects. The hexokinase inhibitor N-acetylglucosamine (NAG) inhibited cotton fiber elongation in the cultured ovules, indicating that Glc-mediated fiber elongation depends on the Glc signal transduced by hexokinase. RNA sequencing (RNA-seq) analysis and hormone content detection showed that 150mM Glc significantly activated brassinosteroid (BR) biosynthesis, and the expression of signaling-related genes was also increased, which promoted fiber elongation. In vitro ovule culture clarified that BR induced cotton fiber elongation in a dose-dependent manner. In hormone recovery experiments, only BR compensated for the inhibitory effects of NAG on fiber elongation in a Glc-containing medium. However, the ovules cultured with the BR biosynthetic inhibitor brassinazole and from the BR-deficient cotton mutant pag1 had greatly reduced fiber elongation at all the Glc concentrations tested. This demonstrates that Glc does not compensate for the inhibition of fiber elongation caused by BR biosynthetic defects, suggesting that the BR signaling pathway works downstream of Glc during cotton fiber elongation. Altogether, our study showed that Glc plays an important role in cotton fibre elongation, and crosstalk occurs between Glc and BR signaling during modulation of fiber elongation.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Liu
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhiqiang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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13
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Kang L, Qian L, Zheng M, Chen L, Chen H, Yang L, You L, Yang B, Yan M, Gu Y, Wang T, Schiessl SV, An H, Blischak P, Liu X, Lu H, Zhang D, Rao Y, Jia D, Zhou D, Xiao H, Wang Y, Xiong X, Mason AS, Chris Pires J, Snowdon RJ, Hua W, Liu Z. Genomic insights into the origin, domestication and diversification of Brassica juncea. Nat Genet 2021; 53:1392-1402. [PMID: 34493868 PMCID: PMC8423626 DOI: 10.1038/s41588-021-00922-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000-14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.
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Affiliation(s)
- Lei Kang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liu Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liang You
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Bin Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yuanguo Gu
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Tianyi Wang
- Novogene Bioinformatics Institute, Beijing, China
| | | | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Paul Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Xianjun Liu
- College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yong Rao
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Donghai Jia
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Huagui Xiao
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yonggang Wang
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xinghua Xiong
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China.
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14
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Chang Y, Bai Y, Wei Y, Shi H. CAMTA3 negatively regulates disease resistance through modulating immune response and extensive transcriptional reprogramming in cassava. TREE PHYSIOLOGY 2020; 40:1520-1533. [PMID: 32705122 DOI: 10.1093/treephys/tpaa093] [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: 03/11/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
As one of the important crops in the world, cassava production is seriously threatened by Xanthomonas axonopodis pv. manihotis (Xam) all year round. Calmodulin-binding transcription activators (CAMTAs) play key roles in biotic stress and abiotic stress in plants, however, their roles in cassava remain elusive. In this study, six MeCAMTAs were identified, and MeCAMTA3 with the highest induction upon Xam infection was confirmed as a transcription factor that binds to the vCGCGb motif. MeCAMTA3 negatively regulates plant disease resistance against Xam. On the one hand, MeCAMTA3 negatively regulated endogenous salicylic acid and reactive oxygen species accumulation, pathogenesis-related genes MePRs' transcripts and callose deposition during cassava-Xam interaction but not under control conditions. On the other hand, RNA sequencing showed extensive transcriptional reprogramming by MeCAMTA3, especially 18 genes with a vCGCGb motif in the promoter region in hormone signaling, antioxidant signaling and other disease resistance signaling. Notably, chromatin immunoprecipitation-polymerase chain reaction showed that eight of these genes might be directly regulated by MeCAMTA3 through transcriptional repression. In summary, MeCAMTA3 negatively regulates plant disease resistance against cassava bacterial blight through modulation of multiple immune responses during cassava-Xam interaction and extensive transcriptional reprogramming.
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Affiliation(s)
- Yanli Chang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Yujing Bai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
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15
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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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16
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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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17
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Zeb Q, Wang X, Hou C, Zhang X, Dong M, Zhang S, Zhang Q, Ren Z, Tian W, Zhu H, Li L, Liu L. The interaction of CaM7 and CNGC14 regulates root hair growth in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:887-896. [PMID: 31755194 DOI: 10.1111/jipb.12890] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Oscillations in cytosolic free calcium determine the polarity of tip-growing root hairs. The Ca2+ channel cyclic nucleotide gated channel 14 (CNGC14) contributes to the dynamic changes in Ca2+ concentration gradient at the root hair tip. However, the mechanisms that regulate CNGC14 are unknown. In this study, we detected a direct interaction between calmodulin 7 (CaM7) and CNGC14 through yeast two-hybrid and bimolecular fluorescence complementation assays. We demonstrated that the third EF-hand domain of CaM7 specifically interacts with the cytosolic C-terminal domain of CNGC14. A two-electrode voltage clamp assay showed that CaM7 completely inhibits CNGC14-mediated Ca2+ influx, suggesting that CaM7 negatively regulates CNGC14-mediated calcium signaling. Furthermore, CaM7 overexpressing lines phenocopy the short root hair phenotype of a cngc14 mutant and this phenotype is insensitive to changes in external Ca2+ concentrations. We, thus, identified CaM7-CNGC14 as a novel interacting module that regulates polar growth in root hairs by controlling the tip-focused Ca2+ signal.
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Affiliation(s)
- Qudsia Zeb
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiaohan Wang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Congcong Hou
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiwen Zhang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Mengqi Dong
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Sisi Zhang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Qian Zhang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Zhijie Ren
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Wang Tian
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Huifen Zhu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Legong Li
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Liangyu Liu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, and College of Life Sciences, Capital Normal University, Beijing, 100048, China
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18
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Song Y, Li L, Yang Z, Zhao G, Zhang X, Wang L, Zheng L, Zhuo F, Yin H, Ge X, Zhang C, Yang Z, Ren M, Li F. Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton. Front Genet 2019; 9:690. [PMID: 30671083 PMCID: PMC6332313 DOI: 10.3389/fgene.2018.00690] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
TOR (Target of Rapamycin) kinase is an evolutionarily conserved protein kinase, which integrates stress-related cues with growth and metabolic outputs. Long non-coding RNAs (lncRNAs) play a vital role in the regulation of eukaryotic genes. However, little is known about TOR's function in regulating the expression of lncRNAs in plants. In this study, four putative homologous genes encoding the TOR protein were identified by utilizing the recently completed cotton genome. Pharmacological experiments with TOR inhibitor AZD8055 and on silencing GhTOR genes resulted in obvious cotton growth retardation, indicating the conserved role of TOR in plant growth. The expression pattern analyses in different tissues reveal that TOR may play a role in root development, and the transcript levels of TOR genes were changed under different stress conditions. Importantly, we found TOR may be a key player in regulating the expression of long non-coding RNAs (lncRNAs). A total of 10,315 lncRNAs were discovered in cotton seedlings, 90.7% of which were long intergenic ncRNAs. Moreover, we identified the differentially expressed lncRNAs, of which 296 were significantly upregulated and 105 were downregulated in TOR inactivated plants. GO and KEGG analyses of differentially expressed lncRNA neighboring genes reveal that these differentially expressed lncRNA-targeted genes are involved in many life processes, including stress response, glutathione, and ribosomes in cotton. A series of differentially expressed lncRNAs potentially involved in plant stress response was identified under TOR inhibition. Collectively, these results suggest that cotton TOR proteins may directly modulate the expression of putative stress-related lncRNAs and eventually play a potential role in the cotton stress response.
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Affiliation(s)
- Yun Song
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Linxuan Li
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ge Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xueyan Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lingling Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lei Zheng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fengping Zhuo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huan Yin
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chaojun Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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19
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Ijaz B, Zhao N, Kong J, Hua J. Fiber Quality Improvement in Upland Cotton ( Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application. FRONTIERS IN PLANT SCIENCE 2019; 10:1585. [PMID: 31921240 PMCID: PMC6917639 DOI: 10.3389/fpls.2019.01585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/12/2019] [Indexed: 05/17/2023]
Abstract
Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Fiber quality traits are controlled by multiple genes and are classified as complex quantitative traits, with a negative relationship with yield potential, so the genetic gain is low in traditional genetic improvement by phenotypic selection. The availability of Gossypium genomic sequences facilitates the development of high-throughput molecular markers, quantitative trait loci (QTL) fine mapping and gene identification, which helps us to validate candidate genes and to use marker assisted selection (MAS) on fiber quality in breeding programs. Based on developments of high density linkage maps, QTLs fine mapping, marker selection and omics, we have performed trait dissection on fiber quality traits in diverse populations of upland cotton. QTL mapping combined with multi-omics approaches such as, RNA sequencing datasets to identify differentially expressed genes have benefited the improvement of fiber quality. In this review, we discuss the application of molecular markers, QTL mapping and MAS for fiber quality improvement in upland cotton.
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Affiliation(s)
- Babar Ijaz
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Jinping Hua,
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20
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YC3.60-Based Imaging Analysis on Calcium Level in Cotton Cells. Methods Mol Biol 2018. [PMID: 30543070 DOI: 10.1007/978-1-4939-8952-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Calcium ion (Ca2+) is a core regulator of cell functions in response to many developmental and environmental stimuli. A hallmark for Ca2+ signaling is the change of this ion in cells. Fluorescent resonance energy transfer (FRET)-based Ca2+ sensors provide a powerful tool for qualitatively and quantitatively measuring cytosolic Ca2+ level. Using YC3.60, one of those sensors, we have imaged cytosolic changes of Ca2+ in cotton fibers during the initiation stage. In this chapter, the imaging method is described in detail. The description is not limited to fiber cells but also examples leaf trichomes and protoplasts of cotton.
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21
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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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22
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Guo K, Tu L, He Y, Deng J, Wang M, Huang H, Li Z, Zhang X. Interaction between calcium and potassium modulates elongation rate in cotton fiber cells. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5161-5175. [PMID: 29045717 PMCID: PMC5853336 DOI: 10.1093/jxb/erx346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/14/2017] [Indexed: 05/20/2023]
Abstract
Calcium (Ca2+) is necessary for fiber cell development in cotton (Gossypium hirsutum), both as a cell wall structural component and for environmental signaling responses. It is also known that potassium (K+) plays a critical role in cotton fiber cell elongation. However, it is unclear whether Ca2+ integrates its activities with K+ to regulate fiber elongation. Here, we report the novel discovery that Ca2+ deficiency, when integrated with K+ signaling, promotes fiber elongation. Using inductively coupled plasma-mass spectrometry (ICP-MS), we determined dynamic profiles of the ionome in ovules and fibers at different developmental stages, and found that a high accumulation of macro-elements, but not Ca2+, was associated with longer fibers. Using an in vitro ovule culture system, we found that under Ca2+-deficient conditions, sufficient K+ (52 mM) rapidly induced ovule and fiber browning, while reduced K+ (2 or 27 mM) not only suppressed tissue browning but also altered fiber elongation. Reduced K+ also enhanced reactive oxygen species scavenging ability and maintained abscisic acid and jasmonic acid levels, which in turn compensated for Ca2+ deficiency. Ca2+ deficiency combined with reduced K+ (0 mM Ca2+ and 27 mM K+) produced longer fibers in cultured ovules, due to cell wall loosening by phytosulfokine (PSK), expansin (EXP), and xyloglucan endotransglycosylase/hydrolase (XTH), and an increase of the K+ content of fiber cells. Using transgenic cotton, we showed that the CBL-INTERACTING PROTEIN KINASE 6 (GhCIPK6) gene mediates the uptake of K+ under Ca2+-deficient conditions. This study establishes a new link between Ca2+, K+, and fiber elongation.
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Affiliation(s)
- Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Correspondence:
| | - Yonghui He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinwu Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hui Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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23
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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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24
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Ullah A, Sun H, Yang X, Zhang X. Drought coping strategies in cotton: increased crop per drop. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:271-284. [PMID: 28055133 PMCID: PMC5316925 DOI: 10.1111/pbi.12688] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/06/2016] [Accepted: 12/27/2016] [Indexed: 05/04/2023]
Abstract
The growth and yield of many crops, including cotton, are affected by water deficit. Cotton has evolved drought specific as well as general morpho-physiological, biochemical and molecular responses to drought stress, which are discussed in this review. The key physiological responses against drought stress in cotton, including stomata closing, root development, cellular adaptations, photosynthesis, abscisic acid (ABA) and jasmonic acid (JA) production and reactive oxygen species (ROS) scavenging, have been identified by researchers. Drought stress induces the expression of stress-related transcription factors and genes, such as ROS scavenging, ABA or mitogen-activated protein kinases (MAPK) signalling genes, which activate various drought-related pathways to induce tolerance in the plant. It is crucial to elucidate and induce drought-tolerant traits via quantitative trait loci (QTL) analysis, transgenic approaches and exogenous application of substances. The current review article highlights the natural as well as engineered drought tolerance strategies in cotton.
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Affiliation(s)
- Abid Ullah
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Heng Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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