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Wu M, Xu Z, Fu C, Wang N, Zhang R, Le Y, Chen M, Yang N, Li Y, Zhang X, Li X, Lin Z. NAC transcription factor GbNTL9 modifies the accumulation and organization of cellulose microfibrils to enhance cotton fiber strength. J Adv Res 2025:S2090-1232(25)00120-1. [PMID: 39971129 DOI: 10.1016/j.jare.2025.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 01/22/2025] [Accepted: 02/17/2025] [Indexed: 02/21/2025] Open
Abstract
INTRODUCTION Fiber strength is a critical determinant of fiber quality, with stronger fibers being highly preferred in the cotton textile industry. However, the genetic basis and the specific regulatory mechanism underlying the formation of cotton fiber strength remain largely unknown. OBJECTIVES To explore fiber strength-related genes, QTL mapping, map-based cloning, and gene function verification were conducted in a backcross inbred line BS41 derived from interspecific hybridization between upland cotton and sea-island cotton. METHODS Upland cotton Emian22 (E22) and an interspecific backcross inbred line (BIL) BS41 were used as parents to construct secondary segregation populations for BSA and QTL mapping of fiber strength. The candidate gene GbNTL9 was identified through map-based cloning and expression analysis. The function of NTL9 was determined through transgenic experiments and cytological observations. The regulatory mechanisms of NTL9 were explored using RNA-seq, RT-qPCR, yeast two-hybrid, bimolecular fluorescence complementation, and yeast one-hybrid. RESULTS A major QTL for fiber strength, qFS-A11-1, was mapped to a 14.6-kb genomic region using segregating populations from E22 × BS41. GbNTL9, which encodes a NAC transcription factor, was identified as the candidate gene. Overexpression of both upland cotton genotype NTL9E22 and sea-island genotype NTL9BS41 in upland cotton enhanced fiber strength by facilitating the dense accumulation and orderly organization of cellulose microfibrils within the cell wall. Transcriptomic analysis revealed that NTL9 inhibited the expression of genes involved in secondary wall synthesis, such as CESA4, CESA7, and CESA8, thereby delaying cell wall cellulose deposition and altering the microfibril deposition pattern. NTL9 interacted with MYB6 and functioned as a downstream gene in the ethylene signaling pathway. Additionally, an effective gene marker NTL9-24 was developed to distinguish haplotypes from G. barbadense and G. hirsutum for fiber quality breeding program. CONCLUSION Our findings demonstrate that GbNTL9 positively regulates fiber strength through altering the microfibril deposition pattern, and provide a new insight into the molecular mechanism underlying fiber strength.
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Affiliation(s)
- Mi Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Zhiyong Xu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Chao Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Yu Le
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Meilin Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Ningyu Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Yuanxue Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
| | - Ximei Li
- 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.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070 Hubei, China.
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Kun W, Shoupu H, Yuxian Z. Cotton2035: From genomics research to optimized breeding. MOLECULAR PLANT 2025; 18:298-312. [PMID: 39844464 DOI: 10.1016/j.molp.2025.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 01/08/2025] [Accepted: 01/12/2025] [Indexed: 01/24/2025]
Abstract
Cotton is the world's most important natural fiber crop and serves as an ideal model for studying plant genome evolution, cell differentiation, elongation, and cell wall biosynthesis. The first draft genome assembly for Gossypium raimondii, completed in 2012, marked the beginning of global efforts in studying cotton genomics. Over the past decade, the cotton research community has continued to assemble and refine the genomes for both wild and cultivated Gossypium species. With the accumulation of de novo genome assemblies and resequencing data across virous cotton populations, significant progress has been made in uncovering the genetic basis of key agronomic traits. Achieving the goal of cotton genomics-to-breeding (G2B) will require a deeper understanding of the spatiotemporal regulatory mechanisms involved in genome information storage and expression. We advocate for a cotton ENCODE project to systematically decode the functional elements and regulatory networks within the cotton genome. Technological advances, particularly on single-cell sequencing and high-resolution spatiotemporal omics, will be essential for elucidating these regulatory mechanisms. By integrating multi-omics data, genome editing tools, and artificial intelligence, these efforts will empower the genomics-driven strategies needed for future cotton G2B breeding.
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Affiliation(s)
- Wang Kun
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430072, China.
| | - He Shoupu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572000, China.
| | - Zhu Yuxian
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430072, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China.
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Fang H, Gao X, Wu Y, Zhang K, Wu Y, Li J, Qian D, Li R, Gu H, Mehari TG, Shen X, Wang B. Unveiling the Role of GhP5CS1 in Cotton Salt Stress Tolerance: A Comprehensive Genomic and Functional Analysis of P5CS Genes. PLANTS (BASEL, SWITZERLAND) 2025; 14:231. [PMID: 39861584 PMCID: PMC11768395 DOI: 10.3390/plants14020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 01/08/2025] [Accepted: 01/14/2025] [Indexed: 01/27/2025]
Abstract
Proline, a critical osmoregulatory compound, is integral to various plant stress responses. The P5CS gene, which encodes the rate-limiting enzyme in proline biosynthesis, known as ∆1-pyrroline-5-carboxylate synthetase, is fundamental to these stress response pathways. While the functions of P5CS genes in plants have been extensively documented, their specific roles in cotton remain inadequately characterized. In this study, we identified 40 P5CS genes across four cotton species with diverse sequence lengths and molecular weights. Phylogenetic analysis of 100 P5CS genes from nine species revealed three subgroups, with Gossypium hirsutum closely related to Gossypium barbadense. Collinearity analysis highlighted significant differences in collinear gene pairs, indicating evolutionary divergence among P5CS genes in tetraploid and diploid cotton. Exon-intron structures and conserved motifs correlated with phylogenetic relationships, suggesting functional differentiation. Stress-responsive elements in P5CS promoters suggest involvement in abiotic stress. Expression analysis under salt stress revealed differential expressions of GhP5CS genes, with GhP5CS1 emerging as a potential key regulator. Virus-induced gene silencing confirmed the pivotal role of GhP5CS1 in cotton's salt stress response, as evidenced by increased salt sensitivity in the silenced plants. This study enhances our understanding of the functional diversity and roles of P5CS genes in cotton under stress conditions.
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Affiliation(s)
- Hui Fang
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Xin Gao
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Yunhao Wu
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Ke Zhang
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Ying Wu
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Junyi Li
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Dongmei Qian
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Ruochen Li
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Haijing Gu
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
| | - Teame Gereziher Mehari
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing) of the Ministry of Agriculture, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Baohua Wang
- Institute of Modern Agriculture, School of Life Sciences, Nantong University, Nantong 226019, China; (H.F.); (X.G.); (Y.W.); (K.Z.); (Y.W.); (J.L.); (D.Q.); (R.L.); (H.G.); (T.G.M.)
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Yan S, Si Z, Qi G, Zang Y, Xuan L, He L, Cao Y, Li X, Zhang T, Hu Y. A CC-NB-ARC-LRR Gene Regulates Bract Morphology in Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2406111. [PMID: 39364742 PMCID: PMC11600217 DOI: 10.1002/advs.202406111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/02/2024] [Indexed: 10/05/2024]
Abstract
Bracts are leaf-like structures in flowering plants. They serve multiple functions such as attracting pollinators, aiding tolerance of abiotic stressors, and conducting photosynthesis. While previous studies extensively examine bract function, the molecular mechanisms underlying bract growth remain unknown. Here, the map-based isolation and characterization of a crucial factor responsible for cotton bract development, identified from a mutant known as frego bract (fg), discovered by Frego in 1945 are presented. This gene, named Ghfg, encodes a CC-NB-ARC-LRR (CNL) family protein. Through analysis of bract form in plants with virus-induced gene silencing (VIGS) and transgenic plants, this gene is confirmed to be the causal gene under the fg locus. Furthermore, high-resolution single-cell transcriptomic landscape of cotton bracts is generated, which reveals differences related to auxin in proliferating cells from TM-1 and T582; differences in auxin distribution and ROS accumulation are experimentally verified. These findings suggest that GhFG is in a self-activated state in the fg mutant, and its activity leads to ROS accumulation that impacts auxin distribution and transport. Finally, an island cotton variety with the frego bract trait is developed, demonstrating a novel solution for reducing the high impurity rate caused by bract remnants.
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Affiliation(s)
- Sunyi Yan
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
- Precision Breeding and Germplasm Innovation Team for Cotton and Economic CropsHainan Institute of Zhejiang UniversitySanya572025China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
| | - Guoan Qi
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
- Precision Breeding and Germplasm Innovation Team for Cotton and Economic CropsHainan Institute of Zhejiang UniversitySanya572025China
| | - Yihao Zang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
| | - Lisha Xuan
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
| | - Lu He
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
- Precision Breeding and Germplasm Innovation Team for Cotton and Economic CropsHainan Institute of Zhejiang UniversitySanya572025China
| | - Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
- Precision Breeding and Germplasm Innovation Team for Cotton and Economic CropsHainan Institute of Zhejiang UniversitySanya572025China
| | - Xiaoran Li
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
- Precision Breeding and Germplasm Innovation Team for Cotton and Economic CropsHainan Institute of Zhejiang UniversitySanya572025China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityZhejiang310058China
- Precision Breeding and Germplasm Innovation Team for Cotton and Economic CropsHainan Institute of Zhejiang UniversitySanya572025China
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Wang P, Abbas M, He J, Zhou L, Cheng H, Guo H. Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding. FRONTIERS IN PLANT SCIENCE 2024; 15:1400201. [PMID: 39015293 PMCID: PMC11250495 DOI: 10.3389/fpls.2024.1400201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024]
Abstract
Cotton production faces challenges in fluctuating environmental conditions due to limited genetic variation in cultivated cotton species. To enhance the genetic diversity crucial for this primary fiber crop, it is essential to augment current germplasm resources. High-throughput sequencing has significantly impacted cotton functional genomics, enabling the creation of diverse mutant libraries and the identification of mutant functional genes and new germplasm resources. Artificial mutation, established through physical or chemical methods, stands as a highly efficient strategy to enrich cotton germplasm resources, yielding stable and high-quality raw materials. In this paper, we discuss the good foundation laid by high-throughput sequencing of cotton genome for mutant identification and functional genome, and focus on the construction methods of mutant libraries and diverse sequencing strategies based on mutants. In addition, the important functional genes identified by the cotton mutant library have greatly enriched the germplasm resources and promoted the development of functional genomes. Finally, an innovative strategy for constructing a cotton CRISPR mutant library was proposed, and the possibility of high-throughput screening of cotton mutants based on a UAV phenotyping platform was discussed. The aim of this review was to expand cotton germplasm resources, mine functional genes, and develop adaptable materials in a variety of complex environments.
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Affiliation(s)
- Peilin Wang
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, Hainan, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhan He
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Hebei Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Lili Zhou
- Yazhouwan National Laboratory, Sanya, Hainan, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiming Guo
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, Hainan, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Song X, Zhu G, Su X, Yu Y, Duan Y, Wang H, Shang X, Xu H, Chen Q, Guo W. Combined genome and transcriptome analysis of elite fiber quality in Gossypium barbadense. PLANT PHYSIOLOGY 2024; 195:2158-2175. [PMID: 38513701 DOI: 10.1093/plphys/kiae175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Gossypium barbadense, which is one of several species of cotton, is well known for its superior fiber quality. However, the genetic basis of its high-quality fiber remains largely unexplored. Here, we resequenced 269 G. barbadense accessions. Phylogenetic structure analysis showed that the set of accessions was clustered into 3 groups: G1 and G2 mainly included modern cultivars from Xinjiang, China, and G3 was related to widely introduced accessions in different regions worldwide. A genome-wide association study of 5 fiber quality traits across multiple field environments identified a total of 512 qtls (main-effect QTLs) and 94 qtlEs (QTL-by-environment interactions) related to fiber quality, of which 292 qtls and 57 qtlEs colocated with previous studies. We extracted the genes located in these loci and performed expression comparison, local association analysis, and introgression segment identification. The results showed that high expression of hormone-related genes during fiber development, introgressions from Gossypium hirsutum, and the recombination of domesticated elite allelic variation were 3 major contributors to improve the fiber quality of G. barbadense. In total, 839 candidate genes with encoding region variations associated with elite fiber quality were mined. We confirmed that haplotype GB_D03G0092H traced to G. hirsutum introgression, with a 1-bp deletion leading to a frameshift mutation compared with GB_D03G0092B, significantly improved fiber quality. GB_D03G0092H is localized in the plasma membrane, while GB_D03G0092B is in both the nucleus and plasma membrane. Overexpression of GB_D03G0092H in Arabidopsis (Arabidopsis thaliana) significantly improved the elongation of longitudinal cells. Our study systematically reveals the genetic basis of the superior fiber quality of G. barbadense and provides elite segments and gene resources for breeding high-quality cotton cultivars.
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Affiliation(s)
- Xiaohui Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiujuan Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yujia Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujia Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Haitang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijiang Xu
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
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Rehman A, Tian C, Li X, Wang X, Li H, He S, Jiao Z, Qayyum A, Du X, Peng Z. GhiPLATZ17 and GhiPLATZ22, zinc-dependent DNA-binding transcription factors, promote salt tolerance in upland cotton. PLANT CELL REPORTS 2024; 43:140. [PMID: 38740586 DOI: 10.1007/s00299-024-03178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE The utilization of transcriptome analysis, functional validation, VIGS, and DAB techniques have provided evidence that GhiPLATZ17 and GhiPLATZ22 play a pivotal role in improving the salt tolerance of upland cotton. PLATZ (Plant AT-rich sequences and zinc-binding proteins) are known to be key regulators in plant growth, development, and response to salt stress. In this study, we comprehensively analyzed the PLATZ family in ten cotton species in response to salinity stress. Gossypium herbaceum boasts 25 distinct PLATZ genes, paralleled by 24 in G. raimondii, 25 in G. arboreum, 46 in G. hirsutum, 48 in G. barbadense, 43 in G. tomentosum, 67 in G. mustelinum, 60 in G. darwinii, 46 in G. ekmanianum, and a total of 53 PLATZ genes attributed to G. stephensii. The PLATZ gene family shed light on the hybridization and allopolyploidy events that occurred during the evolutionary history of allotetraploid cotton. Ka/Ks analysis suggested that the PLATZ gene family underwent intense purifying selection during cotton evolution. Analysis of synteny and gene collinearity revealed a complex pattern of segmental and dispersed duplication events to expand PLATZ genes in cotton. Cis-acting elements and gene expressions revealed that GhiPLATZ exhibited salt stress resistance. Transcriptome analysis, functional validation, virus-induced gene silencing (VIGS), and diaminobenzidine staining (DAB) demonstrated that GhiPLATZ17 and GhiPLATZ22 enhance salt tolerance in upland cotton. The study can potentially advance our understanding of identifying salt-resistant genes in cotton.
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Affiliation(s)
- Abdul Rehman
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Chunyan Tian
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiawen Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoyang Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Hongge Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Shoupu He
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Zhen Jiao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 66000, Pakistan
| | - Xiongming Du
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
| | - Zhen Peng
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
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Chang X, He X, Li J, Liu Z, Pi R, Luo X, Wang R, Hu X, Lu S, Zhang X, Wang M. High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres. PLANT COMMUNICATIONS 2024; 5:100722. [PMID: 37742072 PMCID: PMC10873883 DOI: 10.1016/j.xplc.2023.100722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/16/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023]
Abstract
Centromere positioning and organization are crucial for genome evolution; however, research on centromere biology is largely influenced by the quality of available genome assemblies. Here, we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum (TM-1) and Gossypium barbadense (3-79). Compared with previously published reference genomes, our assemblies show substantial improvements, with the contig N50 improved by 4.6-fold and 5.6-fold, respectively, and thus represent the most complete cotton genomes to date. These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G. hirsutum and G. barbadense, respectively. Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize (CRM) and Tekay long terminal repeat families, and the CRM family reshapes the centromere structure of the At subgenome after polyploidization. These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes, ensuring centromere function and genome stability. In addition, the repositioning and high sequence divergence of centromeres between G. hirsutum and G. barbadense have contributed to speciation and centromere diversity. This study sheds light on centromere evolution in a significant crop and provides an alternative approach for exploring the evolution of polyploid plants.
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Affiliation(s)
- Xing Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xin He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruizhen Pi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuanxuan Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruipeng Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiubao Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Sifan Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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9
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Kangben F, Kumar S, Li Z, Sreedasyam A, Dardick C, Jones D, Saski CA. Phylogenetic and functional analysis of tiller angle control homeologs in allotetraploid cotton. FRONTIERS IN PLANT SCIENCE 2024; 14:1320638. [PMID: 38356867 PMCID: PMC10864623 DOI: 10.3389/fpls.2023.1320638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024]
Abstract
Introduction Plants can adapt their growth to optimize light capture in competitive environments, with branch angle being a crucial factor influencing plant phenotype and physiology. Decreased branch angles in cereal crops have been shown to enhance productivity in high-density plantings. The Tiller Angle Control (TAC1) gene, known for regulating tiller inclination in rice and corn, has been found to control branch angle in eudicots. Manipulating TAC1 in field crops like cotton offers the potential for improving crop productivity. Methods Using a homolog-based methodology, we examined the distribution of TAC1-related genes in cotton compared to other angiosperms. Furthermore, tissue-specific qPCR analysis unveiled distinct expression patterns of TAC1 genes in various cotton tissues. To silence highly expressed specific TAC1 homeologs in the stem, we applied CRISPR-Cas9 gene editing and Agrobacterium-mediated transformation, followed by genotyping and subsequent phenotypic validation of the mutants. Results Gene duplication events of TAC1 specific to the Gossypium lineage were identified, with 3 copies in diploid progenitors and 6 copies in allotetraploid cottons. Sequence analysis of the TAC1 homeologs in Gossypium hirsutum revealed divergence from other angiosperms with 1-2 copies, suggesting possible neo- or sub-functionalization for the duplicated copies. These TAC1 homeologs exhibited distinct gene expression patterns in various tissues over developmental time, with elevated expression of A11G109300 and D11G112200, specifically in flowers and stems, respectively. CRISPR-mediated loss of these TAC1 homeologous genes resulted in a reduction in branch angle and altered petiole angles, and a 5 to 10-fold reduction in TAC1 expression in the mutants, confirming their role in controlling branch and petiole angles. This research provides a promising strategy for genetically engineering branch and petiole angles in commercial cotton varieties, potentially leading to increased productivity.
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Affiliation(s)
- Foster Kangben
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sonika Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Chris Dardick
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Appalachian Fruit Research Station, Kearneysville, WV, United States
| | - Don Jones
- Department of Agricultural Research, Cotton Incorporated, Cary, NC, United States
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
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10
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Zhang L, Ma C, Wang L, Su X, Huang J, Cheng H, Guo H. Repression of GhTUBB1 Reduces Plant Height in Gossypium hirsutum. Int J Mol Sci 2023; 24:15424. [PMID: 37895102 PMCID: PMC10607470 DOI: 10.3390/ijms242015424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
The original 'Green Revolution' genes are associated with gibberellin deficiency. However, in some species, mutations in these genes cause pleiotropic phenotypes, preventing their application in dwarf breeding. The development of novel genotypes with reduced plant height will resolve this problem. In a previous study, we obtained two dwarf lines, L28 and L30, by introducing the Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f. C-repeat-binding factor 1 (AmCBF1) into the upland cotton variety R15. We found that Gossypium hirsutum Tubulin beta-1 (GhTUBB1) was downregulated in L28 and L30, which suggested that this gene may have contributed to the dwarf phenotype of L28 and L30. Here, we tested this hypothesis by silencing GhTUBB1 expression in R15 and found that decreased expression resulted in a dwarf phenotype. Interestingly, we found that repressing AmCBF1 expression in L28 and L30 partly recovered the expression of GhTUBB1. Thus, AmCBF1 expression presented a negative relationship with GhTUBB1 expression in L28 and L30. Moreover, yeast one-hybrid and dual-luciferase assays suggest that AmCBF1 negatively regulates GhTUBB1 expression by directly binding to C-repeat/dehydration-responsive (CRT/DRE) elements in the GhTUBB1 promoter, potentially explaining the dwarf phenotypes of L28 and L30. This study elucidates the regulation of GhTUBB1 expression by AmCBF1 and suggests that GhTUBB1 may be a new target gene for breeding dwarf and compact cultivars.
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Affiliation(s)
- Lihua Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (C.M.); (L.W.); (X.S.)
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Caixia Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (C.M.); (L.W.); (X.S.)
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Lihua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (C.M.); (L.W.); (X.S.)
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (C.M.); (L.W.); (X.S.)
| | - Jinling Huang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (C.M.); (L.W.); (X.S.)
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Huiming Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.Z.); (C.M.); (L.W.); (X.S.)
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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12
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Fan Y, Peng F, Cui R, Wang S, Cui Y, Lu X, Huang H, Ni K, Liu X, Jiang T, Feng X, Liu M, Lei Y, Chen W, Meng Y, Han M, Wang D, Yin Z, Chen X, Wang J, Li Y, Guo L, Zhao L, Ye W. GhIMP10D, an inositol monophosphates family gene, enhances ascorbic acid and antioxidant enzyme activities to confer alkaline tolerance in Gossypium hirsutum L. BMC PLANT BIOLOGY 2023; 23:447. [PMID: 37736713 PMCID: PMC10515029 DOI: 10.1186/s12870-023-04462-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Inositol monophosphates (IMP) are key enzymes in the ascorbic acid (AsA) synthesis pathways, which play vital roles in regulating plant growth and development and stresses tolerance. To date, no comprehensive analysis of the expression profile of IMP genes and their functions under abiotic stress in cotton has been reported. RESULTS In this study, the genetic characteristics, phylogenetic evolution, cis-acting elements and expression patterns of IMP gene family in cotton were systematically analyzed. A total of 28, 27, 13 and 13 IMP genes were identified in Gossypium hirsutum (G. hirsutum), Gossypium barbadense (G. barbadense), Gossypium arboreum (G. arboreum), and Gossypium raimondii (G. raimondii), respectively. Phylogenetic analysis showed that IMP family genes could cluster into 3 clades. Structure analysis of genes showed that GhIMP genes from the same subgroup had similar genetic structure and exon number. And most GhIMP family members contained hormone-related elements (abscisic acid response element, MeJA response element, gibberellin response element) and stress-related elements (low temperature response element, defense and stress response element, wound response element). After exogenous application of abscisic acid (ABA), some GhIMP genes containing ABA response elements positively responded to alkaline stress, indicating that ABA response elements played an important role in response to alkaline stress. qRT-PCR showed that most of GhIMP genes responded positively to alkaline stress, and GhIMP10D significantly upregulated under alkaline stress, with the highest up-regulated expression level. Virus-induced gene silencing (VIGS) experiment showed that compared with 156 plants, MDA content of pYL156:GhIMP10D plants increased significantly, while POD, SOD, chlorophyII and AsA content decreased significantly. CONCLUSIONS This study provides a thorough overview of the IMP gene family and presents a new perspective on the evolution of this gene family. In particular, some IMP genes may be involved in alkaline stress tolerance regulation, and GhIMP10D showed high expression levels in leaves, stems and roots under alkaline stress, and preliminary functional verification of GhIMP10D gene suggested that it may regulate tolerance to alkaline stress by regulating the activity of antioxidant enzymes and the content of AsA. This study contributes to the subsequent broader discussion of the structure and alkaline resistance of IMP genes in cotton.
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Affiliation(s)
- Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Fanjia Peng
- Hunan Institute of Cotton Science, Hunan, 415101, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xiaoyu Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Tiantian Jiang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xixian Feng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Mengyue Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yuqian Lei
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Wenhua Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yuan Meng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yujun Li
- Hunan Institute of Cotton Science, Hunan, 415101, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China.
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Liu Q, Wang Y, Fu Y, Du L, Zhang Y, Wang Q, Sun R, Ai N, Feng G, Li C. Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:205. [PMID: 37668671 DOI: 10.1007/s00122-023-04453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
KEY MESSAGE In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR. The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08 cM, with an average distance of 0.80 cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.
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Affiliation(s)
- Qiao Liu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuanyuan Wang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuanzhi Fu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Lei Du
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Yilin Zhang
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Qinglian Wang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Runrun Sun
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Nijiang Ai
- Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China
| | - Guoli Feng
- Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China
| | - Chengqi Li
- Life Science College, Yuncheng University, Yuncheng, 044000, China.
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Cen Y, Geng S, Gao L, Wang X, Yan X, Hou Y, Wang P. Genome-Wide Identification and Expression Analysis of RLCK-VII Subfamily Genes Reveal Their Roles in Stress Responses of Upland Cotton. PLANTS (BASEL, SWITZERLAND) 2023; 12:3170. [PMID: 37687414 PMCID: PMC10490013 DOI: 10.3390/plants12173170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
Receptor-like cytoplasmic kinase VII (RLCK-VII) subfamily members are vital players in plant innate immunity and are also involved in plant development and abiotic stress tolerance. As a widely cultivated textile crop, upland cotton (Gossypium hirsutum) attaches great importance to the cotton industry worldwide. To obtain details of the composition, phylogeny, and putative function of RLCK-VII genes in upland cotton, genome-wide identification, evolutionary event analysis, and expression pattern examination of RLCK-VII subfamily genes in G. hirsutum were performed. There are 129 RLCK-VII members in upland cotton (GhRLCKs) and they were divided into nine groups based on their phylogenetic relationships. The gene structure and sequence features are relatively conserved within each group, which were divided based on their phylogenetic relationships, and consistent with those in Arabidopsis. The phylogenetic analysis results showed that RLCK-VII subfamily genes evolved in plants before the speciation of Arabidopsis and cotton, and segmental duplication was the major factor that caused the expansion of GhRLCKs. The diverse expression patterns of GhRLCKs in response to abiotic stresses (temperature, salt, and drought) and V. dahliae infection were observed. The candidates that may be involved in cotton's response to these stresses are highlighted. GhRLCK7 (GhRLCK7A and D), which is notably induced by V. dahliae infection, was demonstrated to positively regulate cotton defense against V. dahliae by the loss-of-function assay in cotton. These findings shed light on the details of the RLCK-VII subfamily in cotton and provide a scaffold for the further function elucidation and application of GhRLCKs for the germplasm innovation of cotton.
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Affiliation(s)
- Yuhan Cen
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Shiyi Geng
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Linying Gao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
| | - Xinyue Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Xin Yan
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
| | - Yuxia Hou
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
| | - Ping Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
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15
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Ye Y, Wang P, Zhang M, Abbas M, Zhang J, Liang C, Wang Y, Wei Y, Meng Z, Zhang R. UAV-based time-series phenotyping reveals the genetic basis of plant height in upland cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:937-951. [PMID: 37154288 DOI: 10.1111/tpj.16272] [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: 01/18/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
Plant height (PH) is an important agronomic trait affecting crop architecture, biomass, resistance to lodging and mechanical harvesting. Elucidating the genetic governance of plant height is crucial because of the global demand for high crop yields. However, during the rapid growth period of plants the PH changes a lot on a daily basis, which makes it difficult to accurately phenotype the trait by hand on a large scale. In this study, an unmanned aerial vehicle (UAV)-based remote-sensing phenotyping platform was applied to obtain time-series PHs of 320 upland cotton accessions in three different field trials. The results showed that the PHs obtained from UAV images were significantly correlated with ground-based manual measurements, for three trials (R2 = 0.96, 0.95 and 0.96). Two genetic loci on chromosomes A01 and A11 associated with PH were identified by genome-wide association studies (GWAS). GhUBP15 and GhCUL1 were identified to influence PH in further analysis. We obtained a time series of PH values for three field conditions based on remote sensing with UAV. The key genes identified in this study are of great value for the breeding of ideal plant architecture in cotton.
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Affiliation(s)
- Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Man Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaxin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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16
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Manivannan A, Cheeran Amal T. Deciphering the complex cotton genome for improving fiber traits and abiotic stress resilience in sustainable agriculture. Mol Biol Rep 2023; 50:6937-6953. [PMID: 37349608 DOI: 10.1007/s11033-023-08565-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/31/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Understanding the complex cotton genome is of paramount importance in devising a strategy for sustainable agriculture. Cotton is probably the most economically important cash crop known for its cellulose-rich fiber content. The cotton genome has become an ideal model for deciphering polyploidization due to its polyploidy, setting it apart from other major crops. However, the main challenge in understanding the functional and regulatory functions of many genes in cotton is still the complex cotton polyploidy genome, which is not limited to a single role. Cotton production is vulnerable to the sensitive effects of climate change, which can alter or aggravate soil, pests, and diseases. Thus, conventional plant breeding coupled with advanced technologies has led to substantial progress being made in cotton production. GENOMICS APPROACHES IN COTTON In the frontier areas of genomics research, cotton genomics has gained momentum accomplished by robust high-throughput sequencing platforms combined with novel computational tools to make the cotton genome more tractable. Advances in long-read sequencing have allowed for the generation of the complete set of cotton gene transcripts giving incisive scientific knowledge in cotton improvement. In contrast, the integration of the latest sequencing platforms has been used to generate multiple high-quality reference genomes in diploid and tetraploid cotton. While pan-genome and 3D genomic studies are still in the early stages in cotton, it is anticipated that rapid advances in sequencing, assembly algorithms, and analysis pipelines will have a greater impact on advanced cotton research. CONCLUSIONS This review article briefly compiles substantial contributions in different areas of the cotton genome, which include genome sequencing, genes, and their molecular regulatory networks in fiber development and stress tolerance mechanism. This will greatly help us in understanding the robust genomic organization which in turn will help unearth candidate genes for functionally important agronomic traits.
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Affiliation(s)
- Alagarsamy Manivannan
- ICAR-Central Institute for Cotton Research, Regional Station, Coimbatore, 641 003, Tamil Nadu, India.
| | - Thomas Cheeran Amal
- ICAR-Central Institute for Cotton Research, Regional Station, Coimbatore, 641 003, Tamil Nadu, India
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17
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Han J, Jawad Umer M, Yang M, Hou Y, Gereziher Mehari T, Zheng J, Wang H, Liu J, Dong W, Xu Y, Wang Y, Liu F, Zhou Z, Cai X. Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107708. [PMID: 37116225 DOI: 10.1016/j.plaphy.2023.107708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023]
Abstract
Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.
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Affiliation(s)
- Jiangping Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Mengying Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Teame Gereziher Mehari
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jie Zheng
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China
| | - Heng Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jiajun Liu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenhao Dong
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China; State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
| | - ZhongLi Zhou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xiaoyan Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
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18
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Gui Y, Fu G, Li X, Dai Y. Identification and analysis of isoflavone reductase gene family in Gossypium hirsutum L. Sci Rep 2023; 13:5703. [PMID: 37029187 PMCID: PMC10082034 DOI: 10.1038/s41598-023-32213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/24/2023] [Indexed: 04/09/2023] Open
Abstract
Isoflavone reductase (IFR) is a key enzyme controlling isoflavone synthesis and widely involved in response to various stresses. In this study, the IFR genes in four Gossypium species and other 7 species were identified and analyzed in the whole genome, and the physicochemical properties, gene structures, cis-acting elements, chromosomal locations, collinearity relationships and expression patterns of IFR genes were systematically analyzed. 28, 28, 14 and 15 IFR genes were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii, respectively, which were divided into five clades according to the evolutionary tree and gene structure. Collinear analysis showed that segmental duplication and whole genome duplication were the main driving forces in the process of evolution, and most genes underwent pure selection. Gene structure analysis showed that IFR gene family was relatively conserved. Cis-element analysis of promoter showed that most GhIFR genes contain cis-elements related to abiotic stresses and plant hormones. Analysis of GhIFR gene expression under different stresses showed that GhIFR genes were involved in the response to drought, salt, heat and cold stresses through corresponding network mechanisms, especially GhIFR9A. Phenotypic analysis after silencing GhIFR9A gene by VIGS was shown that GhIFR9A gene was involved in the response to salt stress. This study laid a foundation for the subsequent functional study of cotton IFR genes.
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Affiliation(s)
- Yanting Gui
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China
| | - Guozhan Fu
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China.
| | - Xuelin Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China
| | - Yinghao Dai
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China
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19
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Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, Wang Z, Li F. Recent progression and future perspectives in cotton genomic breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:548-569. [PMID: 36226594 DOI: 10.1111/jipb.13388] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/11/2022] [Indexed: 05/26/2023]
Abstract
Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
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Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yihao Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qingdi Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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20
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Chávez Montes RA, Ulloa M, Biniashvili T, Zackay A, Kfir N, Lopez-Arredondo D, Herrera-Estrella L. Assembly and annotation of the Gossypium barbadense L. 'Pima-S6' genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes. BMC Genomics 2023; 24:11. [PMID: 36627552 PMCID: PMC9830710 DOI: 10.1186/s12864-022-09102-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome assemblies. RESULTS Synteny and orthogroup analyses revealed important differences on chromosome structure and annotated proteins content between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses revealed chromosomal rearrangements between Pima-S6 and other Pima genomes on several chromosomes, with three major inversions in chromosomes A09, A13 and D05, raising questions about the true chromosome structure of Gossypium barbadense genomes. CONCLUSION Analyses of the re-assembled and re-annotated genome of the close relative G. barbadense Pima 3-79 using our Pima-S6 assembly suggest that contig placement of some recent G. barbadense assemblies might have been unduly influenced by the use of the G. hirsutum TM-1 genome as the anchoring reference. The Pima-S6 reference genome provides a valuable genomic resource and offers new insights on genomic structure, and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts.
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Affiliation(s)
- Ricardo A. Chávez Montes
- grid.264784.b0000 0001 2186 7496Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, 79409 Lubbock, TX USA
| | - Mauricio Ulloa
- grid.508981.dPlant Stress and Germplasm Development Research, USDA-ARS, PA, CSRL, 79415 Lubbock, TX USA
| | | | | | | | - Damar Lopez-Arredondo
- grid.264784.b0000 0001 2186 7496Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, 79409 Lubbock, TX USA
| | - Luis Herrera-Estrella
- grid.264784.b0000 0001 2186 7496Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, 79409 Lubbock, TX USA ,grid.512574.0 Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Mexico
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21
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Zhou J, Zhao L, Wu Y, Zhang X, Cheng S, Wei F, Zhang Y, Zhu H, Zhou Y, Feng Z, Feng H. A DEK domain-containing protein GhDEK2D mediated Gossypium hirsutum enhanced resistance to Verticillium dahliae. PLANT SIGNALING & BEHAVIOR 2022; 17:2024738. [PMID: 35034577 PMCID: PMC9176258 DOI: 10.1080/15592324.2021.2024738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, GhDEK2D was identified in Gossypium hirsutum by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under Verticillium dahliae (Vd) challenge. The GhDEK2D-silenced cotton decreased resistance against Vd. In GhDEK2D-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic Arabidopsis lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.
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Affiliation(s)
- Jinglong Zhou
- College of Agriculture, Yangtze University, Jingzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yajie Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xiaojian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Sheng Cheng
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yi Zhou
- College of Agriculture, Yangtze University, Jingzhou, China
- Yi Zhou College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zili Feng State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Hongjie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- CONTACT Hongjie Feng
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22
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Zhou L, Wang Y, Wang P, Wang C, Wang J, Wang X, Cheng H. Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation for gene editing analysis in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1059404. [PMID: 36643290 PMCID: PMC9832336 DOI: 10.3389/fpls.2022.1059404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
CRIPSR/Cas9 gene editing system is an effective tool for genome modification in plants. Multiple target sites are usually designed and the effective target sites are selected for editing. Upland cotton (Gossypium hirsutum L., hereafter cotton) is allotetraploid and is commonly considered as difficult and inefficient to transform, it is important to select the effective target sites that could result in the ideal transgenic plants with the CRISPR-induced mutations. In this study, Agrobacterium rhizogenes-mediated hairy root method was optimized to detect the feasibility of the target sites designed in cotton phytoene desaturase (GhPDS) gene. A. rhizogenes showed the highest hairy root induction (30%) when the bacteria were cultured until OD600 reached to 0.8. This procedure was successfully applied to induce hairy roots in the other three cultivars (TM-1, Lumian-21, Zhongmian-49) and the mutations were detected in GhPDS induced by CRISPR/Cas9 system. Different degrees of base deletions at two sgRNAs (sgRNA5 and sgRNA10) designed in GhPDS were detected in R15 hairy roots. Furthermore, we obtained an albino transgenic cotton seeding containing CRISPR/Cas9-induced gene editing mutations in sgRNA10. The hairy root transformation system established in this study is sufficient for selecting sgRNAs in cotton, providing a technical basis for functional genomics research of cotton.
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Affiliation(s)
- Lili Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yali Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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23
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Cao J, Huang C, Liu J, Li C, Liu X, Zheng Z, Hou L, Huang J, Wang L, Zhang Y, Shangguan X, Chen Z. Comparative Genomics and Functional Studies of Putative m 6A Methyltransferase (METTL) Genes in Cotton. Int J Mol Sci 2022; 23:14111. [PMID: 36430588 PMCID: PMC9694044 DOI: 10.3390/ijms232214111] [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: 09/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m6A RNA methyltransferases in cotton. Here, a systematic analysis of the m6A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis thaliana, and Homo sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m6A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m6A in subsequent studies to improve the agronomic traits in cotton.
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Affiliation(s)
- Junfeng Cao
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chaochen Huang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun’e Liu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenyi Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xia Liu
- Esquel Group, 25 Harbour Road, Wanchai, Hong Kong, China
| | - Zishou Zheng
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lipan Hou
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jinquan Huang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yugao Zhang
- Esquel Group, 25 Harbour Road, Wanchai, Hong Kong, China
| | - Xiaoxia Shangguan
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044099, China
| | - Zhiwen Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Duan Y, Chen Q, Chen Q, Zheng K, Cai Y, Long Y, Zhao J, Guo Y, Sun F, Qu Y. Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense. G3 GENES|GENOMES|GENETICS 2022; 12:6650278. [PMID: 35881688 PMCID: PMC9434320 DOI: 10.1093/g3journal/jkac167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022]
Abstract
Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for Gossypium barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a Gossypium barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0–35 days postanthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using the weighted gene coexpression network analysis. In total, 55 genes were identified as differentially expressed from 4 specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670, and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. Quantitative real-time PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.
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Affiliation(s)
- Yajie Duan
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Qin Chen
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yongsheng Cai
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yilei Long
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Jieyin Zhao
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yaping Guo
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Fenglei Sun
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
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25
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Lu Z, Yin G, Chai M, Sun L, Wei H, Chen J, Yang Y, Fu X, Li S. Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance. BMC Genomics 2022; 23:560. [PMID: 35931984 PMCID: PMC9356423 DOI: 10.1186/s12864-022-08800-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/27/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that participate in a variety of biological functions, such as signaling pathways, plant development, and environmental stress and stimulus responses. Nevertheless, there have been few studies on CNGC gene family in cotton. RESULTS In this study, a total of 114 CNGC genes were identified from the genomes of 4 cotton species. These genes clustered into 5 main groups: I, II, III, IVa, and IVb. Gene structure and protein motif analysis showed that CNGCs on the same branch were highly conserved. In addition, collinearity analysis showed that the CNGC gene family had expanded mainly by whole-genome duplication (WGD). Promoter analysis of the GhCNGCs showed that there were a large number of cis-acting elements related to abscisic acid (ABA). Combination of transcriptome data and the results of quantitative RT-PCR (qRT-PCR) analysis revealed that some GhCNGC genes were induced in response to salt and drought stress and to exogenous ABA. Virus-induced gene silencing (VIGS) experiments showed that the silencing of the GhCNGC32 and GhCNGC35 genes decreased the salt tolerance of cotton plants (TRV:00). Specifically, physiological indexes showed that the malondialdehyde (MDA) content in gene-silenced plants (TRV:GhCNGC32 and TRV:GhCNGC35) increased significantly under salt stress but that the peroxidase (POD) activity decreased. After salt stress, the expression level of ABA-related genes increased significantly, indicating that salt stress can trigger the ABA signal regulatory mechanism. CONCLUSIONS we comprehensively analyzed CNGC genes in four cotton species, and found that GhCNGC32 and GhCNGC35 genes play an important role in cotton salt tolerance. These results laid a foundation for the subsequent study of the involvement of cotton CNGC genes in salt tolerance.
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Affiliation(s)
- Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan, China
| | - Guo Yin
- Handan Academy of Agricultural Sciences, Handan, China
| | - Mao Chai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Lu Sun
- Handan Academy of Agricultural Sciences, Handan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Jie Chen
- Handan Academy of Agricultural Sciences, Handan, China
| | - Yufeng Yang
- Handan Academy of Agricultural Sciences, Handan, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China.
| | - Shiyun Li
- Handan Academy of Agricultural Sciences, Handan, China.
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26
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Han G, Li Y, Yang Z, Wang C, Zhang Y, Wang B. Molecular Mechanisms of Plant Trichome Development. FRONTIERS IN PLANT SCIENCE 2022; 13:910228. [PMID: 35720574 PMCID: PMC9198495 DOI: 10.3389/fpls.2022.910228] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
- Dongying Institute, Shandong Normal University, Dongying, China
| | - Yuxia Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zongran Yang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chengfeng Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
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27
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Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks. Genes (Basel) 2022; 13:genes13060954. [PMID: 35741716 PMCID: PMC9222338 DOI: 10.3390/genes13060954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.
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28
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Zhang L, Liu J, Cheng J, Sun Q, Zhang Y, Liu J, Li H, Zhang Z, Wang P, Cai C, Chu Z, Zhang X, Yuan Y, Shi Y, Cai Y. lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt. PLANT PHYSIOLOGY 2022; 189:264-284. [PMID: 35134243 PMCID: PMC9070856 DOI: 10.1093/plphys/kiac041] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/26/2021] [Indexed: 05/13/2023]
Abstract
In plants, long noncoding RNAs (lncRNAs) regulate disease resistance against fungi and other pathogens. However, the specific mechanism behind this regulation remains unclear. In this study, we identified disease resistance-related lncRNAs as well as their regulating genes and assessed their functions by infection of cotton (Gossypium) chromosome segment substitution lines with Verticillium dahliae. Our results demonstrated that lncRNA7 and its regulating gene Pectin methylesterase inhibitor 13 (GbPMEI13) positively regulated disease resistance via the silencing approach, while ectopic overexpression of GbPMEI13 in Arabidopsis (Arabidopsis thaliana) promoted growth and enhanced resistance to V. dahliae. In contrast, lncRNA2 and its regulating gene Polygalacturonase 12 (GbPG12) negatively regulated resistance to V. dahliae. We further found that fungal disease-related agents, including the pectin-derived oligogalacturonide (OG), could downregulate the expression of lncRNA2 and GbPG12, leading to pectin accumulation. Conversely, OG upregulated the expression of lncRNA7, which encodes a plant peptide phytosulfokine (PSK-α), which was confirmed by lncRNA7 overexpression and Ultra Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS) experiments. We showed that PSK-α promoted 3-Indoleacetic acid (IAA) accumulation and activated GbPMEI13 expression through Auxin Response Factor 5. Since it is an inhibitor of pectin methylesterase (PME), GbPMEI13 promotes pectin methylation and therefore increases the resistance to V. dahliae. Consistently, we also demonstrated that GbPMEI13 inhibits the mycelial growth and spore germination of V. dahliae in vitro. In this study, we demonstrated that lncRNA7, lncRNA2, and their regulating genes modulate cell wall defense against V. dahliae via auxin-mediated signaling, providing a strategy for cotton breeding.
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Affiliation(s)
- Lin Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
- College of life science and agricultural engineering, Nanyang Normal
University, Nanyang 473000, China
| | - Jinlei Liu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Jieru Cheng
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Quan Sun
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of
Bioinformation, Chongqing University of Posts and Telecommunications,
Chongqing 400065, China
| | - Yu Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Jinggao Liu
- Southern Plains Agricultural Research Center, Agricultural Research
Service, USDA, College Station, Texas 77845, USA
| | - Huimin Li
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Ping Wang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Chaowei Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - Zongyan Chu
- Kaifeng Academy of Agriculture and Forestry, Kaifeng 475000,
China
| | - Xiao Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
| | - 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 455000, China
| | - Yuzhen Shi
- 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 455000, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant
Stress Biology, School of Life Sciences, School of Computer and Information
Engineering, Henan University, Kaifeng 475001, China
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29
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Zhang J, Mei H, Lu H, Chen R, Hu Y, Zhang T. Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development. FRONTIERS IN PLANT SCIENCE 2022; 13:864529. [PMID: 35463423 PMCID: PMC9022538 DOI: 10.3389/fpls.2022.864529] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten time points during the fiber developmental period for investigating the dynamics of gene expression changes associated with fiber in G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79. Globally, 44,484 genes expressed in all three cultivars account for 61.14% of the total genes. About 61.39% (N = 3,412) of the cotton transcription factors were involved in fiber development, which consisted of 58 cotton TF families. The differential analysis of intra- and interspecies showed that 3 DPA had more expression changes. To discover the genes with temporally changed expression profiles during the whole fiber development, 1,850 genes predominantly expressed in G. hirsutum and 1,050 in G. barbadense were identified, respectively. Based on the weighted gene co-expression network and time-course analysis, several candidate genes, mainly involved in the secondary cell wall synthesis and phytohormones, were identified in this study, underlying possibly the transcriptional regulation and molecular mechanisms of the fiber quality differences between G. barbadense and G. hirsutum. The quantitative real-time PCR validation of the candidate genes was consistent with the RNA-seq data. Our study provides a strong rationale for the analysis of gene function and breeding of high-quality cotton.
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30
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Zhao N, Wang W, Grover CE, Jiang K, Pan Z, Guo B, Zhu J, Su Y, Wang M, Nie H, Xiao L, Guo A, Yang J, Cheng C, Ning X, Li B, Xu H, Adjibolosoo D, Aierxi A, Li P, Geng J, Wendel JF, Kong J, Hua J. Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:691-710. [PMID: 34800075 PMCID: PMC8989498 DOI: 10.1111/pbi.13747] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Weiran Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhuanxia Pan
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Baosheng Guo
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jiahui Zhu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Ying Su
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Meng Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Hushuai Nie
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Li Xiao
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Anhui Guo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jing Yang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Cheng Cheng
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xinmin Ning
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Haijiang Xu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Daniel Adjibolosoo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Alifu Aierxi
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Pengbo Li
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Junyi Geng
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Jie Kong
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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31
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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: 1.7] [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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32
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Huang C, Li P, Cao J, Zheng Z, Huang J, Zhang X, Shangguan X, Wang L, Chen Z. Comprehensive identification and expression analysis of CRY gene family in Gossypium. BMC Genomics 2022; 23:231. [PMID: 35331129 PMCID: PMC8952943 DOI: 10.1186/s12864-022-08440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/03/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The cryptochromes (CRY) are specific blue light receptors of plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance. RESULTS In the present work, a systematic analysis of the CRY gene family was performed on twelve cotton species, resulting in 18, 17, 17, 17, and 17 CRYs identified in five alloteraploid cottons (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii), respectively, and five to nine CRY genes in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that CRY genes from cottons and Arabidopsis thaliana could be classified into seven clades. Synteny analysis suggested that the homoeolog of G. hirsutum Gh_A02G0384 has undergone an evolutionary loss event in the other four allotetraploid cotton species. Cis-element analysis predicated the possible functions of CRY genes in G. hirsutum. RNA-seq data revealed that Gh_D09G2225, Gh_A09G2012 and Gh_A11G1040 had high expressions in fiber cells of different developmental states. In addition, the expression levels of one (Gh_A03G0120), 15 and nine GhCRY genes were down-regulated following the PEG, NaCl and high-temperature treatments, respectively. For the low-temperature treatment, five GhCRY genes were induced, and five were repressed. These results indicated that most GhCRY genes negatively regulate the abiotic stress treatments. CONCLUSION We report the structures, domains, divergence, synteny, and cis-elements analyses systematically of G. hirsutum CRY genes. Possible biological functions of GhCRY genes in differential tissues as well as in response to abiotic stress during the cotton plant life cycle were predicted.
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Affiliation(s)
- Chaochen Huang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
- University of Chinese Academy of Sciences, Shanghai, 200032 China
| | - Pengbo Li
- Shanxi Key Laboratory of Cotton Germplasm Resources Utilization and Molecular Design Breeding, Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, 044099 China
| | - Junfeng Cao
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zishou Zheng
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jinquan Huang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xiufang Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xiaoxia Shangguan
- Shanxi Key Laboratory of Cotton Germplasm Resources Utilization and Molecular Design Breeding, Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, 044099 China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, 037009 China
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Wang G, Xu Z, Wang F, Huang Y, Xin Y, Liang S, Li B, Si H, Sun L, Wang Q, Ding X, Zhu X, Chen L, Yu L, Lindsey K, Zhang X, Jin S. Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum). BMC Biol 2022; 20:45. [PMID: 35164736 PMCID: PMC8845244 DOI: 10.1186/s12915-022-01232-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/13/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Base editors (BEs) display diverse applications in a variety of plant species such as Arabidopsis, rice, wheat, maize, soybean, and cotton, where they have been used to mediate precise base pair conversions without the collateral generation of undesirable double-stranded breaks (DSB). Studies of single-nucleotide polymorphisms (SNPs) underpinning plant traits are still challenging, particularly in polyploidy species where such SNPs are present in multiple copies, and simultaneous modification of all alleles would be required for functional analysis. Allotetraploid cotton has a number of homoeologous gene pairs located in the A and D sub-genomes with considerable SNPs, and it is desirable to develop adenine base editors (ABEs) for efficient and precise A-to-G single-base editing without DSB in such complex genome. RESULTS We established various ABE vectors based on different engineered adenosine deaminase (TadA) proteins fused to Cas9 variants (dCas9, nCas9), enabling efficient A to G editing up to 64% efficiency on-target sites of the allotetraploid cotton genome. Comprehensive analysis showed that GhABE7.10n exhibited the highest editing efficiency, with the main editing sites specifically located at the position A5 (counting the PAM as positions 21-23). Furthermore, DNA and RNA off-target analysis of cotton plants edited with GhABE7.10n and GhABE7.10d by whole genome and whole-transcriptome sequencing revealed no DNA off-target mutations, while very low-level RNA off-target mutations were detected. A new base editor, namely GhABE7.10dCpf1 (7.10TadA + dCpf1), that recognizes a T-rich PAM, was developed for the first time. Targeted A-to-G substitutions generated a single amino acid change in the cotton phosphatidyl ethanolamine-binding protein (GhPEBP), leading to a compact cotton plant architecture, an ideotype for mechanized harvesting of modern cotton production. CONCLUSIONS Our data illustrate the robustness of adenine base editing in plant species with complex genomes, which provides efficient and precise toolkit for cotton functional genomics and precise molecular breeding.
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Affiliation(s)
- Guanying Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Zhongping Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yanfeng Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Sijia Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Bo Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Wulumuqi, Xinjaing, 830000, People's Republic of China
| | - Huan Si
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Qiongqiong Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xiao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xiangqian Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Luo Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lu Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
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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: 1.0] [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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Pei L, Huang X, Liu Z, Tian X, You J, Li J, Fang DD, Lindsey K, Zhu L, Zhang X, Wang M. Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biol 2022; 23:45. [PMID: 35115029 PMCID: PMC8812185 DOI: 10.1186/s13059-022-02616-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. RESULTS To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes. CONCLUSIONS This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianhui Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xuehan Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Liu X, Yang L, Wang J, Wang Y, Guo Z, Li Q, Yang J, Wu Y, Chen L, Teng Z, Liu D, Liu D, Guo K, Zhang Z. Analyzing Quantitative Trait Loci for Fiber Quality and Yield-Related Traits From a Recombinant Inbred Line Population With Gossypium hirsutum Race palmeri as One Parent. FRONTIERS IN PLANT SCIENCE 2022; 12:817748. [PMID: 35046989 PMCID: PMC8763314 DOI: 10.3389/fpls.2021.817748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Fiber quality and yield-related traits are important agronomic traits in cotton breeding. To detect the genetic basis of fiber quality and yield related traits, a recombinant inbred line (RIL) population consisting of 182 lines was established from a cross between Gossypium hirsutum cultivar CCRI35 and G. hirsutum race palmeri accession TX-832. The RIL population was deeply genotyped using SLAF-seq and was phenotyped in six environments. A high-density genetic linkage map with 15,765 SNP markers and 153 SSR markers was constructed, with an average distance of 0.30 cM between adjacent markers. A total of 210 fiber quality quantitative trait loci (QTLs) and 73 yield-related QTLs were identified. Of the detected QTLs, 62 fiber quality QTLs and 10 yield-related QTLs were stable across multiple environments. Twelve and twenty QTL clusters were detected on the At and Dt subgenome, respectively. Twenty-three major QTL clusters were further validated through associated analysis and five candidate genes of four stable fiber quality QTLs were identified. This study revealed elite loci influencing fiber quality and yield and significant phenotypic selection regions during G. hirsutum domestication, and set a stage for future utilization of molecular marker assisted breeding in cotton breeding programs.
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Peng Z, Li H, Sun G, Dai P, Geng X, Wang X, Zhang X, Wang Z, Jia Y, Pan Z, Chen B, Du X, He S. CottonGVD: A Comprehensive Genomic Variation Database for Cultivated Cottons. FRONTIERS IN PLANT SCIENCE 2021; 12. [PMID: 34992626 PMCID: PMC8724205 DOI: 10.3389/fpls.2021.803736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cultivated cottons are the most important economic crop, which produce natural fiber for the textile industry. In recent years, the genetic basis of several essential traits for cultivated cottons has been gradually elucidated by decoding their genomic variations. Although an abundance of resequencing data is available in public, there is still a lack of a comprehensive tool to exhibit the results of genomic variations and genome-wide association study (GWAS). To assist cotton researchers in utilizing these data efficiently and conveniently, we constructed the cotton genomic variation database (CottonGVD; http://120.78.174.209/ or http://db.cngb.org/cottonGVD). This database contains the published genomic information of three cultivated cotton species, the corresponding population variations (SNP and InDel markers), and the visualized results of GWAS for major traits. Various built-in genomic tools help users retrieve, browse, and query the variations conveniently. The database also provides interactive maps (e.g., Manhattan map, scatter plot, heatmap, and linkage disequilibrium block) to exhibit GWAS and expression GWAS results. Cotton researchers could easily focus on phenotype-associated loci visualization, and they are interested in and screen for candidate genes. Moreover, CottonGVD will continue to update by adding more data and functions.
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Yu J, Jung S, Cheng CH, Lee T, Zheng P, Buble K, Crabb J, Humann J, Hough H, Jones D, Campbell JT, Udall J, Main D. CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122805. [PMID: 34961276 PMCID: PMC8705096 DOI: 10.3390/plants10122805] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/11/2021] [Accepted: 12/12/2021] [Indexed: 05/12/2023]
Abstract
Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.
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Affiliation(s)
- Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - James Crabb
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Don Jones
- Cotton Incorporated, Cary, NC 27513, USA;
| | - J. Todd Campbell
- The Agricultural Research Service of U.S. Department of Agriculture, Florence, SC 29501, USA;
| | - Josh Udall
- The Agricultural Research Service of U.S. Department of Agriculture, College Station, TX 77845, USA;
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
- Correspondence: ; Tel.: +1-509-335-2774
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Jiang X, Gong J, Zhang J, Zhang Z, Shi Y, Li J, Liu A, Gong W, Ge Q, Deng X, Fan S, Chen H, Kuang Z, Pan J, Che J, Zhang S, Jia T, Wei R, Chen Q, Wei S, Shang H, Yuan Y. Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2021; 12:753755. [PMID: 34975939 PMCID: PMC8716697 DOI: 10.3389/fpls.2021.753755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.
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Affiliation(s)
- Xiao Jiang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haodong Chen
- Cotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde, China
| | - Zhengcheng Kuang
- Cotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jincan Che
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renhui Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quanjia Chen
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
| | - Shoujun Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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Zhang H, Zhang Y, Xu N, Rui C, Fan Y, Wang J, Han M, Wang Q, Sun L, Chen X, Lu X, Wang D, Chen C, Ye W. Genome-wide expression analysis of phospholipase A1 (PLA1) gene family suggests phospholipase A1-32 gene responding to abiotic stresses in cotton. Int J Biol Macromol 2021; 192:1058-1074. [PMID: 34656543 DOI: 10.1016/j.ijbiomac.2021.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 01/01/2023]
Abstract
Cotton is the most important crop for the production of natural fibres used in the textile industry. High salinity, drought, cold and high temperature represent serious abiotic stresses, which seriously threaten cotton production. Phospholipase AS has an irreplaceable role in lipid signal transmission, growth and development and stress events. Phospholipase A can be divided into three families: PLA1, PLA2 and pPLA. Among them, the PLA1 family is rarely studied in plants. In order to study the potential functions of the PLA1 family in cotton, the bioinformatics analysis of the PLA1 family was correlated with cotton adversity, and tissue-specific analysis was performed. Explore the structure-function relationship of PLA1 members. It is found that the expression of GbPLA1-32 gene is affected by a variety of environmental stimuli, indicating that it plays a very important role in stress and hormone response, and closely associates the cotton adversity with this family. Through further functional verification, we found that virus-induced GbPLA1-32 gene silencing (VIGS) caused Gossypium barbadense to be sensitive to salt stress. This research provides an important basis for further research on the molecular mechanism of cotton resistance to abiotic stress.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China; Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052 Urumqi, China
| | - Yuexin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Nan Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Cun Rui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Yapeng Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Jing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Mingge Han
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052 Urumqi, China
| | - Qinqin Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052 Urumqi, China
| | - Liangqing Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Chao Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China; Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052 Urumqi, China.
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Peng Z, Jiang X, Wang Z, Wang X, Li H, He S, Pan Z, Qayyum A, Rehman A, Du X. Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton. Int J Mol Sci 2021; 22:12649. [PMID: 34884455 PMCID: PMC8657469 DOI: 10.3390/ijms222312649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.
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Affiliation(s)
- Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xuran Jiang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
| | - Zhenzhen Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Zhaoe Pan
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan;
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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Wang N, Dong WL, Zhang XJ, Zhou T, Huang XJ, Li BG, Liu JN, Ma XF, Li ZH. Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs. PLANTA 2021; 254:116. [PMID: 34750674 DOI: 10.1007/s00425-021-03775-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The novel structural variations were identified in cotton chloroplast tRNAs and gene loss events were more obvious than duplications in chloroplast tRNAs. Transfer RNAs (tRNA) have long been believed an evolutionary-conserved molecular family, which play the key roles in the process of protein biosynthesis in plant life activities. In this study, we detected the evolutionary characteristics and phylogeny of chloroplast tRNAs in cotton plants, an economic and fibered important taxon in the world. We firstly annotated the chloroplast tRNAs of 27 Gossypium species to analyze their genetic composition, structural characteristics and evolution. Compared with the traditional view of evolutionary conservation of tRNA, some novel tRNA structural variations were identified in cotton plants. I.g., tRNAVal-UAC and tRNAIle-GAU only contained one intron in the anti-condon loop region of tRNA secondary structure, respectively. In the variable region, some tRNAs contained a circle structure with a few nucleotides. Interestingly, the calculation result of free energy indicated that the variation of novel tRNAs contributed to the stability of tRNA structure. Phylogenetic analysis suggested that chloroplast tRNAs have evolved from multiple common ancestors, and the tRNAMet seemed to be an ancestral tRNA, which can be duplicated and diversified to produce other tRNAs. The chloroplast tRNAs contained a group I intron in cotton plants, and the evolutionary analysis of introns indicated that group I intron of chloroplast tRNA originated from cyanobacteria. Analysis of gene duplication and loss events showed that gene loss events were more obvious than duplications in Gossypium chloroplast tRNAs. Additionally, we found that the rate of transition was higher than the ones of transversion in cotton chloroplast tRNAs. This study provided new insights into the structural characteristics and evolution of chloroplast tRNAs in cotton plants.
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Affiliation(s)
- Ning Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Wan-Lin Dong
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiao-Jing Zhang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tong Zhou
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiao-Juan Huang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jian-Ni Liu
- State Key Laboratory of Continental Dynamics, Department of Geology, Early Life Institute, Northwest University, Xi'an, 710069, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhong-Hu Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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Grover CE, Yuan D, Arick MA, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA. The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. G3 (BETHESDA, MD.) 2021; 11:jkab319. [PMID: 34549783 PMCID: PMC8527517 DOI: 10.1093/g3journal/jkab319] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/30/2021] [Indexed: 11/14/2022]
Abstract
Cotton is an important crop that has been the beneficiary of multiple genome sequencing efforts, including diverse representatives of wild species for germplasm development. Gossypium anomalum is a wild African diploid species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. In addition, this species is a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Here, we report a high-quality de novo genome assembly for G. anomalum and characterize this genome relative to existing genome sequences in cotton. In addition, we use the synthetic allopolyploids 2(A2D1) and 2(A2D3) to discover regions in the G. anomalum genome potentially involved in hybrid lethality, a possibility enabled by introgression of regions homologous to the D3 (Gossypium davidsonii) lethality loci into the synthetic 2(A2D3) allopolyploid.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, MS 39762, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Guanjing Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Shenzhen 518120, China
- Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, MS 39762, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Joshua A Udall
- USDA/Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845, USA
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Favorable pleiotropic loci for fiber yield and quality in upland cotton (Gossypium hirsutum). Sci Rep 2021; 11:15935. [PMID: 34354212 PMCID: PMC8342446 DOI: 10.1038/s41598-021-95629-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Upland cotton (Gossypium hirsutum L.) is an important economic crop for renewable textile fibers. However, the simultaneous improvement of yield and fiber quality in cotton is difficult as the linkage drag. Compared with breaking the linkage drag, identification of the favorable pleiotropic loci on the genome level by genome-wide association study (GWAS) provides a new way to improve the yield and fiber quality simultaneously. In our study restriction-site-associated DNA sequencing (RAD-seq) was used to genotype 316 cotton accessions. Eight major traits in three categories including yield, fiber quality and maturation were investigated in nine environments (3 sites × 3 years). 231 SNPs associated with these eight traits (− log10(P) > 5.27) were identified, located in 27 genomic regions respectively by linkage disequilibrium analysis. Further analysis showed that four genomic regions (the region 1, 6, 8 and 23) held favorable pleiotropic loci and 6 candidate genes were identified. Through genotyping, 14 elite accessions carrying the favorable loci on four pleiotropic regions were identified. These favorable pleiotropic loci and elite genotypes identified in this study will be utilized to improve the yield and fiber quality simultaneously in future cotton breeding.
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Zhang X, Xue Y, Guan Z, Zhou C, Nie Y, Men S, Wang Q, Shen C, Zhang D, Jin S, Tu L, Yin P, Zhang X. Structural insights into homotrimeric assembly of cellulose synthase CesA7 from Gossypium hirsutum. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1579-1587. [PMID: 33638282 PMCID: PMC8384604 DOI: 10.1111/pbi.13571] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 05/06/2023]
Abstract
Cellulose is one of the most abundant organic polymers in nature. It contains multiple β-1,4-glucan chains synthesized by cellulose synthases (CesAs) on the plasma membrane of higher plants. CesA subunits assemble into a pseudo-sixfold symmetric cellulose synthase complex (CSC), known as a 'rosette complex'. The structure of CesA remains enigmatic. Here, we report the cryo-EM structure of the homotrimeric CesA7 from Gossypium hirsutum at 3.5-angstrom resolution. The GhCesA7 homotrimer shows a C3 symmetrical assembly. Each protomer contains seven transmembrane helices (TMs) which form a channel potentially facilitating the release of newly synthesized glucans. The cytoplasmic glycosyltransferase domain (GT domain) of GhCesA7 protrudes from the membrane, and its catalytic pocket is directed towards the TM pore. The homotrimer GhCesA7 is stabilized by the transmembrane helix 7 (TM7) and the plant-conserved region (PCR) domains. It represents the building block of CSCs and facilitates microfibril formation. This structure provides insight into how eukaryotic cellulose synthase assembles and provides a mechanistic basis for the improvement of cotton fibre quality in the future.
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Affiliation(s)
- Xiangnan Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yuan Xue
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Chen Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yangfan Nie
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - She Men
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Cuicui Shen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
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Hong S, Lim YP, Kwon SY, Shin AY, Kim YM. Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:702243. [PMID: 34290729 PMCID: PMC8288248 DOI: 10.3389/fpls.2021.702243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/14/2021] [Indexed: 05/03/2023]
Abstract
In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.
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Affiliation(s)
- Seongmin Hong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yong-Min Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
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47
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Huang G, Huang JQ, Chen XY, Zhu YX. Recent Advances and Future Perspectives in Cotton Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:437-462. [PMID: 33428477 DOI: 10.1146/annurev-arplant-080720-113241] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cotton is not only the world's most important natural fiber crop, but it is also an ideal system in which to study genome evolution, polyploidization, and cell elongation. With the assembly of five different cotton genomes, a cotton-specific whole-genome duplication with an allopolyploidization process that combined the A- and D-genomes became evident. All existing A-genomes seemed to originate from the A0-genome as a common ancestor, and several transposable element bursts contributed to A-genome size expansion and speciation. The ethylene production pathway is shown to regulate fiber elongation. A tip-biased diffuse growth mode and several regulatory mechanisms, including plant hormones, transcription factors, and epigenetic modifications, are involved in fiber development. Finally, we describe the involvement of the gossypol biosynthetic pathway in the manipulation of herbivorous insects, the role of GoPGF in gland formation, and host-induced gene silencing for pest and disease control. These new genes, modules, and pathways will accelerate the genetic improvement of cotton.
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Affiliation(s)
- Gai Huang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin-Quan Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Xian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
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48
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Myo T, Wei F, Zhang H, Hao J, Zhang B, Liu Z, Cao G, Tian B, Shi G. Genome-wide identification of the BASS gene family in four Gossypium species and functional characterization of GhBASSs against salt stress. Sci Rep 2021; 11:11342. [PMID: 34059742 PMCID: PMC8166867 DOI: 10.1038/s41598-021-90740-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
Bile acid sodium symporter (BASS) family proteins encode a class of sodium/solute symporters. Even though the sodium transporting property of BASSs in mammals was well studied, their sodium transportability and functional roles in plant salt tolerance remained largely unknown. Here, BASS family members from 4 cotton species, as well as 30 other species were identified. Then, they were designated as members of BASS1 to BASS5 subfamilies according to their sequence similarity and phylogenetic relationships. There were 8, 11, 16 and 18 putative BASS genes in four cotton species. While whole-genome duplications (WGD) and segmental duplications rendered the expansion of the BASS gene family in cotton, BASS gene losses occurred in the tetraploid cotton during the evolution from diploids to allotetraploids. Concerning functional characterizations, the transcript profiling of GhBASSs revealed that they not only preferred tissue-specific expression but also were differently induced by various stressors and phytohormones. Gene silencing and overexpression experiments showed that GhBASS1 and GhBASS3 positively regulated, whereas GhBASS2, GhBASS4 and GhBASS5 negatively regulated plant salt tolerance. Taken together, BASS family genes have evolved before the divergence from the common ancestor of prokaryotes and eukaryotes, and GhBASSs are plastidial sodium-dependent metabolite co-transporters that can influence plant salt tolerance.
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Affiliation(s)
- Thwin Myo
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Fang Wei
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Honghao Zhang
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jianfeng Hao
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Bin Zhang
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhixian Liu
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Gangqiang Cao
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Baoming Tian
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Gongyao Shi
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
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Zhu G, Hou S, Song X, Wang X, Wang W, Chen Q, Guo W. Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum). BMC PLANT BIOLOGY 2021; 21:250. [PMID: 34059007 PMCID: PMC8167989 DOI: 10.1186/s12870-021-03009-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/05/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND Numerous quantitative trait loci (QTLs) and candidate genes associated with yield-related traits have been identified in cotton by genome-wide association study (GWAS) analysis. However, most of the phenotypic data were from a single or few environments, and the stable loci remained to be validated under multiple field environments. RESULTS Here, 242 upland cotton accessions collected from different origins were continuously investigated for phenotypic data of four main yield components, including boll weight (BW) and lint percentage (LP) under 13 field environments, and boll number per plant (BN) and seed index (SI) under 11 environments. Correlation analysis revealed a positive correlation between BN and LP, BW and SI, while SI had a negative correlation with LP and BN. Genetic analysis indicated that LP had the highest heritability estimates of 94.97%, followed by 92.08% for SI, 86.09% for BW, and 72.92% for BN, indicating LP and SI were more suitable traits for genetic improvement. Based on 56,010 high-quality single nucleotide polymorphisms (SNPs) and GWAS analysis, a total of 95 non-redundant QTLs were identified, including 12 of BN, 23 of BW, 45 of LP, and 33 of SI, respectively. Of them, 10 pairs of homologous QTLs were detected between A and D sub-genomes. We also found that 15 co-located QTLs with more than two traits and 12 high-confidence QTLs were detected under more than six environments, respectively. Further, two NET genes (GH_A08G0716 and GH_A08G0783), located in a novel QTL hotspot (qtl24, qtl25 and qlt26) were predominately expressed in early fiber development stages, exhibited significant correlation with LP and SI. The GH_A07G1389 in the stable qtl19 region encoded a tetratricopeptide repeat (TPR)-like superfamily protein and was a homologous gene involved in short fiber mutant ligon lintless-y (Liy), implying important roles in cotton yield. CONCLUSIONS The present study provides a foundation for understanding the regulatory mechanisms of yield components and may enhance yield improvement through molecular breeding in cotton.
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Affiliation(s)
- Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Sen Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaohui Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Xing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Wei Wang
- Institute of Agricultural Sciences in Coastal Area of Jiangsu Province, Yancheng, 224002 China
| | - Quanjia Chen
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
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Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes (Basel) 2021; 12:genes12060822. [PMID: 34071968 PMCID: PMC8228828 DOI: 10.3390/genes12060822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
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