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Zhou J, Wu Y, Zhang X, Zhao L, Feng Z, Wei F, Zhang Y, Feng H, Zhou Y, Zhu H. MPK homolog GhNTF6 was involved in cotton against Verticillium wilt by interacted with VdEPG1. Int J Biol Macromol 2022; 195:456-465. [PMID: 34920061 DOI: 10.1016/j.ijbiomac.2021.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/10/2021] [Accepted: 12/05/2021] [Indexed: 11/18/2022]
Abstract
Mitogen-activated protein kinases (MPKs) are important in regulating plant development and stress response. Rapid activation of MPKs in plants usually depends on its phosphorylated. In view of this situation, a phosphorylated GhNTF6 belonged to MPKs family was screened in cotton roots under Verticillium dahliae challenge by phosphoproteomics analysis. Expression of GhNTF6 in cotton plants was did not induce by V. dahliae infection, while, silencing GhNTF6 results to enhance cotton plants susceptibility to V. dahliae, overexpression - GhNTF6 enhance Arabidopsis plants survivability to V. dahliae. Moreover, the mutation of GhNTF6 at site Thr195 and Thy197 with the phosphorylation decreased the plant resistance to V. dahliae. Therefore, GhNTF6 phosphorylation is important in plants against V. dahliae. Further analysis demonstrated that GhNTF6 interacted with a V. dahliae endopolygalacturonase (VdEPG1) on the cell nucleus. We propose that GhNTF6 is a potential molecular target for improving resistance to Verticillium wilt in cotton.
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Affiliation(s)
- Jinglong Zhou
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Yajie Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xiaojian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yalin Zhang
- 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, Henan 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Yi Zhou
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China.
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lima LFD, Oliveira JOD, Carneiro JNP, Lima CNF, Coutinho HDM, Morais-Braga MFB. Ethnobotanical and antimicrobial activities of the Gossypium (Cotton) genus: A review. J Ethnopharmacol 2021; 279:114363. [PMID: 34216726 DOI: 10.1016/j.jep.2021.114363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The Malvaceae family, an important group of plants that have the Gossypium (cotton) genus has been used in folk medicine to treat microbial diseases and symptoms. AIMS OF THE STUDY This article aims to understand its ethnobotany expression in communities and scientific elucidation of antimicrobial activities of this genus through literature review. MATERIALS AND METHODS The bibliographic survey was carried out from 1999 to 2019 with keywords combinations such as "Gossypium + ethnobotanical", " Gossypium + medicinal ", "Gossypium + the biological activity" in scientific databases as Pubmed, Scopus, Web of Science, DOAJ, Scielo, Bireme. RESULTS After data analysis, we found that the Gossypium genus, specifically Gossypium hirsutum, G. barbadense, G. herbaceum, G. arboreum are the species most cited in the treatment of microbial diseases and symptoms in communities all over the world. In light of scientific elucidation of biological activities, the Gossypium genus has been used to treat protozoal, bacterial, fungal, and viral diseases. CONCLUSIONS The review demonstrated that the Gossypium genus is a promising source of biological activities against microbial diseases, especially in the treatment of protozoal diseases like malaria.
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Rehman A, Peng Z, Li H, Qin G, Jia Y, Pan Z, He S, Qayyum A, Du X. Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.). Int J Biol Macromol 2021; 184:1035-1061. [PMID: 34174315 DOI: 10.1016/j.ijbiomac.2021.06.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/31/2021] [Accepted: 06/16/2021] [Indexed: 12/25/2022]
Abstract
Calmodulin (CaM) is considered as the most significant Ca2+ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.
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Affiliation(s)
- Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China
| | - Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China
| | - Hongge Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China
| | - Guangyong Qin
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya university, Multan 66000, Pakistan
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China.
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Dai P, Sun G, Jia Y, Pan Z, Tian Y, Peng Z, Li H, He S, Du X. Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum). Theor Appl Genet 2020; 133:3273-3285. [PMID: 32844253 DOI: 10.1007/s00122-020-03668-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/08/2020] [Indexed: 05/06/2023]
Abstract
Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.
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Affiliation(s)
- Panhong Dai
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Gaofei Sun
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Computer Science & Information Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoe Pan
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yingbing Tian
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongge Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Shang X, Zhu L, Duan Y, Guo W. A cotton α1,3-/4-fucosyltransferase-encoding gene, FucT4, plays an important role in cell elongation and is significantly associated with fiber quality. Mol Genet Genomics 2020; 295:1141-1153. [PMID: 32462532 DOI: 10.1007/s00438-020-01687-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/11/2020] [Indexed: 11/25/2022]
Abstract
Fucosylation, one of the key posttranslational modifications, plays an important role in plants. It is involved in the development, signal transduction, reproduction, and disease resistance. α1,3-/4-Fucosyltransferase is responsible for transferring L-fucose from GDP-L-fucose to the N-glycan to exert fucosylational functions. However, the roles of the fucosyltransferase gene in cotton remain unknown. This study provided a comprehensive investigation of its possible functions. A genome-wide analysis identified four, four, eight, and eight FucT genes presented in the four sequenced cotton species, diploid Gossypium raimondii, G. arboreum, tetraploid G. hirsutum acc. TM-1, and G. barbadense cv. H7124, respectively. These FucTs were classified into two groups, with FucT4 homologs alone as a group. We isolated FucT4 in TM-1 and H7124, and named it GhFucT4 and GbFucT4, respectively. Quantitative RT-PCR and transcriptome data demonstrated that GhFucT4 had the highest expression levels in fibers among all GhFucT genes. Association studies and QTL co-localization supported the possible involvement of GhFucT4 in cotton fiber development. GhFucT4 and GbFucT4 shared high sequence identities, and FucT4 had higher expression in H7124 fiber tissues compared with TM-1. Furthermore, ectopic expression of FucT4 in transgenic Arabidopsis promoted root cell elongation, upregulated expression of genes related to cell wall loosening, and led to longer primary root. These results collectively indicate that FucT4 plays an important role in promoting cell elongation and modulating fiber development, which could be utilized to improve fiber quality traits in cotton breeding.
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Affiliation(s)
- Xiaoguang Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijie Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yujia Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
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Yu J, Xie Q, Li C, Dong Y, Zhu S, Chen J. Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium. Planta 2020; 251:81. [PMID: 32185507 DOI: 10.1007/s00425-020-03364-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/13/2020] [Indexed: 05/16/2023]
Abstract
A comprehensive account of the LBD gene family of Gossypium was provided in this work. Expression analysis and functional characterization revealed that LBD genes might play different roles in G. hirsutum and G. barbadense. The Lateral Organ Boundaries Domain (LBD) proteins comprise a plant-specific transcription factor family, which plays crucial roles in physiological processes of plant growth, development, and stress tolerance. In the present work, a systematical analysis of LBD gene family from two allotetraploid cotton species, G. hirsutum and G. barbadense, together with their genomic donor species, G. arboreum and G. raimondii, was conducted. There were 131, 128, 62, and 68 LBDs identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. The LBD proteins could be classified into two main classes, class I and class II, based on the structure of their lateral organ boundaries domain and traits of phylogenetic tree, and class I was further divided into five subgroups. The gene structure and motif composition analyses conducted in both G. hirsutum and G. barbadense revealed that LBD genes kept relatively conserved within the subfamilies. Synteny analysis suggested that segmental duplication acted as an important mechanism in expansion of the cotton LBD gene family. Cis-element analysis predicated the possible functions of LBD genes. Public RNA-seq data were investigated to analyze the expression patterns of cotton LBD genes in various tissues as well as gene expression under abiotic stress treatments. Furthermore, RT-qPCR results found that GhLBDs had various expression regulation under MeJA treatments. Expression analysis indicated the differential functions of cotton LBD genes in response to abiotic stress and hormones.
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Affiliation(s)
- Jingwen Yu
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qianwen Xie
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Li
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yating Dong
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shuijin Zhu
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Jinhong Chen
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Hu W, Huang Y, Loka DA, Bai H, Liu Y, Wang S, Zhou Z. Drought-induced disturbance of carbohydrate metabolism in anthers and male abortion of two Gossypium hirsutum cultivars differing in drought tolerance. Plant Cell Rep 2020; 39:195-206. [PMID: 31680208 DOI: 10.1007/s00299-019-02483-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Cotton pollen abortion, under drought stress, was closely associated with changes in anther carbohydrate metabolism, and pollen abortion rate due to drought was higher in drought-sensitive cultivars than drought-tolerant cultivars. Cotton reproductive failure under drought stress is intrinsically connected with altered male fertility, however, studies investigating the effect of drought stress on cotton male fertility are nonexistent. Thus, a drought stress experiment was conducted with two cotton cultivars, differing in drought tolerance, to study pollen fertility and anthers' physiology. Results indicated that drought stress reduced pollen fertility of both cultivars due to decreases in anther starch and adenosine triphosphate (ATP) synthesis. Lower assimilate supply capacity in conjunction with impaired activities of ADP-glucose pyrophosphorylase and soluble starch synthase were the main reasons for the decreased starch levels in drought-stressed anthers. The decreased activities of sucrose synthetase and acid invertase were responsible for the higher sucrose level in drought-stressed anthers than well-watered anthers and the changing trend of sucrose was intensified by the decreased expressions of sucrose synthase genes (GhSusA, GhSusB, GhSusD) and acid invertase genes (GhINV1, GhINV2). However, despite sucrose degradation being limited in drought-stressed anthers, glucose level was higher in droughted anthers than well-watered ones, and that might be attributed to the down-regulated respiration since decreased anther ATP levels were detected in drought-stressed plants. Furthermore, compared to the drought-tolerant cultivar, pollen fertility was more suppressed by drought stress for the drought-sensitive cultivar, and that was attributed to the larger decrease in starch and ATP contents.
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Affiliation(s)
- Wei Hu
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yanjun Huang
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dimitra A Loka
- Institute of Industrial and Forage Crops, Hellenic Agricultural Organization, 41335, Larissa, Greece
| | - Hua Bai
- School of Agricultural Sciences, Northwest Missouri State University, Maryville, MO, 64468, USA
| | - Yu Liu
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shanshan Wang
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiguo Zhou
- College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
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Ma J, Pei W, Ma Q, Geng Y, Liu G, Liu J, Cui Y, Zhang X, Wu M, Li X, Li D, Zang X, Song J, Tang S, Zhang J, Yu S, Yu J. QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense. Theor Appl Genet 2019; 132:2663-2676. [PMID: 31236630 DOI: 10.1007/s00122-019-03380-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/14/2019] [Indexed: 05/24/2023]
Abstract
We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27-14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
- College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Wenfeng Pei
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830001, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Yanhui Geng
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Yupeng Cui
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Xia Zhang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Xingli Li
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Dan Li
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - XinShan Zang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Shurong Tang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.
- College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.
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Shen C, Wang N, Huang C, Wang M, Zhang X, Lin Z. Population genomics reveals a fine-scale recombination landscape for genetic improvement of cotton. Plant J 2019; 99:494-505. [PMID: 31002209 DOI: 10.1111/tpj.14339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/17/2019] [Accepted: 04/01/2019] [Indexed: 05/28/2023]
Abstract
Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population-scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population-scaled recombination rate between Gossypium hirsutum and G. arboreum and sub-genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome-wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high-recombination regions than were those of yield and early maturity traits. These results provide insights into the population-scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.
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Affiliation(s)
- Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Yang W, Yu M, Zou C, Lu C, Yu D, Cheng H, Jiang P, Feng X, Zhang Y, Wang Q, Zhang H, Song G, Zhou Z. Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii. PLoS One 2019; 14:e0218938. [PMID: 31242257 PMCID: PMC6594650 DOI: 10.1371/journal.pone.0218938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/12/2019] [Indexed: 11/18/2022] Open
Abstract
RB-GRP (RNA-binding Glycine-rich protein gene) family belongs to the fourth subfamily of the GRP (Glycine-rich protein gene) superfamily, which plays a great role in plant growth and development, as well as in abiotic stresses response, while it has not been identified in cotton. Here, we identified 37 and 32 RB-GRPs from two cotton species (Gossypium arboreum and Gossypium raimondii, respectively), which were divided into four distinct subfamilies based on the presence of additional motifs and the arrangement of the glycine repeats. The distribution of RB-GRPs was nonrandom and uneven among the chromosomes both in two cotton species. The expansion of RB-GRP gene family between two cultivars was mainly attributed to segmental and tandem duplication events indicated by synteny analysis, and the tandem duplicated genes were mapped into homologous collinear blocks, indicated that they shared a common ancestral gene in both species. Furthermore, most RB-GRPs in two cotton species undergone stronger negative selective pressure by evolutionary analysis of RB-GRP orthologous genes. Meanwhile, RB-GRPs participated in different abiotic stresses (Abscisic acid, salt and Polyethylene glycol) responses and tissues at different developmental stages between two cotton species were showed by gene expression analysis. This research would provide insight into the evolution and function of the RB-GRPs in Gossypium species.
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Affiliation(s)
- Wencui Yang
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Min Yu
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changsong Zou
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Cairui Lu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Daoqian Yu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pengfei Jiang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hong Zhang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
- * E-mail: (GS); (ZZ)
| | - Zhuqing Zhou
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (GS); (ZZ)
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Lu Y, Chen W, Zhao L, Yao J, Li Y, Yang W, Liu Z, Zhang Y, Sun J. Different divergence events for three pairs of PEBPs in Gossypium as implied by evolutionary analysis. Genes Genomics 2019; 41:445-458. [PMID: 30610620 DOI: 10.1007/s13258-018-0775-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/06/2018] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The phosphatidylethanolamine-binding protein (PEBP) gene family plays a crucial role in seed germination, reproductive transformation, and other important developmental processes in plants, but its distribution in Gossypium genomes or species, evolutionary properties, and the fates of multiple duplicated genes remain unclear. OBJECTIVES The primary objectives of this study were to elucidate the distribution and characteristics of PEBP genes in Gossypium, as well as the evolutionary pattern of duplication and deletion, and functional differentiation of PEBPs in plants. METHODS Using the PEBP protein sequences in Arabidopsis thaliana as queries, blast alignment was carried out for the identification of PEBP genes in four sequenced cotton species. Using the primers designed according to the PEBP genome sequences, PEBP genes were cloned from 15 representative genomes of Gossypium genus, and the gene structure, CDS sequence, protein sequence and properties were predicted and phylogenetic analysis was performed. Taking PEBP proteins of grape as reference, grouping of orthologous gene, analysis of phylogeny and divergence of PEBPs in nine species were conducted to reconstruct the evolutionary pattern of PEBP genes in plants. RESULTS We identified and cloned 160 PEBPs from 15 cotton species, and the phylogenetic analysis showed that the genes could be classified into the following three subfamilies: MFT-like, FT-like and TFL1-like. There were eight single orthologous group (OG) members in each diploid and 16 double OG members in each tetraploid. An analysis of the expression and selective pressure indicated that expression divergence and strong purification selection within the same OG presented in the PEBP gene family. CONCLUSION An evolutionary pattern of duplication and deletion of the PEBP family in the evolutionary history of Gossypium was suggested, and three pairs of genes resulted from different whole-genome duplication events.
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Affiliation(s)
- Youjun Lu
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Huanghe Road, Anyang, 455000, Henan, China
| | - Wei Chen
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Jinbo Yao
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yan Li
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Weijun Yang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Huanghe Road, Anyang, 455000, Henan, China
| | - Ziyang Liu
- University of Saskatchewan, Saskatoon, SK, S7N 5A5, Canada
| | - Yongshan Zhang
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
| | - Jie Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China.
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13
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Li P, Xue Y, Shi J, Pan A, Tang X, Ming F. The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties. Microbiome 2018; 6:184. [PMID: 30336777 PMCID: PMC6194802 DOI: 10.1186/s40168-018-0570-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/02/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear. RESULTS We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content. CONCLUSIONS In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.
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Affiliation(s)
- Peng Li
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Yong Xue
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jialiang Shi
- Dezhou Academy of Agricultural Sciences, Dezhou, 253000, China
| | - Aihu Pan
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Xueming Tang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Feng Ming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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14
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Zhang Z, Zou X, Huang Z, Fan S, Qun G, Liu A, Gong J, Li J, Gong W, Shi Y, Fan L, Zhang Z, Liu R, Jiang X, Lei K, Shang H, Xu A, Yuan Y. Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus. Gene 2018; 680:72-83. [PMID: 30253181 DOI: 10.1016/j.gene.2018.09.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/28/2018] [Accepted: 09/21/2018] [Indexed: 12/30/2022]
Abstract
GATA transcription factors (TFs), which bind to DNA in regulatory regions, are involved in cell differentiation and possess a type-IV zinc finger and a DNA-binding domain. GATA genes have been characterized in plant species such as Arabidopsis thaliana, Oryza sativa, and Glycine max, and their functions have been elucidated in A. thaliana. Although many Gossypium quantitative trait loci for fiber quality harbor GATA TFs, GATA genes have not yet been characterized in cotton. In this study, we identified 179 GATA genes from the genomes of three Gossypium species. We analyzed the phylogenetic relationships, chromosomal distribution, gene structure, expression pattern, and predicted promoters of all 179 Gossypium GATA genes (46 in G. raimondii, 46 in G. arboreum, and 87 in G. hirsutum). Phylogenetic analysis grouped the 179 GATA genes into four subfamilies. Domain analysis revealed that GATA domains in subfamilies I, II, and III were located near the C-terminal, whereas those in subfamily IV were adjacent to the N-terminal. RNA-seq and (Real-time PCR) qRT-PCR revealed that 39.1% (34/87) of GATA genes were expressed in growing plant tissues in G. hirsutum, but only 12.6% (11/87) were expressed during fiber development. In addition, 45.7% (21/46) and 26.1% (12/46) of GATA genes were expressed in G. arboreum and G. raimondii, respectively. Our results may be useful for elucidating the evolution, expression patterns, and functional divergence of GATA genes in Gossypium.
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Affiliation(s)
- Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xianyan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ge Qun
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Liqiang Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhibin Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ruixian Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Kang Lei
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Yuan N, Rai KM, Balasubramanian VK, Upadhyay SK, Luo H, Mendu V. Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum). BMC Plant Biol 2018; 18:185. [PMID: 30189845 PMCID: PMC6128003 DOI: 10.1186/s12870-018-1395-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/27/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND As one of the largest subfamilies of the receptor-like protein kinases (RLKs) in plants, Leucine Rich Repeats-RLKs (LRR-RLKs) are involved in many critical biological processes including growth, development and stress responses in addition to various physiological roles. Arabidopsis contains 234 LRR-RLKs, and four members of Stress Induced Factor (SIF) subfamily (AtSIF1-AtSIF4) which are involved in abiotic and biotic stress responses. Herein, we aimed at identification and functional characterization of SIF subfamily in cultivated tetraploid cotton Gossypium hirsutum. RESULTS Genome-wide analysis of cotton LRR-RLK gene family identified 543 members and phylogenetic analysis led to the identification of 6 cotton LRR-RLKs with high homology to Arabidopsis SIFs. Of the six SIF homologs, GhSIF1 is highly conserved exhibiting 46-47% of homology with AtSIF subfamily in amino acid sequence. The GhSIF1 was transiently silenced using Virus-Induced Gene Silencing system specifically targeting the 3' Untranslated Region. The transiently silenced cotton seedlings showed enhanced salt tolerance compared to the control plants. Further, the transiently silenced plants showed better growth, lower electrolyte leakage, and higher chlorophyll and biomass contents. CONCLUSIONS Overall, 543 LRR-RLK genes were identified using genome-wide analysis in cultivated tetraploid cotton G. hirsutum. The present investigation also demonstrated the conserved salt tolerance function of SIF family member in cotton. The GhSIF1 gene can be knocked out using genome editing technologies to improve salt tolerance in cotton.
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Affiliation(s)
- Ning Yuan
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Krishan Mohan Rai
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Vimal Kumar Balasubramanian
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | | | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
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16
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Hasan MMU, Ma F, Prodhan ZH, Li F, Shen H, Chen Y, Wang X. Molecular and Physio-Biochemical Characterization of Cotton Species for Assessing Drought Stress Tolerance. Int J Mol Sci 2018; 19:E2636. [PMID: 30200561 PMCID: PMC6163957 DOI: 10.3390/ijms19092636] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 01/24/2023] Open
Abstract
Drought stress significantly limits cotton growth and production due to the necessity of water at every stage of crop growth. Hence, it is essential to identify tolerant genetic resources and understand the mechanisms of drought tolerance in economically and socially important plants such as cotton. In this study, molecular and physio-biochemical investigations were conducted by analyzing different parameters by following standard protocols in three different cotton species, namely TM-1 (Gossypium hirsutum), Zhongmian-16 (Gossypium arboreum), and Pima4-S (Gossypium barbadense). Drought stress significantly decreased plant growth, chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), maximum photochemical efficiency of PSII (Fv/Fm), and relative water content. TM-1 resulted in more tolerance than the other two species. The accumulation of proline, soluble proteins, soluble sugars, hydrogen peroxide (H₂O₂), and superoxide radicals (O₂•-) increased significantly in TM-1. In addition, TM-1 maintained the integrity of the chloroplast structure under drought conditions. The relative expression level of drought-responsive genes including coding for transcription factors and other regulatory proteins or enzymes controlling genes (ERF, ERFB, DREB, WRKY6, ZFP1, FeSOD, CuZnSOD, MAPKKK17, P5CR, and PRP5) were higher in TM-1 under drought, conferring a more tolerant status than in Zhongmian-16 and Pima4-S. The findings of this research could be utilized for predicting a tolerant cotton genotype as well as evaluating prospective cotton species in the variety development program.
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Affiliation(s)
- Md Mosfeq-Ul Hasan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
- Examination Control Section, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh.
| | - Fanglu Ma
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Zakaria Hossain Prodhan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Feng Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Hao Shen
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Yadong Chen
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Xuede Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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17
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Seyoum M, Du XM, He SP, Jia YH, Pan Z, Sun JL. Analysis of genetic diversity and population structure in upland cotton ( Gossypium hirsutum L.) germplasm using simple sequence repeats. J Genet 2018; 97:513-522. [PMID: 29932072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Improvement of cotton fibre yield and quality is challenging due to the narrow genetic base of modern cotton cultivars, which emphasizes the great need to effectively explore the existing germplasm resources. With major objective to assess the genetic diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions (253 Chinese and 49 different exotic origins), were genotyped using 198 simple sequence repeats (SSRs) markers. Each of the 198 markers differed greatly in its ability to detect variations in the panel of cotton germplasm. The SSRs amplified 897 alleles, of which 77.7% were polymorphic. The number of alleles varied from 2 to 12 (mean 4.53). Gene diversity ranged from 0.020 to 0.492 with a mean of 0.279. The polymorphic information content (PIC) values ranged from 0.371 to 0.019 (mean 0.225). Genetic distances in the whole cotton germplasm ranged from 0.451 to 0.052 (mean 0.270), demonstrating relatively wider genetic diversity range. Chinese-origin cotton germplasm showed the highest level of SSR polymorphisms (gene diversity=0.268, PIC=0.218), whereas American-origin revealed the highest mean genetic distance (0.274). Model-based Bayesian analysis clustered the whole cotton germplasm into three subpopulations, and the highest molecular variation ws revealed between subpopulations (4%, P<0.001). The SSRs revealed moderate level of genetic diversity at DNA level, identified three structured subpopulations, suggesting a potential use of these markers for genomewide association mapping studies and for identifying and conserving useful alleles in upland cotton germplasm.
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Affiliation(s)
- Mulugeta Seyoum
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia. mulugeta.
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18
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Chen W, Si GY, Zhao G, Abdullah M, Guo N, Li DH, Sun X, Cai YP, Lin Y, Gao JS. Genomic Comparison of the P-ATPase Gene Family in Four Cotton Species and Their Expression Patterns in Gossypium hirsutum. Molecules 2018; 23:molecules23051092. [PMID: 29734726 PMCID: PMC6102550 DOI: 10.3390/molecules23051092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 11/21/2022] Open
Abstract
Plant P-type H+-ATPase (P-ATPase) is a membrane protein existing in the plasma membrane that plays an important role in the transmembrane transport of plant cells. To understand the variety and quantity of P-ATPase proteins in different cotton species, we combined four databases from two diploid cotton species (Gossypium raimondii and G. arboreum) and two tetraploid cotton species (G. hirsutum and G. barbadense) to screen the P-ATPase gene family and resolved the evolutionary relationships between the former cotton species. We identified 53, 51, 99 and 98 P-ATPase genes from G. arboretum, G. raimondii, G. barbadense and G. hirsutum, respectively. The structural and phylogenetic analyses revealed that the gene structure was consistent between P-ATPase genes, with a close evolutionary relationship. The expression analysis of P-ATPase genes showed that many P-ATPase genes were highly expressed in various tissues and at different fiber developmental stages in G. hirsutum, suggesting that they have potential functions during growth and fiber development in cotton.
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Affiliation(s)
- Wen Chen
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Guo-Yang Si
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Gang Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Ning Guo
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Da-Hui Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Xu Sun
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Yong-Ping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Jun-Shan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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19
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Wang L, Xing H, Yuan Y, Wang X, Saeed M, Tao J, Feng W, Zhang G, Song X, Sun X. Genome-wide analysis of codon usage bias in four sequenced cotton species. PLoS One 2018; 13:e0194372. [PMID: 29584741 PMCID: PMC5870960 DOI: 10.1371/journal.pone.0194372] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/01/2018] [Indexed: 01/06/2023] Open
Abstract
Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.
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Affiliation(s)
- Liyuan Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Huixian Xing
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Yanchao Yuan
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Xianlin Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Muhammad Saeed
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Jincai Tao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Wei Feng
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Guihua Zhang
- Heze Academy of Agricultural Sciences, Heze, China
| | - Xianliang Song
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
- * E-mail: (XSO); (XSU)
| | - Xuezhen Sun
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
- * E-mail: (XSO); (XSU)
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20
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Li W, Ren Z, Wang Z, Sun K, Pei X, Liu Y, He K, Zhang F, Song C, Zhou X, Zhang W, Ma X, Yang D. Evolution and Stress Responses of Gossypium hirsutum SWEET Genes. Int J Mol Sci 2018; 19:E769. [PMID: 29517986 PMCID: PMC5877630 DOI: 10.3390/ijms19030769] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
The SWEET (sugars will eventually be exported transporters) proteins are sugar efflux transporters containing the MtN3_saliva domain, which affects plant development as well as responses to biotic and abiotic stresses. These proteins have not been functionally characterized in the tetraploid cotton, Gossypium hirsutum, which is a widely cultivated cotton species. In this study, we comprehensively analyzed the cotton SWEET gene family. A total of 55 putative G. hirsutumSWEET genes were identified. The GhSWEET genes were classified into four clades based on a phylogenetic analysis and on the examination of gene structural features. Moreover, chromosomal localization and an analysis of homologous genes in Gossypium arboreum, Gossypium raimondii, and G. hirsutum suggested that a whole-genome duplication, several tandem duplications, and a polyploidy event contributed to the expansion of the cotton SWEET gene family, especially in Clade III and IV. Analyses of cis-acting regulatory elements in the promoter regions, expression profiles, and artificial selection revealed that the GhSWEET genes were likely involved in cotton developmental processes and responses to diverse stresses. These findings may clarify the evolution of G. hirsutum SWEET gene family and may provide a foundation for future functional studies of SWEET proteins regarding cotton development and responses to abiotic stresses.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhenyu Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kuan Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Chengxiang Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaojian Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Wensheng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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21
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Gu L, Li L, Wei H, Wang H, Su J, Guo Y, Yu S. Identification of the group IIa WRKY subfamily and the functional analysis of GhWRKY17 in upland cotton (Gossypium hirsutum L.). PLoS One 2018; 13:e0191681. [PMID: 29370286 PMCID: PMC5784973 DOI: 10.1371/journal.pone.0191681] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
WRKY transcription factors play important roles in plant defense, stress response, leaf senescence, and plant growth and development. Previous studies have revealed the important roles of the group IIa GhWRKY genes in cotton. To comprehensively analyze the group IIa GhWRKY genes in upland cotton, we identified 15 candidate group IIa GhWRKY genes in the Gossypium hirsutum genome. The phylogenetic tree, intron-exon structure, motif prediction and Ka/Ks analyses indicated that most group IIa GhWRKY genes shared high similarity and conservation and underwent purifying selection during evolution. In addition, we detected the expression patterns of several group IIa GhWRKY genes in individual tissues as well as during leaf senescence using public RNA sequencing data and real-time quantitative PCR. To better understand the functions of group IIa GhWRKYs in cotton, GhWRKY17 (KF669857) was isolated from upland cotton, and its sequence alignment, promoter cis-acting elements and subcellular localization were characterized. Moreover, the over-expression of GhWRKY17 in Arabidopsis up-regulated the senescence-associated genes AtWRKY53, AtSAG12 and AtSAG13, enhancing the plant’s susceptibility to leaf senescence. These findings lay the foundation for further analysis and study of the functions of WRKY genes in cotton.
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Affiliation(s)
- Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
| | - Junji Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
| | - Yaning Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
- * E-mail:
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22
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Magwanga RO, Lu P, Kirungu JN, Lu H, Wang X, Cai X, Zhou Z, Zhang Z, Salih H, Wang K, Liu F. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet 2018; 19:6. [PMID: 29334890 PMCID: PMC5769447 DOI: 10.1007/s11033-012-2250-3fang 10.1186/s12863-017-0596-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/29/2017] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally. RESULTS In this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant genotypes have a greater ability to modulate genes under drought stress than the more susceptible upland cotton cultivars. CONCLUSION The finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress.
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Affiliation(s)
- Richard Odongo Magwanga
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
- School of physical and biological sciences (SPBS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Pu Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Joy Nyangasi Kirungu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Hejun Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Xingxing Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Xiaoyan Cai
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Zhongli Zhou
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Zhenmei Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
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23
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Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biol Evol 2017; 9:3328-3344. [PMID: 29194487 PMCID: PMC5737505 DOI: 10.1093/gbe/evx248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium. In addition, we explore processes underlying the genome downsizing that characterizes Kokia and Gossypioides relative to other genera in the tribe. Using 13,000 gene orthologs and synonymous substitution rates, we show that the two disjuncts last shared a common ancestor ∼5 Ma, or half as long ago as their divergence from Gossypium. We report relative stasis in the transposable element fraction. In comparison to Gossypium, there is loss of ∼30% of the gene content in the two disjunct genera and a history of genome-wide accumulation of deletions. In both genera, there is a genome-wide bias toward deletions over insertions, and the number of gene losses exceeds the number of gains by ∼2- to 4-fold. The genomic analyses presented here elucidate genomic consequences of the demographic and biogeographic history of these closest relatives of Gossypium, and enhance their value as phylogenetic outgroups.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
- Department of Computer Science & Engineering, Mississippi State University, Mississippi State, MS
- The Jackson Laboratory, Connecticut, Farmington, CT
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico
| | | | - Joshua A Udall
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
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Chandnani R, Wang B, Draye X, Rainville LK, Auckland S, Zhuang Z, Lubbers EL, May OL, Chee PW, Paterson AH. Segregation distortion and genome-wide digenic interactions affect transmission of introgressed chromatin from wild cotton species. Theor Appl Genet 2017; 130:2219-2230. [PMID: 28801756 DOI: 10.1007/s00122-017-2952-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species. From an interspecific cross, Gossypium hirsutum × Gossypium mustelinum, we studied G. mustelinum (the most distant tetraploid relative of Upland cotton) allele retention in 35 BC3F1 plants and segregation patterns in BC3F2 populations totaling 3202 individuals, using 216 DNA marker loci. The average retention of donor alleles across BC3F1 plants was higher than expected and the average frequency of G. mustelinum alleles in BC3F2 segregating families was less than expected. Despite surprisingly high retention of G. mustelinum alleles in BC3F1, 46 genomic regions showed no introgression. Regions on chromosomes 3 and 15 lacking introgression were closely associated with possible small inversions previously reported. Nonlinear two-locus interactions are abundant among loci with single-locus segregation distortion, and among loci originating from one of the two subgenomes. Comparison of the present results with those of prior studies indicates different permeability of Upland cotton for donor chromatin from different allotetraploid relatives. Different contributions of subgenomes to two-locus interactions suggest different fates of subgenomes in the evolution of allotetraploid cottons. Transmission genetics of G. hirsutum × G. mustelinum crosses reveals allelic interactions, constraints on fixation and selection of donor alleles, and challenges with retention of introgressed chromatin for crop improvement.
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Affiliation(s)
- Rahul Chandnani
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Baohua Wang
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Xavier Draye
- Unité d'écophysiologie et amélioration végétale, Université Catholique de Louvain, Croix du Sud 1-10, 1348, Louvain-la-Neuve, Belgium
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Susan Auckland
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Zhimin Zhuang
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Edward L Lubbers
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
| | - O Lloyd May
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
- Monsanto Cotton Breeding, Tifton, GA, 31793, USA
| | - Peng W Chee
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA.
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25
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Song W, Wang M, Su W, Lu Q, Xiao X, Cai J, Zhang Z, Li S, Li P, Gong J, Gong W, Shang H, Liu A, Li J, Chen T, Ge Q, Shi Y, Yuan Y. Genetic and phenotypic effects of chromosome segments introgressed from Gossypium barbadense into Gossypium hirsutum. PLoS One 2017; 12:e0184882. [PMID: 28931074 PMCID: PMC5607130 DOI: 10.1371/journal.pone.0184882] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/03/2017] [Indexed: 01/30/2023] Open
Abstract
MBI9915 is an introgression cotton line with excellent fiber quality. It was obtained by advanced backcrossing and continuous inbreeding from an interspecific cross between the upland cotton (Gossypium hirsutum) cultivar CCRI36 as the recurrent parent and the sea island cotton (G. barbadense) cultivar Hai1, as the donor parent. To study the genetic effects of the introgressed chromosome segments in G. hirsutum, an F2 secondary segregating population of 1537 individuals was created by crossing MBI9915 and CCRI36, and an F2:3 population was created by randomly selecting 347 individuals from the F2 generation. Quantitative trait locus (QTL) mapping and interaction for fiber length and strength were identified using IciMapping software. The genotype analysis showed that the recovery rate for MBI9915 was 97.9%, with a total 6 heterozygous segments and 13 homozygous segments. A total of 18 QTLs for fiber quality and 6 QTLs for yield related traits were detected using the two segregating generations. These QTLs were distributed across 7 chromosomes and collectively explained 0.81%–9.51% of the observed phenotypic variations. Six QTLs were consistently detected in two generations and 6 QTLs were identified in previous studies. A total of 13 pairs of interaction for fiber length and 13 pairs of interaction for fiber strength were identified in two generations. Among them, 3 pairs of interaction for fiber length and 3 pairs of interaction for fiber strength could be identified in all generations; 4 pairs of interactions affected fiber length and fiber strength simultaneously. The results clearly showed that 5 chromosome segments (Seg-5-1, Seg-7-1, Seg-8-1, Seg-20-2 and Seg-20-3) have important effects on fiber yield and quality. This study provides the useful information for gene cloning and marker-assisted breeding for excellent fiber related quality.
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Affiliation(s)
- Weiwu Song
- 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, Henan, China
- Enshi Academy of Agricultural Sciences. Enshi, Hubei, China
| | - Mi Wang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Wei Su
- 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, Henan, China
| | - Quanwei Lu
- 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, Henan, China
| | - Xianghui Xiao
- 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, Henan, China
| | - Juan Cai
- 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, Henan, China
- Enshi Academy of Agricultural Sciences. Enshi, Hubei, China
| | - Zhen Zhang
- 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, Henan, China
| | - Shaoqi Li
- 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, Henan, China
| | - Pengtao Li
- 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, Henan, China
| | - Juwu Gong
- 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, Henan, China
| | - Wankui Gong
- 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, Henan, 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, Henan, China
| | - Aiying Liu
- 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, Henan, China
| | - Junwen Li
- 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, Henan, China
| | - Tingting Chen
- 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, Henan, 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, Henan, 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, Henan, China
- * E-mail: (YZS); (YLY)
| | - 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, Henan, China
- * E-mail: (YZS); (YLY)
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Liu Y, Kim HJ. Characterization of Developmental Immature Fiber ( im) Mutant and Texas Marker-1 (TM-1) Cotton Fibers Using Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy. Appl Spectrosc 2017; 71:1689-1695. [PMID: 28106475 DOI: 10.1177/0003702816684639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The immature fiber ( im) mutant is one type of cotton fiber mutant with unique characteristics of non-fluffy cotton bolls. Compared to its near-isogenic wild type Texas Marker-1 (TM-1), im fiber has a thin secondary cell wall and is less mature. In this work, we applied the previously proposed principal component analysis (PCA) and simple algorithms to analyze the attenuated total reflection Fourier transform infrared (ATR FT-IR) spectra of developmental im and TM-1 fibers. The results from these approaches could not effectively and consistently indicate the inherent difference between TM-1 and im fibers at the same developmental stage. The difference between TM-1 and corresponding im fibers was detected when comparing the normalized intensity variations of the 730 cm-1 bands. The 730 cm-1 band intensities in developmental im fibers are temporally lower than those in developmental TM-1 fibers although they became similar when the TM-1 and im fibers are fully mature. The observation might imply the likelihood of temporal reduction of amorphous regions in developmental im fibers rather than in developmental TM-1 fibers.
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Affiliation(s)
- Yongliang Liu
- 1 USDA, ARS, Cotton Structure & Quality Research Unit, Southern Regional Research Center (SRRC), New Orleans, LA, USA
| | - Hee-Jin Kim
- 2 USDA, ARS, Cotton Fiber Bioscience Research Unit, Southern Regional Research Center (SRRC), New Orleans, LA, USA
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27
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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28
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Xu J, Xu X, Tian L, Wang G, Zhang X, Wang X, Guo W. Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton. Sci Rep 2016; 6:29022. [PMID: 27354165 PMCID: PMC4926273 DOI: 10.1038/srep29022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/14/2016] [Indexed: 12/02/2022] Open
Abstract
Verticillium dahliae, a destructive and soil-borne fungal pathogen, causes massive losses in cotton yields. However, the resistance mechanism to V. dahilae in cotton is still poorly understood. Accumulating evidence indicates that chitinases are crucial hydrolytic enzymes, which attack fungal pathogens by catalyzing the fungal cell wall degradation. As a large gene family, to date, the chitinase genes (Chis) have not been systematically analyzed and effectively utilized in cotton. Here, we identified 47, 49, 92, and 116 Chis from four sequenced cotton species, diploid Gossypium raimondii (D5), G. arboreum (A2), tetraploid G. hirsutum acc. TM-1 (AD1), and G. barbadense acc. 3-79 (AD2), respectively. The orthologous genes were not one-to-one correspondence in the diploid and tetraploid cotton species, implying changes in the number of Chis in different cotton species during the evolution of Gossypium. Phylogenetic classification indicated that these Chis could be classified into six groups, with distinguishable structural characteristics. The expression patterns of Chis indicated their various expressions in different organs and tissues, and in the V. dahliae response. Silencing of Chi23, Chi32, or Chi47 in cotton significantly impaired the resistance to V. dahliae, suggesting these genes might act as positive regulators in disease resistance to V. dahliae.
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Affiliation(s)
- Jun Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyang Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangliang Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Guilin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
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29
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Yang JS, Hu W, Zhao W, Meng Y, Chen B, Wang Y, Zhou Z. Soil Potassium Deficiency Reduces Cotton Fiber Strength by Accelerating and Shortening Fiber Development. Sci Rep 2016; 6:28856. [PMID: 27350236 PMCID: PMC4924092 DOI: 10.1038/srep28856] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 06/10/2016] [Indexed: 11/24/2022] Open
Abstract
Low potassium (K)-induced premature senescence in cotton has been observed worldwide, but how it affects cotton fiber properties remain unclear. We hypothesized that K deficiency affects cotton fiber properties by causing disordered fiber development, which may in turn be caused by the induction of a carbohydrate acquisition difficulty. To investigate this issue, we employed a low-K-sensitive cotton cultivar Siza 3 and a low-K-tolerant cultivar Simian 3 and planted them in three regions of different K supply. Data concerning lint yield, Pn and main fiber properties were collected from three years of testing. Soil K deficiency significantly accelerated fiber cellulose accumulation and dehydration processes, which, together with previous findings, suggests that the low-K induced carbohydrate acquisition difficulty could cause disordered fiber development by stimulating the expression of functional proteins such as CDKA (cyclin-dependent kinase). As a result, fiber strength and lint weight were reduced by up to 7.8% and 2.1%, respectively. Additional quantitative analysis revealed that the degree of accelerated fiber development negatively correlated with fiber strength. According to the results of this study, it is feasible to address the effects of soil K deficiency on fiber properties using existing cultivation strategies to prevent premature senescence of cotton plants.
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Affiliation(s)
- Jia-Shuo Yang
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Wei Hu
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Wenqing Zhao
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Yali Meng
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Binglin Chen
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Youhua Wang
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Zhiguo Zhou
- Key Laboratory of Crop Physiology & Ecology, Department of Agronomy, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
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30
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Egamberdiev SS, Saha S, Salakhutdinov I, Jenkins JN, Deng D, Y Abdurakhmonov I. Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton. Genetica 2016; 144:289-306. [PMID: 27155886 DOI: 10.1007/s10709-016-9898-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/07/2016] [Indexed: 02/05/2023]
Abstract
The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton.
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Affiliation(s)
- Sharof S Egamberdiev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215
| | - Sukumar Saha
- Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA.
| | - Ilkhom Salakhutdinov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215
| | - Johnie N Jenkins
- Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Dewayne Deng
- Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Ibrokhim Y Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215
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31
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Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid HO, Gong W, Yuan Y. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.). BMC Plant Biol 2016; 16:79. [PMID: 27067834 PMCID: PMC4827241 DOI: 10.1186/s12870-016-0741-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. RESULTS In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. CONCLUSIONS This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.
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Affiliation(s)
- Zhen Zhang
- />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 Henan 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, 455000 Henan 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 Henan China
| | - Long Huang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Junwen Li
- />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 Henan 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, 455000 Henan China
| | - Juwu Gong
- />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 Henan China
| | - Aiying Liu
- />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 Henan China
| | - Tingting Chen
- />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 Henan China
| | - Dan Wang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Yanling Wang
- />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 Henan China
| | - Koffi Kibalou Palanga
- />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 Henan China
| | - Jamshed Muhammad
- />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 Henan China
| | - Weijie Li
- />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 Henan China
| | - Quanwei Lu
- />Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Xiaoying Deng
- />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 Henan China
| | - Yunna Tan
- />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 Henan China
| | - Weiwu Song
- />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 Henan China
| | - Juan Cai
- />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 Henan China
| | - Pengtao Li
- />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 Henan China
| | - Harun or Rashid
- />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 Henan China
| | - Wankui Gong
- />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 Henan 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 Henan China
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Zhang J, Wu M, Yu J, Li X, Pei W. Breeding Potential of Introgression Lines Developed from Interspecific Crossing between Upland Cotton (Gossypium hirsutum) and Gossypium barbadense: Heterosis, Combining Ability and Genetic Effects. PLoS One 2016; 11:e0143646. [PMID: 26730964 PMCID: PMC4701505 DOI: 10.1371/journal.pone.0143646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/07/2015] [Indexed: 12/04/2022] Open
Abstract
Upland cotton (Gossypium hirstum L.), which produces more than 95% of the world natural cotton fibers, has a narrow genetic base which hinders progress in cotton breeding. Introducing germplasm from exotic sources especially from another cultivated tetraploid G. barbadense L. can broaden the genetic base of Upland cotton. However, the breeding potential of introgression lines (ILs) in Upland cotton with G. barbadense germplasm integration has not been well addressed. This study involved six ILs developed from an interspecific crossing and backcrossing between Upland cotton and G. barbadense and represented one of the first studies to investigate breeding potentials of a set of ILs using a full diallel analysis. High mid-parent heterosis was detected in several hybrids between ILs and a commercial cultivar, which also out-yielded the high-yielding cultivar parent in F1, F2 and F3 generations. A further analysis indicated that general ability (GCA) variance was predominant for all the traits, while specific combining ability (SCA) variance was either non-existent or much lower than GCA. The estimated GCA effects and predicted additive effects for parents in each trait were positively correlated (at P<0.01). Furthermore, GCA and additive effects for each trait were also positively correlated among generations (at P<0.05), suggesting that F2 and F3 generations can be used as a proxy to F1 in analyzing combining abilities and estimating genetic parameters. In addition, differences between reciprocal crosses in F1 and F2 were not significant for yield, yield components and fiber quality traits. But maternal effects appeared to be present for seed oil and protein contents in F3. This study identified introgression lines as good general combiners for yield and fiber quality improvement and hybrids with high heterotic vigor in yield, and therefore provided useful information for further utilization of introgression lines in cotton breeding.
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Affiliation(s)
- Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
- * E-mail: (JFZ); (JWY)
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- * E-mail: (JFZ); (JWY)
| | - Xingli Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Yan S, Zhu J, Zhu W, Li Z, Shelton AM, Luo J, Cui J, Zhang Q, Liu X. Pollen-mediated gene flow from transgenic cotton under greenhouse conditions is dependent on different pollinators. Sci Rep 2015; 5:15917. [PMID: 26525573 PMCID: PMC4630633 DOI: 10.1038/srep15917] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/05/2015] [Indexed: 11/27/2022] Open
Abstract
With the large-scale release of genetically modified (GM) crops, there are ecological concerns on transgene movement from GM crops to non-GM counterparts and wild relatives. In this research, we conducted greenhouse experiments to measure pollen-mediated gene flow (PGF) in the absence and presence of pollinators (Bombus ignitus, Apis mellifera and Pieris rapae) in one GM cotton (resistant to the insect Helicoverpa armigera and the herbicide glyphosate) and two non-GM lines (Shiyuan321 and Hai7124) during 2012 and 2013. Our results revealed that: (1) PGF varied depending on the pollinator species, and was highest with B. ignitus (10.83%) and lowest with P. rapae (2.71%); (2) PGF with B. ignitus depended on the distance between GM and non-GM cottons; (3) total PGF to Shiyuan321 (8.61%) was higher than to Hai7124 (4.10%). To confirm gene flow, we tested hybrids carrying transgenes for their resistance to glyphosate and H. armigera, and most hybrids showed strong resistance to the herbicide and insect. Our research confirmed that PGF depended on pollinator species, distance between plants and the receptor plant.
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Affiliation(s)
- Shuo Yan
- Department of Entomology, China Agricultural University, Beijing, 100193, P.R. China
- National Agricultural Technology Extension and Service Center, Beijing, 100125, P.R. China
| | - Jialin Zhu
- Department of Entomology, China Agricultural University, Beijing, 100193, P.R. China
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing, 100026, P.R. China
| | - Weilong Zhu
- Department of Entomology, China Agricultural University, Beijing, 100193, P.R. China
| | - Zhen Li
- Department of Entomology, China Agricultural University, Beijing, 100193, P.R. China
| | - Anthony M. Shelton
- Department of Entomology, Cornell University/New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Junyu Luo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, P.R. China
| | - Jinjie Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, P.R. China
| | - Qingwen Zhang
- Department of Entomology, China Agricultural University, Beijing, 100193, P.R. China
| | - Xiaoxia Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, P.R. China
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Nie X, Tu J, Wang B, Zhou X, Lin Z. A BIL Population Derived from G. hirsutum and G. barbadense Provides a Resource for Cotton Genetics and Breeding. PLoS One 2015; 10:e0141064. [PMID: 26517274 PMCID: PMC4627741 DOI: 10.1371/journal.pone.0141064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
To provide a resource for cotton genetics and breeding, an interspecific hybridization between Gossypium hirsutum cv. Emian22 and G. barbadense acc. 3–79 was made. A population of 54 BILs (backcross inbred lines, BC1F8) was developed with the aim of transferring G. barbadense genes into G. hirsutum in order to genetically analyze these genes’ function in a G. hirsutum background and create new germplasms for breeding. Preliminary investigation of the morphological traits showed that the BILs had diverse variations in plant architecture, seed size, and fuzz color; the related traits of yield and fiber quality evaluated in 4 environments also showed abundant phenotypic variation. In order to explore the molecular diversity of the BIL population, 446 SSR markers selected at an average genetic distance of 10 cM from our interspecific linkage map were used to genotype the BIL population. A total of 393 polymorphic loci accounting for 84.4% MAF (major allele frequency) > 0.05 and 922 allele loci were detected, and the Shannon diversity index (I) was 0.417 per locus. The average introgression segment length was 16.24 cM, and an average of 29.53 segments were introgressed in each BIL line with an average background recovery of 79.8%. QTL mapping revealed 58 QTL associated with fiber quality and yield traits, and 47 favored alleles derived from the donor parent were discovered. This study demonstrated that the interspecific BIL population was enriched with much phenotypic and molecular variation which could be a resource for cotton genetics and breeding.
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Affiliation(s)
- Xinhui Nie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianli Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaofeng Zhou
- Cotton Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, Xinjiang, China
- * E-mail: (ZL); (XZ)
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- * E-mail: (ZL); (XZ)
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Thyssen GN, Fang DD, Turley RB, Florane C, Li P, Naoumkina M. Mapping-by-sequencing of Ligon-lintless-1 (Li 1 ) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2015; 128:1703-1712. [PMID: 26021293 DOI: 10.1007/s00122-015-2539-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
Mapping-by-sequencing and SNP marker analysis were used to fine map the Ligon-lintless-1 ( Li 1 ) short fiber mutation in tetraploid cotton to a 255-kb region that contains 16 annotated proteins. The Ligon-lintless-1 (Li 1 ) mutant of cotton (Gossypium hirsutum L.) has been studied as a model for cotton fiber development since its identification in 1929; however, the causative mutation has not been identified yet. Here we report the fine genetic mapping of the mutation to a 255-kb region that contains only 16 annotated genes in the reference Gossypium raimondii genome. We took advantage of the incompletely dominant dwarf vegetative phenotype to identify 100 mutants (Li 1 /Li 1 ) and 100 wild-type (li 1 /li 1 ) homozygotes from a mapping population of 2567 F2 plants, which we bulked and deep sequenced. Since only homozygotes were sequenced, we were able to use a high stringency in SNP calling to rapidly narrow down the region harboring the Li 1 locus, and designed subgenome-specific SNP markers to test the population. We characterized the expression of all sixteen genes in the region by RNA sequencing of elongating fibers and by RT-qPCR at seven time points spanning fiber development. One of the most highly expressed genes found in this interval in wild-type fiber cells is 40-fold under-expressed at the day of anthesis (DOA) in the mutant fiber cells. This gene is a major facilitator superfamily protein, part of the large family of proteins that includes auxin and sugar transporters. Interestingly, nearly all genes in this region were most highly expressed at DOA and showed a high degree of co-expression. Further characterization is required to determine if transport of hormones or carbohydrates is involved in both the dwarf and lintless phenotypes of Li 1 plants.
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Affiliation(s)
- Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA,
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Zhai C, Xu P, Zhang X, Guo Q, Zhang X, Xu Z, Shen X. Development of Gossypium anomalum-derived microsatellite markers and their use for genome-wide identification of recombination between the G. anomalum and G. hirsutum genomes. Theor Appl Genet 2015; 128:1531-1540. [PMID: 25957115 DOI: 10.1007/s00122-015-2528-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
We reported the first development of Gossypium anomalum -derived microsatellite markers and identification of recombination between sexually incompatible species by a synthesized hexaploid on genome level. To continue to develop improved cotton varieties, it is essential to transfer desired characters from diploid wild cotton species such as Gossypium anomalum to cultivated allotetraploid cotton species. However, interspecific reproductive barriers limit gene transfer between species. In a previous study, we used colchicine treatment to produce a synthesized hexaploid derived from an interspecific hybrid between Gossypium hirsutum and G. anomalum and demonstrated its hybridity and doubled status using morphological, cytological and molecular marker methods. In the current study, to effectively monitor G. anomalum genome components in the G. hirsutum background, we developed 5974 non-redundant G. anomalum-derived SSR primer pairs using RNA-Seq technology, which were combined with a publicly available physical map. Based on this combined map and segregation data from the BC2F1 population, we identified a set of 230 informative G. anomalum-specific SSR markers distributed on the chromosomes, which cover 95.72% of the cotton genome. After analyzing BC2F1 segregation data, 50 recombination types from 357 recombination events were identified, which cover 81.48% of the corresponding G. anomalum genome. A total of 203 recombination events occurred on chromosome 11, accounting for 56.86% of the recombination events on all chromosomes. Recombination hotspots were observed at marker intervals JAAS1148-NAU5100 on chromosome 1 and JAAS0426-NAU998 on chromosome 2. Therefore, all G. anomalum chromosomes are capable of recombining with At chromosomes in G. hirsutum. This study represents an important step towards introgressing desirable traits into cultivated cotton from the wild cotton species G. anomalum.
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Affiliation(s)
- Caijiao Zhai
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
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Chen Y, Wang Y, Zhao T, Yang J, Feng S, Nazeer W, Zhang T, Zhou B. A New Synthetic Amphiploid (AADDAA) between Gossypium hirsutum and G. arboreum Lays the Foundation for Transferring Resistances to Verticillium and Drought. PLoS One 2015; 10:e0128981. [PMID: 26061996 PMCID: PMC4465178 DOI: 10.1371/journal.pone.0128981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/04/2015] [Indexed: 11/18/2022] Open
Abstract
Gossypium arboreum, a cultivated cotton species (2n = 26, AA) native to Asia, possesses invaluable characteristics unavailable in the tetraploid cultivated cotton gene pool, such as resistance to pests and diseases and tolerance to abiotic stresses. However, it is quite difficult to transfer favorable traits into Upland cotton through conventional methods due to the cross-incompatibility of G. hirsutum (2n = 52, AADD) and G. arboreum. Here, we improved an embryo rescue technique to overcome the cross-incompatibility between these two parents for transferring favorable genes from G. arboreum into G. hirsutum. Our results indicate that MSB2K supplemented with 0.5 mgl-1 kinetin and 250 mg-1 casein hydrolysate is an efficient initial medium for rescuing early (3 d after pollination) hybrid embryos. Eight putative hybrids were successfully obtained, which were further verified and characterized by cytology, molecular markers and morphological analysis. The putative hybrids were subsequently treated with different concentrations of colchicine solution to double their chromosomes. The results demonstrate that four putative hybrid plants were successfully chromosome-doubled by treatment with 0.1% colchicine for 24 h and become amphiploid, which were confirmed by cytological observation, self-fertilization and backcrossing. Preliminary assessments of resistance at seedling stage indicate that the synthetic amphiploid showed highly resistant to Verticillium and drought. The synthetic amphiploid between G. hirsutum × G. arboreum would lay the foundation for developing G. arboreum-introgressed lines with the uniform genetic background of G. hirsutum acc TM-1, which would greatly enhance and simplify the mining, isolation, characterization, cloning and use of G. arboreum-specific desirable genes in future cotton breeding programs.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yingying Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Ting Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Jianwei Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Shouli Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Wajad Nazeer
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
- * E-mail:
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Hinze LL, Fang DD, Gore MA, Scheffler BE, Yu JZ, Frelichowski J, Percy RG. Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection. Theor Appl Genet 2015; 128:313-327. [PMID: 25431191 DOI: 10.1007/s00122-014-2431-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
A core marker set containing markers developed to be informative within a single commercial cotton species can elucidate diversity structure within a multi-species subset of the Gossypium germplasm collection. An understanding of the genetic diversity of cotton (Gossypium spp.) as represented in the US National Cotton Germplasm Collection is essential to develop strategies for collecting, conserving, and utilizing these germplasm resources. The US collection is one of the largest world collections and includes not only accessions with improved yield and fiber quality within cultivated species, but also accessions possessing sources of abiotic and biotic stress resistance often found in wild species. We evaluated the genetic diversity of a subset of 272 diploid and 1,984 tetraploid accessions in the collection (designated the Gossypium Diversity Reference Set) using a core set of 105 microsatellite markers. Utility of the core set of markers in differentiating intra-genome variation was much greater in commercial tetraploid genomes (99.7 % polymorphic bands) than in wild diploid genomes (72.7 % polymorphic bands), and may have been influenced by pre-selection of markers for effectiveness in the commercial species. Principal coordinate analyses revealed that the marker set differentiated interspecific variation among tetraploid species, but was only capable of partially differentiating among species and genomes of the wild diploids. Putative species-specific marker bands in G. hirsutum (73) and G. barbadense (81) were identified that could be used for qualitative identification of misclassifications, redundancies, and introgression within commercial tetraploid species. The results of this broad-scale molecular characterization are essential to the management and conservation of the collection and provide insight and guidance in the use of the collection by the cotton research community in their cotton improvement efforts.
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Affiliation(s)
- Lori L Hinze
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, USA
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Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol 2014; 6:559-71. [PMID: 24558256 PMCID: PMC3971588 DOI: 10.1093/gbe/evu037] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/25/2022] Open
Abstract
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Joseph P. Gallagher
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Emmanuel Szadkowski
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | | | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
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Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2014; 127:283-95. [PMID: 24170350 DOI: 10.1007/s00122-013-2217-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 10/14/2013] [Indexed: 05/09/2023]
Abstract
Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.
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Affiliation(s)
- Priyanka Tyagi
- Crop Science Department, North Carolina State University, Raleigh, NC, 27695, USA
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Li Y, Jiang J, Li L, Wang XL, Wang NN, Li DD, Li XB. A cotton LIM domain-containing protein (GhWLIM5) is involved in bundling actin filaments. Plant Physiol Biochem 2013; 66:34-40. [PMID: 23466745 DOI: 10.1016/j.plaphy.2013.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/18/2013] [Indexed: 06/01/2023]
Abstract
LIM-domain proteins play important roles in cellular processes in eukaryotes. In this study, a LIM protein gene, GhWLIM5, was identified in cotton. Quantitative RT-PCR analysis showed that GhWLIM5 was expressed widely in different cotton tissues and had a peak in expression during fiber elongation. GFP fluorescence assay revealed that cotton cells expressing GhWLIM5:eGFP fusion gene displayed a network distribution of eGFP fluorescence, suggesting that GhWLIM5 protein is mainly localized to the cell cytoskeleton. When GhWLIM5:eGFP transformed cells were stained with rhodamine-phalloidin there was consistent overlap in eGFP and rhodamine-palloidin signals, demonstrating that GhWLIM5 protein is colocalized with the F-actin cytoskeleton. In addition, high-speed cosedimentation assay verified that GhWLIM5 directly bound actin filaments, while low cosedimentation assay and microscopic observation indicated that GhWLIM5 bundled F-actin in vitro. Increasing amounts of GhWLIM5 protein were able to protect F-actin from depolymerization in vitro in the presence of Lat B (an F-actin depolymerizer). Our results contribute to a better understanding of the biochemical role of GhWLIM5 in modulating the dynamic F-actin network in cotton.
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Affiliation(s)
- Yang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
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Abstract
The detection and identification of genetically modified (GM) plants are challenging issues that have arisen from the potential negative impacts of extensive cultivation of transgenic plants. The screening process is a long-term focus and needs specific detection strategies. Surface plasmon resonance (SPR) has been used to detect a variety of biomolecules including proteins and nucleic acids due to its ability to monitor specific intermolecular interactions. In the present study, two high-throughput, label-free, and specific methods based on SPR technology were developed to detect transgenic Cry1Ac cotton ( Gossypium spp.) by separately targeting protein and DNA. In the protein-based detection system, monoclonal anti-Cry1Ac antibodies were immobilized on the surface of a CM5 sensor chip. Conventional cotton samples were used to define the detection threshold. Transgenic cotton was easily identified within 5 min per sample. For the DNA-based model, a 25-mer biotinylated oligonucleotide probe was immobilized on an SA sensor chip. PCR products of Cry1Ac (230 bp) were used to investigate the reaction conditions. The sensitivity of the constructed sensor chip was identified at concentrations as low as 0.1 nM based on its complementary base pairing.
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Affiliation(s)
- Zhuoya Zhao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, People's Republic of China
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Xu NY, Zhang GW, Li J, Zhou ZG. [Ecological regionalization of cotton varieties based on GGE biplot]. Ying Yong Sheng Tai Xue Bao 2013; 24:771-776. [PMID: 23755494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
By using the heritability-adjusted GGE biplot analysis method, and taking the trial sites Anqing, Nanyang, Huanggang, Jingzhou, Wuhan, Xiangyang, Changde, Yueyang, Nanjing, Nantong, Yancheng, Jiujiang, Jianyang, Shehong, and Cixi as the representative cotton-planting areas in the Yangtze River basin, the ecological regionalization of cotton varieties in the basin was made based on the lint cotton yield, and the regionalization results were adjusted by the information ratio (IR) method, aimed to provide scientific basis for the selection of cotton varieties in the cotton-planting areas of the basin. The cotton-planting areas in the Yangtze River basin could be divided into three ecological regions, i.e., the "Sichuan basin cotton region" with Jianyang and Shehong as the representative, the "Nan-Xiang basin cotton region" with Xiangyang and Nanyang as the representative, and the "majority complex cotton region in the Yangtze River basin" including all the other sites in the basin.
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Affiliation(s)
- Nai-Yin Xu
- Ministry of Agriculture Key Laboratory of Crop Growth Regulation, Nanjing Agricultural University, Nanjing 210095, China.
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Xu Q, Xiong G, Li P, He F, Huang Y, Wang K, Li Z, Hua J. Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids. PLoS One 2012; 7:e37128. [PMID: 22876273 PMCID: PMC3411646 DOI: 10.1371/journal.pone.0037128] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/16/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time. METHODOLOGY/PRINCIPAL FINDINGS The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43-0.68 million years ago (MYA). CONCLUSION Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1-3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in Gossypium is the maternal source of extant allotetraploid species and allotetraploids have a monophyletic origin. G. hirsutum AD1 lineages have experienced more sequence variations than other allotetraploids in intergenic regions. The available complete nucleotide sequences of 12 Gossypium chloroplast genomes should facilitate studies to uncover the molecular mechanisms of compartmental co-evolution and speciation of Gossypium allotetraploids.
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Affiliation(s)
- Qin Xu
- College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
| | - Guanjun Xiong
- College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
| | - Pengbo Li
- College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
- Institute of Cotton, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Fei He
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Huang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kunbo Wang
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhaohu Li
- College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
| | - Jinping Hua
- College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
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Zhang GW, Zhang L, Tang MX, Zhou LL, Chen BL, Zhou ZG. [Diurnal variation of gas exchange and chlorophyll fluorescence parameters of cotton functional leaves under effects of soil salinity]. Ying Yong Sheng Tai Xue Bao 2011; 22:1771-1781. [PMID: 22007454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A two-year (2007-2008) pot experiment with cotton varieties Sumian 12 (salinity-sensitive) and Zhongmiansuo 44 (salinity-tolerance) was conducted at the Pailou experimental station of Nanjing Agricultural University to study the diurnal variation of the gas exchange and chlorophyll fluorescence parameters of cotton functional leaves under five levels (0, 0.35%, 0.60% , 0.85%, and 1.00%) of soil salinity. With the increase of soil salinity, the concentrations of Na+, Cl-, and Mg2+ in functional leaves increased, whereas the concentrations of K+ and Ca2+ decreased. The salinity level <0. 35% had little effects on the gas exchange and chlorophyll fluorescence parameters, but that >0.35% depressed the net photosynthetic rate (Pn) dramatically. At the salinity level >0.35%, the sensitivity of functional leaves to daytime photon flux density (PFD) and air temperature (Ta) enhanced, which in turn resulted in more severe photo- and temperature inhibition, and changed the diurnal variation patterns of Pn and stomatal conductance (Gs) from a one-peak curve to a constantly decreasing one. Along with the variations of daytime PED and Ta, the diurnal variation patterns of the maximum photochemical efficiency (F(v)/F(m)), quantum yield of electron transport (phi(PS II), and photochemical quenching coefficient (q(P)) of functional leaves presented a V-shaped curve, with the minimum value appeared at 12:00-13:00, while the non-photochemical quenching coefficient (q(N)) showed a single-peak curve. Soil salinity decreased the F(v)/F(m), phi(PS II), and q(P) significantly, but increased the q(N) and enlarged its change trend. The comparatively low concentrations of Na+ and Cl- and the relatively high concentrations of K+ and Ca2+ in salt-tolerant Zhongmiansuo 44 functional leaves benefited the relative stability of PS II, and the maintenance of a relatively high thermal dissipation capacity could be one of the reasons for a high level of Pn at high salinity level.
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Affiliation(s)
- Guo-wei Zhang
- Ministry of Agriculture Key Laboratory of Crop Physiology and Ecology in Southern China, Nanjing Agricultural University, Nanjing 210095, China.
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Zhang F, Zuo K, Zhang J, Liu X, Zhang L, Sun X, Tang K. An L1 box binding protein, GbML1, interacts with GbMYB25 to control cotton fibre development. J Exp Bot 2010; 61:3599-613. [PMID: 20667961 PMCID: PMC2921199 DOI: 10.1093/jxb/erq173] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/24/2010] [Accepted: 05/25/2010] [Indexed: 05/19/2023]
Abstract
Transcription factors play key roles in plant development through their interaction with cis-elements and/or other transcription factors. A HD-Zip IV family transcription factor, Gossypium barbadense Meristem Layer 1 (GbML1) has been identified and characterized here. GbML1 specifically bound to the L1 box and the promoters of GbML1 and GbRDL1. GbML1 physically interacted with a key regulator of cotton fibre development, GbMYB25. Truncated and point mutation assays indicated the START-SAD domain was required for the binding to the C terminal domain (CTD) of GbMYB25. GbML1 overexpression in Arabidopsis increased the number of trichomes on stems and leaves and increased the accumulation of anthocyanin in leaves. Taken together, the L1 box binding protein, GbML1 was identified as the first partner for GbMYB25 and the role of START domain was discovered to be a protein binding domain in plants. Our findings will help the improvement of cotton fibre production and the understanding of the key role of HD-Zip family and MYB family in plants.
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Affiliation(s)
- Fei Zhang
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Kaijing Zuo
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jieqiong Zhang
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiang Liu
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Lida Zhang
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiaofen Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Kexuan Tang
- Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
- To whom correspondence should be addressed. E-mail: or
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Park W, Scheffler BE, Bauer PJ, Campbell BT. Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 2010; 10:142. [PMID: 20626869 PMCID: PMC3095289 DOI: 10.1186/1471-2229-10-142] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 07/13/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cotton (Gossypium spp.) is produced in over 30 countries and represents the most important natural fiber in the world. One of the primary factors affecting both the quantity and quality of cotton production is water. A major facilitator of water movement through cell membranes of cotton and other plants are the aquaporin proteins. Aquaporin proteins are present as diverse forms in plants, where they function as transport systems for water and other small molecules. The plant aquaporins belong to the large major intrinsic protein (MIP) family. In higher plants, they consist of five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). Although a great deal is known about aquaporins in plants, very little is known in cotton. RESULTS From a molecular cloning effort, together with a bioinformatic homology search, 71 upland cotton (G. hirsutum) aquaporin genes were identified. The cotton aquaporins consist of 28 PIP and 23 TIP members with high sequence similarity. We also identified 12 NIP and 7 SIP members that showed more divergence. In addition, one XIP member was identified that formed a distinct 5th subfamily. To explore the physiological roles of these aquaporin genes in cotton, expression analyses were performed for a select set of aquaporin genes from each subfamily using semi-quantitative reverse transcription (RT)-PCR. Our results suggest that many cotton aquaporin genes have high sequence similarity and diverse roles as evidenced by analysis of sequences and their expression. CONCLUSION This study presents a comprehensive identification of 71 cotton aquaporin genes. Phylogenetic analysis of amino acid sequences divided the large and highly similar multi-gene family into the known 5 aquaporin subfamilies. Together with expression and bioinformatic analyses, our results support the idea that the genes identified in this study represent an important genetic resource providing potential targets to modify the water use properties of cotton.
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Affiliation(s)
- Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, 2611 West Lucas St., Florence, 29501, SC, USA
| | - Brian E Scheffler
- USDA-ARS, MSA Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, 38776, MS, USA
| | - Philip J Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, 2611 West Lucas St., Florence, 29501, SC, USA
| | - B Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, 2611 West Lucas St., Florence, 29501, SC, USA
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Hawkins JS, Proulx SR, Rapp RA, Wendel JF. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci U S A 2009; 106:17811-6. [PMID: 19815511 PMCID: PMC2764891 DOI: 10.1073/pnas.0904339106] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Indexed: 11/18/2022] Open
Abstract
Transposable elements, particularly LTR-retrotransposons, comprise the primary vehicle for genome size expansion in plants, while DNA removal through illegitimate recombination and intrastrand homologous recombination serve as the most important counteracting forces to plant genomic obesity. Despite extensive research, the relative impact of these opposing forces and hence the directionality of genome size change remains unknown. In Gossypium (cotton), the 3-fold genome size variation among diploids is due largely to copy number variation of the gypsy-like retrotransposon Gorge3. Here we combine comparative sequence analysis with a modeling approach to study the directionality of genome size change in Gossypium. We demonstrate that the rate of DNA removal in the smaller genomes is sufficient to reverse genome expansion through Gorge3 proliferation. These data indicate that rates of DNA loss can be highly variable even within a single plant genus, and that the known mechanisms of DNA loss can indeed reverse the march toward genomic obesity.
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Affiliation(s)
- Jennifer S Hawkins
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
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Shu HM, Zhou ZG, Zheng M, Wang YH. [Low-temperature responses of enzyme activities related to fiber development of two cotton (Gossvpium hirsutum L.) cultivars with different temperature-sensitivity]. Ying Yong Sheng Tai Xue Bao 2009; 20:2157-2165. [PMID: 20030137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Taking two cotton cultivars with difterent temperature-sensitivity during tneir liner strength formation as test materials, a field experiment of different sowing dates was conducted in Nanjing of Jiangsu Province in 2006 and 2007 to study the effects of low temperature on the activities and gene expression of the enzymes related to fiber development. The low temperature induced by late sowing (with the mean daily minimum temperature being 21.1, 20.5, and 18.1 degrees C during fiber development period) had definite effects on the enzyme activities, and accordingly, the fiber strength formation. Low temperature increased the invertase and beta-1, 3-glucanase activities, decreased the sucrose synthase and sucrose phosphate synthase activities, prolonged the time with higher gene expression level of Expansin and sucrose synthase, and delayed the expression peak and decreased the gene expression quantity of beta-1,3-glucanase. There existed significant differences in the low-temperature responses of related enzymes activities between the two cultivars, with the change ranges of the enzyme activities being larger for temperature-sensitive cultivar Sumian 15 than for temperature-insensitive cultivar Kemian 1, which could be the main reasons leading to the different temnerature-sensitivitv of the two cotton cultivars during their fiber strength formation.
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Affiliation(s)
- Hong-mei Shu
- Ministry of Agriculture Key Laboratory of Grop Physiology & Ecology, Nanjing Agricultural University, Nanjing 210095, China.
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Deng JS, Shi YY, Chen LS, Wang K, Zhu JX. [Cotton identification and extraction using near infrared sensor and object-oriented spectral segmentation technique]. Guang Pu Xue Yu Guang Pu Fen Xi 2009; 29:1754-1758. [PMID: 19798933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The real-time, effective and reliable method of identifying crop is the foundation of scientific management for crop in the precision agriculture. It is also one of the key techniques for the precision agriculture. However, this expectation cannot be fulfilled by the traditional pixel-based information extraction method with respect to complicated image processing and accurate objective identification. In the present study, visible-near infrared image of cotton was acquired using high-resolution sensor. Object-oriented segmentation technique was performed on the image to produce image objects and spatial/spectral features of cotton. Afterwards, nearest neighbor classifier integrated the spectral, shape and topologic information of image objects to precisely identify cotton according to various features. Finally, 300 random samples and an error matrix were applied to undertake the accuracy assessment of identification. Although errors and confusion exist, this method shows satisfying results with an overall accuracy of 96.33% and a KAPPA coefficient of 0.926 7, which can meet the demand of automatic management and decision-making in precision agriculture.
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Affiliation(s)
- Jin-Song Deng
- Institute of Remote Sensing & Information Technique, Zhejiang University, Hangzhou 310029, China.
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