1
|
Iqbal A, Aslam S, Ahmed M, Khan F, Ali Q, Han S. Role of Actin Dynamics and GhACTIN1 Gene in Cotton Fiber Development: A Prototypical Cell for Study. Genes (Basel) 2023; 14:1642. [PMID: 37628693 PMCID: PMC10454433 DOI: 10.3390/genes14081642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Cotton crop is considered valuable for its fiber and seed oil. Cotton fiber is a single-celled outgrowth from the ovule epidermis, and it is a very dynamic cell for study. It has four distinct but overlapping developmental stages: initiation, elongation, secondary cell wall synthesis, and maturation. Among the various qualitative characteristics of cotton fiber, the important ones are the cotton fiber staple length, tensile strength, micronaire values, and fiber maturity. Actin dynamics are known to play an important role in fiber elongation and maturation. The current review gives an insight into the cotton fiber developmental stages, the qualitative traits associated with cotton fiber, and the set of genes involved in regulating these developmental stages and fiber traits. This review also highlights some prospects for how biotechnological approaches can improve cotton fiber quality.
Collapse
Affiliation(s)
- Adnan Iqbal
- School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui 553004, China;
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Sibgha Aslam
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Mukhtar Ahmed
- Government Boys College Sokasan, Higher Education Department, Azad Jammu and Kashmir, Bhimber 10040, Pakistan
| | - Fahad Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan 33001, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Shiming Han
- School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui 553004, China;
| |
Collapse
|
2
|
Han J, Jawad Umer M, Yang M, Hou Y, Gereziher Mehari T, Zheng J, Wang H, Liu J, Dong W, Xu Y, Wang Y, Liu F, Zhou Z, Cai X. Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107708. [PMID: 37116225 DOI: 10.1016/j.plaphy.2023.107708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023]
Abstract
Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.
Collapse
Affiliation(s)
- Jiangping Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Mengying Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Teame Gereziher Mehari
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jie Zheng
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China
| | - Heng Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jiajun Liu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenhao Dong
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China; State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
| | - ZhongLi Zhou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xiaoyan Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
| |
Collapse
|
3
|
Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
Collapse
Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Abdul Hafeez
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | | | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Li Pengtao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Maozhi Ren
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Youlu Yuan
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| |
Collapse
|
4
|
Ijaz B, Zhao N, Kong J, Hua J. Fiber Quality Improvement in Upland Cotton ( Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application. FRONTIERS IN PLANT SCIENCE 2019; 10:1585. [PMID: 31921240 PMCID: PMC6917639 DOI: 10.3389/fpls.2019.01585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/12/2019] [Indexed: 05/17/2023]
Abstract
Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Fiber quality traits are controlled by multiple genes and are classified as complex quantitative traits, with a negative relationship with yield potential, so the genetic gain is low in traditional genetic improvement by phenotypic selection. The availability of Gossypium genomic sequences facilitates the development of high-throughput molecular markers, quantitative trait loci (QTL) fine mapping and gene identification, which helps us to validate candidate genes and to use marker assisted selection (MAS) on fiber quality in breeding programs. Based on developments of high density linkage maps, QTLs fine mapping, marker selection and omics, we have performed trait dissection on fiber quality traits in diverse populations of upland cotton. QTL mapping combined with multi-omics approaches such as, RNA sequencing datasets to identify differentially expressed genes have benefited the improvement of fiber quality. In this review, we discuss the application of molecular markers, QTL mapping and MAS for fiber quality improvement in upland cotton.
Collapse
Affiliation(s)
- Babar Ijaz
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Jinping Hua,
| |
Collapse
|
5
|
Xu Z, Yu J, Kohel RJ, Percy RG, Beavis WD, Main D, Yu JZ. Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome. Genomics 2015; 106:61-9. [PMID: 25796538 DOI: 10.1016/j.ygeno.2015.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 02/05/2015] [Accepted: 03/11/2015] [Indexed: 01/15/2023]
Abstract
Cotton fiber represents the largest single cell in plants and they serve as models to study cell development. This study investigated the distribution and evolution of fiber Unigenes anchored to recombination hotspots between tetraploid cotton (Gossypium hirsutum) At and Dt subgenomes, and within a parental diploid cotton (Gossypium raimondii) D genome. Comparative analysis of At vs D and Dt vs D showed that 1) the D genome provides many fiber genes after its merger with another parental diploid cotton (Gossypium arboreum) A genome although the D genome itself does not produce any spinnable fiber; 2) similarity of fiber genes is higher between At vs D than between Dt vs D genomic hotspots. This is the first report that fiber genes have higher similarity between At and D than between Dt and D. The finding provides new insights into cotton genomic regions that would facilitate genetic improvement of natural fiber properties.
Collapse
Affiliation(s)
- Zhanyou Xu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Jing Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA; Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Russell J Kohel
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Richard G Percy
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - William D Beavis
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - John Z Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA.
| |
Collapse
|
6
|
Zhang R, Ding J, Liu C, Cai C, Zhou B, Zhang T, Guo W. Molecular evolution and phylogenetic analysis of eight COL superfamily genes in group I related to photoperiodic regulation of flowering time in wild and domesticated cotton (Gossypium) species. PLoS One 2015; 10:e0118669. [PMID: 25710777 PMCID: PMC4339614 DOI: 10.1371/journal.pone.0118669] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/07/2015] [Indexed: 12/02/2022] Open
Abstract
Flowering time is an important ecological trait that determines the transition from vegetative to reproductive growth. Flowering time in cotton is controlled by short-day photoperiods, with strict photoperiod sensitivity. As the CO-FT (CONSTANS-FLOWER LOCUS T) module regulates photoperiodic flowering in several plants, we selected eight CONSTANS genes (COL) in group I to detect their expression patterns in long-day and short-day conditions. Further, we individually cloned and sequenced their homologs from 25 different cotton accessions and one outgroup. Finally, we studied their structures, phylogenetic relationship, and molecular evolution in both coding region and three characteristic domains. All the eight COLs in group I show diurnal expression. In the orthologous and homeologous loci, each gene structure in different cotton species is highly conserved, while length variation has occurred due to insertions/deletions in intron and/or exon regions. Six genes, COL2 to COL5, COL7 and COL8, exhibit higher nucleotide diversity in the D-subgenome than in the A-subgenome. The Ks values of 98.37% in all allotetraploid cotton species examined were higher in the A-D and At-Dt comparison than in the A-At and D-Dt comparisons, and the Pearson’s correlation coefficient (r) of Ks between A vs. D and At vs. Dt also showed positive, high correlations, with a correlation coefficient of at least 0.797. The nucleotide polymorphism in wild species is significantly higher compared to G. hirsutum and G. barbadense, indicating a genetic bottleneck associated with the domesticated cotton species. Three characteristic domains in eight COLs exhibit different evolutionary rates, with the CCT domain highly conserved, while the B-box and Var domain much more variable in allotetraploid species. Taken together, COL1, COL2 and COL8 endured greater selective pressures during the domestication process. The study improves our understanding of the domestication-related genes/traits during cotton evolutionary process.
Collapse
Affiliation(s)
- Rui Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
| | - Jian Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
| | - Chunxiao Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
| | - Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, China
- * E-mail:
| |
Collapse
|
7
|
Mansoor S, Paterson AH. Genomes for jeans: cotton genomics for engineering superior fiber. Trends Biotechnol 2012; 30:521-7. [PMID: 22831638 DOI: 10.1016/j.tibtech.2012.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/25/2012] [Accepted: 06/25/2012] [Indexed: 12/22/2022]
Abstract
Twenty years ago, scientists predicted that better understanding of fiber development would lead to novel ways to engineer superior cotton fiber. Advances in genetic resources, DNA markers, DNA sequence information, and gene expression data have indeed provided new insights into fiber initiation, elongation and maturation. Many exciting applications of this knowledge offer the potential to select better cotton genotypes more effectively in mainstream breeding programs or engineer genotypes with improved agronomic and/or quality traits. Here, we discuss recent progress in understanding genes involved in fiber development, and their regulation and manipulation to engineer improved fibers. Better understanding of quantitative trait loci/gene interactions that influence fiber quality and yield may help to tailor superior cotton genotypes to diverse environments.
Collapse
Affiliation(s)
- Shahid Mansoor
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA.
| | | |
Collapse
|