251
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Exploration of miRNAs and target genes of cytoplasmic male sterility line in cotton during flower bud development. Funct Integr Genomics 2018; 18:457-476. [PMID: 29626311 DOI: 10.1007/s10142-018-0606-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 12/13/2022]
Abstract
Cytoplasmic male sterility (CMS) lines provide crucial material to harness heterosis for crop plants, which serves as an important strategy for hybrid seed production. However, the molecular mechanism remains obscure. Although microRNAs (miRNAs) play important roles in vegetative growth and reproductive growth, there are few reports on miRNAs regulating the development of male sterility in Upland cotton. In present study, 12 small RNA libraries were constructed and sequenced for two development stages of flower buds from a CMS line and its maintainer line. Based on the results, 256 novel miRNAs were allocated to 141 new miRNA families, and 77 known miRNAs belonging to 54 conserved miRNA families were identified as well. Comparative analysis revealed that 61 novel and 10 conserved miRNAs were differentially expressed. Further transcriptome analysis identified 232 target genes for these miRNAs, which participated in cellular developmental process, cell death, pollen germination, and sexual reproduction. In addition, expression patterns of typical miRNA and the negatively regulated target genes, such as PPR, ARF, AP2, and AFB, were verified by qRT-PCR in cotton flower buds. These targets were previously reported to be related to reproduction development and male sterility, suggesting that miRNAs might act as regulators of CMS occurrence. Some miRNAs displayed specific expression profiles in special developmental stages of CMS line and its fertile hybrid (F1). Present study offers new information on miRNAs and their related target genes in exploiting CMS mechanism, and revealing the miRNA regulatory networks in Upland cotton.
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252
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Ding M, Chen ZJ. Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:37-48. [PMID: 29502038 PMCID: PMC6058195 DOI: 10.1016/j.pbi.2018.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 05/19/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.
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Affiliation(s)
- Mingquan Ding
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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253
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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: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [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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254
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Ashraf J, Zuo D, Wang Q, Malik W, Zhang Y, Abid MA, Cheng H, Yang Q, Song G. Recent insights into cotton functional genomics: progress and future perspectives. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:699-713. [PMID: 29087016 PMCID: PMC5814580 DOI: 10.1111/pbi.12856] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/03/2017] [Accepted: 10/18/2017] [Indexed: 05/11/2023]
Abstract
Functional genomics has transformed from futuristic concept to well-established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re-sequencing broad diversity panels with the development of high-throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.
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Affiliation(s)
- Javaria Ashraf
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Dongyun Zuo
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Qiaolian Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Waqas Malik
- Genomics LabDepartment of Plant Breeding and GeneticsFaculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultanPunjabPakistan
| | - Youping Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Muhammad Ali Abid
- Genomics LabDepartment of Plant Breeding and GeneticsFaculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultanPunjabPakistan
| | - Hailiang Cheng
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Qiuhong Yang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
| | - Guoli Song
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenanChina
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255
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Wen T, Wu M, Shen C, Gao B, Zhu D, Zhang X, You C, Lin Z. Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum). PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1654-1666. [PMID: 29476651 PMCID: PMC6097129 DOI: 10.1111/pbi.12902] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 05/14/2023]
Abstract
Brown fibre cotton is an environmental-friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine-mapped the brown fibre region, Lc1 , and dissected it into 2 loci, qBF-A07-1 and qBF-A07-2. The qBF-A07-1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF-A07-1 and qBF-A07-2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF-A07-1 and qBF-A07-2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome-wide association study (GWAS) and found that qBF-A07-2 negatively affects fibre yield and quality through an epistatic interaction with qBF-A07-1. This study sheds light on the genetics of fibre colour and lint-related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.
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Affiliation(s)
- Tianwang Wen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Mi Wu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chao Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Bin Gao
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - De Zhu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chunyuan You
- Cotton Research InstituteShihezi Academy of Agriculture ScienceShiheziXinjiangChina
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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256
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Wang M, Wang P, Lin M, Ye Z, Li G, Tu L, Shen C, Li J, Yang Q, Zhang X. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton. NATURE PLANTS 2018; 4:90-97. [PMID: 29379149 DOI: 10.1038/s41477-017-0096-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/22/2017] [Indexed: 05/21/2023]
Abstract
The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
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257
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Affiliation(s)
- Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, USA.
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258
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Huang L, Yang M, Li L, Li H, Yang D, Shi T, Yang P. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:2-15. [PMID: 29052958 DOI: 10.1111/jipb.12606] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/28/2017] [Indexed: 05/11/2023]
Abstract
Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.
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Affiliation(s)
- Longyu Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Ling Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
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259
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Sun Z, Li H, Zhang Y, Li Z, Ke H, Wu L, Zhang G, Wang X, Ma Z. Identification of SNPs and Candidate Genes Associated With Salt Tolerance at the Seedling Stage in Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1011. [PMID: 30050555 PMCID: PMC6050395 DOI: 10.3389/fpls.2018.01011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 06/21/2018] [Indexed: 05/02/2023]
Abstract
Salt tolerance in cotton is highly imperative for improvement in the response to decreasing farmland and soil salinization. However, little is known about the genetic basis underlying salt tolerance in cotton, especially the seedling stage. In this study, we evaluated two salt-tolerance-related traits of a natural population comprising 713 upland cotton (Gossypium hirsutum L.) accessions worldwide at the seedling stage and performed a genome-wide association study (GWAS) to identify marker-trait associations under salt stress using the Illumina Infinium CottonSNP63K array. A total of 23 single nucleotide polymorphisms (SNPs) that represented seven genomic regions on chromosomes A01, A10, D02, D08, D09, D10, and D11 were significantly associated with the two salt-tolerance-related traits, relative survival rate (RSR) and salt tolerance level (STL). Of these, the two SNPs i46598Gh and i47388Gh on D09 were simultaneously associated with the two traits. Based on all loci, we screened 280 possible candidate genes showing different expression levels under salt stress. Most of these genes were involved in transcription factors, transporters and enzymes and were previously reported as being involved in plant salt tolerance, such as NAC, MYB, NXH, WD40, CDPK, LEA, and CIPK. We further validated six putative candidate genes by qRT-PCR and found a differential expression level between salt-tolerant and salt-sensitive varieties. Our findings provide valuable information for enhancing the understanding of complicated mechanisms of salt tolerance in G. hirsutum seedlings and cotton salt tolerance breeding by molecular marker-assisted selection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhiying Ma
- *Correspondence: Xingfen Wang, Zhiying Ma,
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260
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Hou S, Zhu G, Li Y, Li W, Fu J, Niu E, Li L, Zhang D, Guo W. Genome-Wide Association Studies Reveal Genetic Variation and Candidate Genes of Drought Stress Related Traits in Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1276. [PMID: 30233620 PMCID: PMC6129771 DOI: 10.3389/fpls.2018.01276] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/14/2018] [Indexed: 05/18/2023]
Abstract
Cotton is an important industrial crop worldwide and upland cotton (Gossypium hirsutum L.) is most widely cultivated in the world. Due to ever-increasing water deficit, drought stress brings a major threat to cotton production. Thus, it is important to reveal the genetic basis under drought stress and develop drought tolerant cotton cultivars. To address this issue, in present study, 319 upland cotton accessions were genotyped by 55,060 single nucleotide polymorphisms (SNPs) from high-density CottonSNP80K array and phenotyped nine drought tolerance related traits. The two datasets were used to identify quantitative trait nucleotides (QTNs) for the above nine traits using multi-locus random-SNP-effect mixed linear model method. As a result, a total of 20 QTNs distributed on 16 chromosomes were found to be significantly associated with six drought tolerance related traits. Of the 1,326 genes around the 20 QTNs, 205 were induced after drought stress treatment, and 46 were further mapped to Gene ontology (GO) term "response to stress." Taken genome-wide association study (GWAS) analysis, RNA-seq data and qRT-PCR verification, four genes, RD2 encoding a response to desiccation 2 protein, HAT22 encoding a homeobox-leucine zipper protein, PIP2 encoding a plasma membrane intrinsic protein 2, and PP2C encoding a protein phosphatase 2C, were proposed to be potentially important for drought tolerance in cotton. These results will deepen our understanding of the genetic basis of drought stress tolerance in cotton and provide candidate markers to accelerate the development of drought-tolerant cotton cultivars.
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261
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Wang M, Wang P, Liang F, Ye Z, Li J, Shen C, Pei L, Wang F, Hu J, Tu L, Lindsey K, He D, Zhang X. A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation. THE NEW PHYTOLOGIST 2018; 217:163-178. [PMID: 28892169 DOI: 10.1111/nph.14762] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/25/2017] [Indexed: 05/21/2023]
Abstract
Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high-throughput next-generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity between coexisting subgenomes. Here we characterize AS in the polyploid species cotton. Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an integrated pipeline for Iso-Seq transcriptome data analysis (https://github.com/Nextomics/pipeline-for-isoseq). We identified 176 849 full-length transcript isoforms from 44 968 gene models and updated gene annotation. These data led us to identify 15 102 fibre-specific AS events and estimate that c. 51.4% of homoeologous genes produce divergent isoforms in each subgenome. We reveal that AS allows differential regulation of the same gene by miRNAs at the isoform level. We also show that nucleosome occupancy and DNA methylation play a role in defining exons at the chromatin level. This study provides new insights into the complexity and regulation of AS, and will enhance our understanding of AS in polyploid species. Our methodology for Iso-Seq data analysis will be a useful reference for the study of AS in other species.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Fan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Feng Wang
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Jiang Hu
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Daohua He
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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262
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Genome sequencing brought Gossypium biology research into a new era. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1463-1466. [PMID: 29285713 DOI: 10.1007/s11427-017-9233-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 10/18/2022]
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263
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Sun H, Chen L, Li J, Hu M, Ullah A, He X, Yang X, Zhang X. The JASMONATE ZIM-Domain Gene Family Mediates JA Signaling and Stress Response in Cotton. PLANT & CELL PHYSIOLOGY 2017; 58:2139-2154. [PMID: 29036515 DOI: 10.1093/pcp/pcx148] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/26/2017] [Indexed: 05/18/2023]
Abstract
JASMONATE ZIM-domain (JAZ) family proteins are involved in regulating diverse biological processes in plants. However, their functions have not been well characterized in cotton (Gossypium spp.). In the present study, 13, 15, 25 and 30 JAZ genes were identified in Gossypium arboretum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively, based on gene homology. Selection and variation analyses showed that the single nucleotide polymorphism (SNP) density of GhJAZ genes in wild species was much higher than that in domesticated species. Expression pattern analysis showed that all the GhJAZ genes are expressed in at least one tissue and respond to one or more stress factors, as well as being induced by some phytohormones. The co-expression network indicated that GhJAZ genes might mediate multiple stress response pathways. Yeast two-hybrid (Y2H) experiments showed extensive interactions among GhJAZ proteins, including homo- and heteromeric interactions. Overexpressing one member of the JAZ gene family, GhJAZ2 (Gh_D06G0810), significantly enhanced sensitivity to salt stress in transgenic cotton. Transcriptome analysis indicated that GhJAZ2 regulates stress responses possibly by participating in α-linolenic acid metabolism and jasmonate signaling, and is involved in the repression of GhMYC2 regulated by GhJAZ2. Our data provide important clues for further elucidating the functions of JAZ genes in cotton.
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Affiliation(s)
- Heng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Lin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Meiling Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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264
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Wu Z, Yang Y, Huang G, Lin J, Xia Y, Zhu Y. Cotton functional genomics reveals global insight into genome evolution and fiber development. J Genet Genomics 2017; 44:511-518. [PMID: 29169921 DOI: 10.1016/j.jgg.2017.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/22/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022]
Abstract
Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution. Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.
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Affiliation(s)
- Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Gai Huang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Lin
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuying Xia
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yuxian Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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265
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Wen Y, He Y, Ji X, Li S, Chen L, Zhou Y, Wang M, Chen B. Isolation of an indigenous Chlorella vulgaris from swine wastewater and characterization of its nutrient removal ability in undiluted sewage. BIORESOURCE TECHNOLOGY 2017; 243:247-253. [PMID: 28672187 DOI: 10.1016/j.biortech.2017.06.094] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/12/2017] [Accepted: 06/17/2017] [Indexed: 05/13/2023]
Abstract
Bio-treatment of wastewater mediated by microalgae is considered as a promising solution. This work aimed to isolate an indigenous microalgal strain (named MBFJNU-1) from swine wastewater effluent and identify as Chlorella vulgaris. After 12days, the removal efficiencies of total nitrogen (TN) and total phosphorus (TP) in undiluted swine slurry were 90.51% and 91.54%, respectively. Stress tolerance in response to wastewater was verified by cultivating in artificial wastewater containing different levels of chemical oxygen demand (COD), TN and TP. MBFJNU-1 could grow well in undiluted swine slurry and artificial wastewater containing 30,000mg/L COD or 2000mg/L TN. Furthermore, global nuclear DNA methylation (5-mC) of MBFJNU-1 was employed to explore the possible mechanism in response to wastewater stress. The results showed that the level of 5-mC was inversely proportional to the growth of MBFJNU-1 in different diluted swine slurry, helping to understand 5-mC variation in response to stress environment.
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Affiliation(s)
- Yangmin Wen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Quanzhou Medical College, Quanzhou 362000, China
| | - Yongjin He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Xiaowei Ji
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Shaofeng Li
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Ling Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Youcai Zhou
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Mingzi Wang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Bilian Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China.
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266
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Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, Qian W. A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4791-4801. [PMID: 28992309 PMCID: PMC5853444 DOI: 10.1093/jxb/erx311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.
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Affiliation(s)
- Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Chaobo Tong
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Correspondence:
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267
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Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet 2017; 49:1089-1098. [DOI: 10.1038/ng.3887] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/03/2017] [Indexed: 12/18/2022]
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268
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Liang C, Liu Y, Li Y, Meng Z, Yan R, Zhu T, Wang Y, Kang S, Ali Abid M, Malik W, Sun G, Guo S, Zhang R. Activation of ABA Receptors Gene GhPYL9-11A Is Positively Correlated with Cotton Drought Tolerance in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:1453. [PMID: 28878793 PMCID: PMC5572150 DOI: 10.3389/fpls.2017.01453] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 05/05/2023]
Abstract
The sensitivity to abscisic acid (ABA) by its receptors, pyrabactin resistance-like proteins (PYLs), is considered a most important factor in activating the ABA signal pathway in response to abiotic stress. However, it is still unknown which PYL is the crucial ABA receptor mediating response to drought stress in cotton (Gossypium hirsutum L.). Here, we reported the identification and characterization of highly induced ABA receptor GhPYL9-11A in response to drought in cotton. It is observed that GhPYL9-11A was highly induced by ABA treatment. GhPYL9-11A binds to protein phosphatase 2Cs (PP2Cs) in an ABA-independent manner. Moreover, the GhPYL-11A-PP2C interactions are partially disrupted by mutations, proline (P84) and histidine (H111), in the gate-latch region. Transgenic Arabidopsis overexpressing GhPYL9-11A plants were hypersensitive to ABA during seed germination and early seedling stage. Further, the increased in root growth and up regulation of drought stress-related genes in transgenic Arabidopsis as compared to wild type confirmed the potential role of GhPYL9-11A in abiotic stress tolerance. Consistently, the expression level of GhPYL9-11A is on average higher in drought-tolerant cotton cultivars than in drought-sensitive cottons under drought treatment. In conclusion, the manipulation of GhPYL9-11A expression could be a useful strategy for developing drought-tolerant cotton cultivars.
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Affiliation(s)
- Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yan Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yanyan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Rong Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Tao Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shujing Kang
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Waqas Malik
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
- Genomics Lab, Department of Plant Breeding and Genetics, Bahauddin Zakariya UniversityMultan, Pakistan
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Rui Zhang, Sandui Guo,
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Rui Zhang, Sandui Guo,
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269
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Ma L, Zhao Y, Wang Y, Shang L, Hua J. QTLs Analysis and Validation for Fiber Quality Traits Using Maternal Backcross Population in Upland Cotton. FRONTIERS IN PLANT SCIENCE 2017; 8:2168. [PMID: 29312408 PMCID: PMC5744017 DOI: 10.3389/fpls.2017.02168] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/11/2017] [Indexed: 05/04/2023]
Abstract
Cotton fiber is renewable natural fiber source for textile. Improving fiber quality is an essential goal for cotton breeding project. In present study, F14 recombinant inbred line (RIL) population was backcrossed by the maternal parent to obtain a backcross (BC) population, derived from one Upland cotton hybrid. Three repetitive field trials were performed by randomized complete block design with two replicates in three locations in 2015, together with the BC population, common male parent and the RIL population. Totally, 26 QTLs in BC population explained 5.00-14.17% of phenotype variation (PV) and 37 quantitative trait loci (QTL) were detected in RIL population explaining 5.13-34.00% of PV. Seven common QTLs detected simultaneously in two populations explained PV from 7.69 to 23.05%. A total of 20 QTLs in present study verified the previous results across three environments in 2012. Particularly, qFL-Chr5-2 controlling fiber length on chromosome 5 explained 34.00% of PV, while qFL-Chr5-3 only within a 0.8 cM interval explained 13.93% of PV on average in multiple environments. These stable QTLs explaining great variation offered essential information for marker-assisted selection (MAS) to improve fiber quality traits. Lots of epistasis being detected in both populations acted as one of important genetic compositions of fiber quality traits.
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Affiliation(s)
- Lingling Ma
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, China
| | - Yanpeng Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, China
| | - Yumei Wang
- Department of Cotton Breeding, Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Lianguang Shang
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing, China
- *Correspondence: Jinping Hua
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