1
|
Chen Y, Niu S, Deng X, Song Q, He L, Bai D, He Y. Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:196. [PMID: 37046207 PMCID: PMC10091845 DOI: 10.1186/s12870-023-04192-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. RESULTS In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. CONCLUSIONS In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.
Collapse
Affiliation(s)
- Yanjun Chen
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Xinyue Deng
- School of Architecture, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Limin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| |
Collapse
|
2
|
Genome-Wide Analyses of Tea Plant Stress-Associated Proteins (SAPs) Reveal the Role of CsSAP12 in Increased Drought Tolerance in Transgenic Tomatoes. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Plant stress-associated proteins (SAPs) contain A20/AN1 zinc finger domains and are involved in plant response to abiotic stresses. In this study, we aimed to explore the biological function of tea plant CsSAPs. A total of 14 CsSAP genes were identified in the tea plant genome using a reference genome database (Camellia sinensis var. sinensis). The CsSAPs were divided into the following two groups: Group I, containing one AN1 domain and/or one A20 domain; and Group II, containing two AN1 domains and/or two C2H2 domains. The sequence alignments and conserved domains analysis indicated that the CsSAPs were highly structurally conserved in terms of amino acid sequence and protein structure. The CsSAPs showed different transcript levels in spatio-temporal expression and in response to cold and drought stress in tea plants. Furthermore, the expression of CsSAP12 was considerably upregulated under drought stress. The overexpression of CsSAP12 in transgenic tomatoes showed increased tolerance to drought stress compared with the wild type. Altogether, the results showed that CsSAP12 might be involved in drought stress. Thus, CsSAP12 might be a target gene in genetic engineering to improve drought tolerance in tea plants.
Collapse
|
3
|
Xu J, Hu P, Tao Y, Song P, Gao H, Guan Y. Genome-wide identification and characterization of the Lateral Organ Boundaries Domain ( LBD) gene family in polyploid wheat and related species. PeerJ 2021; 9:e11811. [PMID: 34447619 PMCID: PMC8364319 DOI: 10.7717/peerj.11811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. METHODS Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a-e, II a and II b). RESULTS The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.
Collapse
Affiliation(s)
- Jun Xu
- Henan Institute of Science and Technology, Xinxiang, China
| | - Ping Hu
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Ye Tao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Puwen Song
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Huanting Gao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Yuanyuan Guan
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| |
Collapse
|
4
|
Marcianò D, Ricciardi V, Marone Fassolo E, Passera A, Bianco PA, Failla O, Casati P, Maddalena G, De Lorenzis G, Toffolatti SL. RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy. FRONTIERS IN PLANT SCIENCE 2021; 12:667319. [PMID: 34127927 PMCID: PMC8196239 DOI: 10.3389/fpls.2021.667319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/20/2021] [Indexed: 05/07/2023]
Abstract
Downy mildew, caused by the oomycete Plasmopara viticola, is one of the diseases causing the most severe economic losses to grapevine (Vitis vinifera) production. To date, the application of fungicides is the most efficient method to control the pathogen and the implementation of novel and sustainable disease control methods is a major challenge. RNA interference (RNAi) represents a novel biotechnological tool with a great potential for controlling fungal pathogens. Recently, a candidate susceptibility gene (VviLBDIf7) to downy mildew has been identified in V. vinifera. In this work, the efficacy of RNAi triggered by exogenous double-stranded RNA (dsRNA) in controlling P. viticola infections has been assessed in a highly susceptible grapevine cultivar (Pinot noir) by knocking down VviLBDIf7 gene. The effects of dsRNA treatment on this target gene were assessed by evaluating gene expression, disease severity, and development of vegetative and reproductive structures of P. viticola in the leaf tissues. Furthermore, the effects of dsRNA treatment on off-target (EF1α, GAPDH, PEPC, and PEPCK) and jasmonic acid metabolism (COI1) genes have been evaluated. Exogenous application of dsRNA led to significant reductions both in VviLBDIf7 gene expression, 5 days after the treatment, and in the disease severity when artificial inoculation was carried out 7 days after dsRNA treatments. The pathogen showed clear alterations to both vegetative (hyphae and haustoria) and reproductive structures (sporangiophores) that resulted in stunted growth and reduced sporulation. Treatment with dsRNA showed signatures of systemic activity and no deleterious off-target effects. These results demonstrated the potential of RNAi for silencing susceptibility factors in grapevine as a sustainable strategy for pathogen control, underlying the possibility to adopt this promising biotechnological tool in disease management strategies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
5
|
Sheng X, Zhao Z, Wang J, Yu H, Shen Y, Gu H. Identification of Brassica oleracea orthologs of the PEBP family and their expression patterns in curd development and flowering in cauliflower. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1790418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, PR China
| | - Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, PR China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, PR China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, PR China
| | - Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, PR China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, PR China
| |
Collapse
|
6
|
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] [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.
Collapse
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.
| |
Collapse
|