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Zhou L, Li Y, Ye L, Li J, Liang T, Liu Y, Xie W, Xie Y, Chen S, Chen H. Genetic Variation in a Crossing Population of Camellia oleifera Based on ddRAD Sequencing and Analysis of Association with Fruit Traits. Curr Issues Mol Biol 2025; 47:92. [PMID: 39996813 PMCID: PMC11854439 DOI: 10.3390/cimb47020092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 01/29/2025] [Accepted: 01/29/2025] [Indexed: 02/26/2025] Open
Abstract
Tea oil is an important high-quality edible oil derived from woody plants. Camellia oleifera is the largest and most widely planted oil-producing plant in the Camellia genus in China, and its seeds are the most important source for obtaining tea oil. In current research, improving the yield and quality of tea oil is the main goal of oil tea genetic breeding. The aim of this study was to investigate the degree of genetic variation in an early crossing population of C. oleifera and identify single nucleotide polymorphisms (SNPs) and genes significantly associated with fruit traits, which can provide a basis for marker-assisted selection and gene editing for achieving trait improvement in the future. In this study, we selected a crossing population of approximately 40-year-old C. oleifera with a total of 330 samples. Then, ddRAD sequencing was used for SNP calling and population genetic analysis, and association analysis was performed on fruit traits measured repeatedly for two consecutive years. The research results indicate that over 8 million high-quality SNPs have been identified, but the vast majority of SNPs occur in intergenic regions. The nucleotide polymorphism of this population is at a low level, and Tajima's D values are mostly greater than 0, indicating that the change in this population was not suitable for the model of central evolution. The population structure analysis shows that the population has seven theoretical sources of genetic material and can be divided into seven groups, and the clustering analysis results support the population structure analysis results. Association analysis identified significant SNPs associated with genes related to the seed number of a single fruit and seed kernel oil content. Our findings provide a basis for molecular breeding and future genetic improvement of cultivated oil tea.
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Affiliation(s)
- Lexin Zhou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- Fujian Academy of Forestry, Fuzhou 350012, China;
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Yu Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Ling Ye
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Jiani Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Tian Liang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Yanxuan Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Weiwei Xie
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- Fujian Academy of Forestry, Fuzhou 350012, China;
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Yiqing Xie
- Fujian Academy of Forestry, Fuzhou 350012, China;
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
| | - Hui Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (L.Y.); (J.L.); (T.L.); (Y.L.); (W.X.); (S.C.); (H.C.)
- The Oil Tea Engineering Technological Research Center of Fujian Province, Fuzhou 350002, China
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Zhang C, Shao W, Ren H, Shen F, Xu Q, Chang J, Wang K, Yao X. Association mapping revealed phenolic content-related SNPs and haplotypes in pecan (Carya illinoinensis). EUPHYTICA 2024; 220:188. [DOI: 10.1007/s10681-024-03445-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/22/2024] [Indexed: 01/04/2025]
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Zhu H, Wang F, Xu Z, Wang G, Hu L, Cheng J, Ge X, Liu J, Chen W, Li Q, Xue F, Liu F, Li W, Wu L, Cheng X, Tang X, Yang C, Lindsey K, Zhang X, Ding F, Hu H, Hu X, Jin S. The complex hexaploid oil-Camellia genome traces back its phylogenomic history and multi-omics analysis of Camellia oil biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2890-2906. [PMID: 38923257 PMCID: PMC11536451 DOI: 10.1111/pbi.14412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
Oil-Camellia (Camellia oleifera), belonging to the Theaceae family Camellia, is an important woody edible oil tree species. The Camellia oil in its mature seed kernels, mainly consists of more than 90% unsaturated fatty acids, tea polyphenols, flavonoids, squalene and other active substances, which is one of the best quality edible vegetable oils in the world. However, genetic research and molecular breeding on oil-Camellia are challenging due to its complex genetic background. Here, we successfully report a chromosome-scale genome assembly for a hexaploid oil-Camellia cultivar Changlin40. This assembly contains 8.80 Gb genomic sequences with scaffold N50 of 180.0 Mb and 45 pseudochromosomes comprising 15 homologous groups with three members each, which contain 135 868 genes with an average length of 3936 bp. Referring to the diploid genome, intragenomic and intergenomic comparisons of synteny indicate homologous chromosomal similarity and changes. Moreover, comparative and evolutionary analyses reveal three rounds of whole-genome duplication (WGD) events, as well as the possible diversification of hexaploid Changlin40 with diploid occurred approximately 9.06 million years ago (MYA). Furthermore, through the combination of genomics, transcriptomics and metabolomics approaches, a complex regulatory network was constructed and allows to identify potential key structural genes (SAD, FAD2 and FAD3) and transcription factors (AP2 and C2H2) that regulate the metabolism of Camellia oil, especially for unsaturated fatty acids biosynthesis. Overall, the genomic resource generated from this study has great potential to accelerate the research for the molecular biology and genetic improvement of hexaploid oil-Camellia, as well as to understand polyploid genome evolution.
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Affiliation(s)
- Huaguo Zhu
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhongping Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningHainanChina
| | | | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jinxuan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Fei Xue
- College of Agriculture, Shihezi UniversityShiheziXinjiangChina
| | - Feng Liu
- College of Agriculture, Shihezi UniversityShiheziXinjiangChina
| | - Wenying Li
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | - Lan Wu
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | - Xinqi Cheng
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | - Xinxin Tang
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | - Chaochen Yang
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | | | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Haiyan Hu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication)Hainan UniversitySanyaHainanChina
| | - Xiaoming Hu
- College of Biology and Agricultural Resources, Huanggang Normal UniversityHuanggangHubeiChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
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Lin P, Chai J, Wang A, Zhong H, Wang K. High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing. Int J Mol Sci 2024; 25:8840. [PMID: 39201527 PMCID: PMC11354348 DOI: 10.3390/ijms25168840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jingyu Chai
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Anni Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Huiqi Zhong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Zheng J, Su H, Pu S, Chen H, El-Kassaby YA, Yang Z, Feng J. High-yield hybrid breeding of Camellia oleifolia based on ISSR molecular markers. BMC PLANT BIOLOGY 2024; 24:517. [PMID: 38851667 PMCID: PMC11162053 DOI: 10.1186/s12870-024-05218-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND C. Oleifera is among the world's largest four woody plants known for their edible oil production, yet the contribution rate of improved varieties is less than 20%. The species traditional breeding is lengthy cycle (20-30 years), occupation of land resources, high labor cost, and low accuracy and efficiency, which can be enhanced by molecular marker-assisted selection. However, the lack of high-quality molecular markers hinders the species genetic analysis and molecular breeding. RESULTS Through quantitative traits characterization, genetic diversity assessment, and association studies, we generated a selection population with wide genetic diversity, and identified five excellent high-yield parental combinations associated with four reliable high-yield ISSR markers. Early selection criteria were determined based on kernel fresh weight and cultivated 1-year seedling height, aided by the identification of these 4 ISSR markers. Specific assignment of selected individuals as paternal and maternal parents was made to capitalize on their unique attributes. CONCLUSIONS Our results indicated that molecular markers-assisted breeding can effectively shorten, enhance selection accuracy and efficiency and facilitate the development of a new breeding system for C. oleifera.
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Affiliation(s)
- Jinjia Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haiqi Su
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shaosheng Pu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Zhijian Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jinling Feng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Ye C, He Z, Peng J, Wang R, Wang X, Fu M, Zhang Y, Wang A, Liu Z, Jia G, Chen Y, Tian B. Genomic and genetic advances of oiltea-camellia ( Camellia oleifera). FRONTIERS IN PLANT SCIENCE 2023; 14:1101766. [PMID: 37077639 PMCID: PMC10106683 DOI: 10.3389/fpls.2023.1101766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Oiltea-camellia (C. oleifera) is a widely cultivated woody oil crop in Southern China and Southeast Asia. The genome of oiltea-camellia was very complex and not well explored. Recently, genomes of three oiltea-camellia species were sequenced and assembled, multi-omic studies of oiltea-camellia were carried out and provided a better understanding of this important woody oil crop. In this review, we summarized the recent assembly of the reference genomes of oiltea-camellia, genes related to economic traits (flowering, photosynthesis, yield and oil component), disease resistance (anthracnose) and environmental stress tolerances (drought, cold, heat and nutrient deficiency). We also discussed future directions of integrating multiple omics for evaluating genetic resources and mining key genes of important traits, and the application of new molecular breeding and gene editing technologies to accelerate the breeding process of oiltea-camellia.
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Affiliation(s)
- Changrong Ye
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Zhilong He
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Jiayu Peng
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Rui Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Xiangnan Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Mengjiao Fu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Ying Zhang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Ai Wang
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Zhixian Liu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Gaofeng Jia
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Yongzhong Chen
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Bingchuan Tian
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
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Wang Z, Huang B, Ye J, He Y, Tang S, Wang H, Wen Q. Comparative transcriptomic analysis reveals genes related to the rapid accumulation of oleic acid in Camellia chekiangoleosa, an oil tea plant with early maturity and large fruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:95-104. [PMID: 34974387 DOI: 10.1016/j.plaphy.2021.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Camellia chekiangoleosa has a higher oleic acid content and a shorter reproductive cycle than typical oil tea plants. It was intensively sampled over six C. chekiangoleosa seed development stages. The content of fatty acids determined by GC showed that the accumulation of fatty acids gradually increased from the S1 to S5 stages, and the maximum concentration was reached in S5. Then, fatty acids declined slightly in S6. The main fatty acid component showed the same accumulation trend as the total fatty acids, except linolenic acid, which remained at a low level throughout seed developmental stages. Changes in the expression of fatty acid accumulation-related genes were monitored using second-generation and SMRT full-length transcriptome sequencing. Finally, 18.92 G accurate and reliable data were obtained. Differential expression analysis and weighted coexpression analysis revealed two "gene modules" significantly associated with oleic acid and linoleic acid contents, and the high expression of ENR, KAS I, and KAS II, which accumulate substrates for oleic acid synthesis, was thought to be responsible for the rapid accumulation of fatty acids in the early stage. The rapid increase in fatty acids in the second stage may be closely related to the synergy between the high expression of SAD and low expression of FAD2. In addition, many transcription factors, such as ERF, GRAS, GRF, MADS, MYB and WRKY, may be involved in the fatty acid synthesis. Our data provide a rich resource for further studies on the regulation of fatty acid synthesis in C. chekiangoleosa.
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Affiliation(s)
- Zhongwei Wang
- Key Laboratory of Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang, 330032, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Bin Huang
- Key Laboratory of Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang, 330032, China.
| | - Jinshan Ye
- Key Laboratory of Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang, 330032, China.
| | - Yichang He
- Key Laboratory of Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang, 330032, China.
| | - Shijie Tang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Huanli Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Qiang Wen
- Key Laboratory of Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang, 330032, China.
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Lin P, Wang K, Wang Y, Hu Z, Yan C, Huang H, Ma X, Cao Y, Long W, Liu W, Li X, Fan Z, Li J, Ye N, Ren H, Yao X, Yin H. The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. Genome Biol 2022; 23:14. [PMID: 35012630 PMCID: PMC8744323 DOI: 10.1186/s13059-021-02599-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/31/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production. However, the molecular mechanism of the domestication of oil-Camellia is still limited due to the lack of sufficient genomic information. RESULTS To elucidate the genetic and genomic basis of evolution and domestication, here we report a chromosome-scale reference genome of wild oil-Camellia (2.95 Gb), together with transcriptome sequencing data of 221 cultivars. The oil-Camellia genome, assembled by an integrative approach of multiple sequencing technologies, consists of a large proportion of repetitive elements (76.1%) and high heterozygosity (2.52%). We construct a genetic map of high-density corrected markers by sequencing the controlled-pollination hybrids. Genome-wide association studies reveal a subset of artificially selected genes that are involved in the oil biosynthesis and phytohormone pathways. Particularly, we identify the elite alleles of genes encoding sugar-dependent triacylglycerol lipase 1, β-ketoacyl-acyl carrier protein synthase III, and stearoyl-acyl carrier protein desaturases; these alleles play important roles in enhancing the yield and quality of seed oil during oil-Camellia domestication. CONCLUSIONS We generate a chromosome-scale reference genome for oil-Camellia plants and demonstrate that the artificial selection of elite alleles of genes involved in oil biosynthesis contributes to oil-Camellia domestication.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Kailiang Wang
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Chao Yan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Hu Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Yongqing Cao
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Wei Long
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Weixin Liu
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Xinlei Li
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Zhengqi Fan
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Jiyuan Li
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Ning Ye
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Huadong Ren
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
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Yang C, Wu P, Yao X, Sheng Y, Zhang C, Lin P, Wang K. Integrated Transcriptome and Metabolome Analysis Reveals Key Metabolites Involved in Camellia oleifera Defense against Anthracnose. Int J Mol Sci 2022; 23:536. [PMID: 35008957 PMCID: PMC8745097 DOI: 10.3390/ijms23010536] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/19/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
Camellia oleifera (Ca. oleifera) is a woody tree species cultivated for the production of edible oil from its seed. The growth and yield of tea-oil trees are severely affected by anthracnose (caused by Colletotrichum gloeosporioides). In this study, the transcriptomic and metabolomic analyses were performed to detect the key transcripts and metabolites associated with differences in the susceptibility between anthracnose-resistant (ChangLin150) and susceptible (ChangLin102) varieties of Ca. oleifera. In total, 5001 differentially expressed genes (DEGs) were obtained, of which 479 DEGs were common between the susceptible and resistant varieties and further analyzed. KEGG enrichment analysis showed that these DEGs were significantly enriched in tyrosine metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis and isoquinoline alkaloid biosynthesis pathways. Furthermore, 68 differentially accumulated metabolites (DAMs) were detected, including flavonoids, such as epicatechin, phenethyl caffeate and procyanidin B2. Comparison of the DEGs and DAMs revealed that epicatechin, procyanidin B2 and arachidonic acid (peroxide free) are potentially important. The expression patterns of genes involved in flavonoid biosynthesis were confirmed by qRT-PCR. These results suggested that flavonoid biosynthesis might play an important role in the fight against anthracnose. This study provides valuable molecular information about the response of Ca. oleifera to Co. gloeosporioides infection and will aid the selection of resistant varieties using marker-assisted breeding.
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Affiliation(s)
| | | | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (C.Y.); (P.W.); (Y.S.); (C.Z.); (P.L.); (K.W.)
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