茶树花表型性状及全基因组关联分析

阳虹; 邵陈禹; 姚林; 饶佳怡; 彭律文; 黄飞毅; 段继华; 谢念祠; 陈宇宏; 李赛君; 刘硕谦; 雷雨

PDF(2091 KB)

茶叶科学 ›› 2026, Vol. 46 ›› Issue (3) : 435-448.

研究报告

茶树花表型性状及全基因组关联分析

阳虹^1,2,3, 邵陈禹¹, 姚林^1,2,3, 饶佳怡^1,2,3, 彭律文^1,2,3, 黄飞毅^2,3, 段继华^2,3, 谢念祠^2,3, 陈宇宏^2,3, 李赛君^2,3, 刘硕谦^1,2,*, 雷雨^1,2,*

作者信息 +

Phenotypic Traits and Genome-Wide Association Study of Camellia sinensis Flowers

YANG Hong^1,2,3, SHAO Chenyu¹, YAO Lin^1,2,3, RAO Jiayi^1,2,3, PENG Lüwen^1,2,3, HUANG Feiyi^2,3, DUAN Jihua^2,3, XIE Nianci^2,3, CHEN Yuhong^2,3, LI Saijun^2,3, LIU Shuoqian^1,2,*, LEI Yu^1,2,*

Author information +

文章历史 +

摘要

花作为茶树主要的生殖器官,其表型性状多样性研究对茶树遗传改良具有重要意义。以64份茶树种质为材料,系统鉴定了其花部9个质量性状与12个数量性状的表型多样性,并利用47 111个高质量单核苷酸多态性（Single nucleotide polymorphism,SNP）标记进行了群体遗传结构与全基因组关联分析（Genome-wide association study,GWAS）。结果表明,供试材料花部性状遗传多样性丰富,其中子房茸毛、百花质量及分裂部位长度占花柱全长比例变异较大,可作为核心评价指标。群体结构分析将材料划分为3个遗传亚群,且与表型聚类结果高度一致。通过GWAS,共鉴定出245个SNP位点与10个重要花部性状显著关联,并进一步筛选出5个核心候选基因（GWHTASIV003067、GWHTASIV018433、GWHTASIV032688、GWHTASIV001183、GWHTASIV044042）,其功能涉及生长调节、RNA编辑、细胞周期调控、染色质重塑及转录调控等关键生物学过程。研究从多维度系统解析了茶树花性状的遗传基础,为茶树花部性状的分子机制研究和分子标记辅助育种提供了重要的基因资源与理论依据。

Abstract

As the primary reproductive organ of the tea plant (Camellia sinensis), the flower exhibits rich phenotypic diversity, which holds significant importance for the genetic improvement of tea plants. In this study, 64 tea germplasm accessions were used to systematically investigate the phenotypic diversity of nine qualitative traits and twelve quantitative traits related to floral morphology. Based on 47 111 high-quality SNP markers, population genetic structure analysis and genome-wide association study (GWAS) were performed. The results reveal abundant genetic diversity in floral traits among the tested materials, with ovary villi, weight per 100 flowers, and the proportion of the bifurcation to the columella showing relatively large variation, which could serve as core evaluation indicators. Population structure analysis divided the materials into three genetic subgroups, which were highly consistent with the phenotypic clustering results. Through GWAS, 245 SNP loci significantly associated with 10 important floral traits were identified. Furthermore, five core candidate genes (GWHTASIV003067, GWHTASIV018433, GWHTASIV032688, GWHTASIV001183, GWHTASIV044042) were identified, which are involved in key biological processes such as growth regulation, RNA editing, cell cycle control, chromatin remodeling and transcriptional regulation. This study provided a systematic multidimensional analysis of the genetic basis of floral traits in tea plants for the first time, offering important gene resources and a theoretical foundation for research into the molecular mechanisms of floral traits and for molecular marker-assisted breeding in tea plants.

导出引用

阳虹, 邵陈禹, 姚林, 饶佳怡, 彭律文, 黄飞毅, 段继华, 谢念祠, 陈宇宏, 李赛君, 刘硕谦, 雷雨. 茶树花表型性状及全基因组关联分析[J]. 茶叶科学. 2026, 46(3): 435-448

YANG Hong, SHAO Chenyu, YAO Lin, RAO Jiayi, PENG Lüwen, HUANG Feiyi, DUAN Jihua, XIE Nianci, CHEN Yuhong, LI Saijun, LIU Shuoqian, LEI Yu. Phenotypic Traits and Genome-Wide Association Study of Camellia sinensis Flowers[J]. Journal of Tea Science. 2026, 46(3): 435-448

中图分类号： S571.1 S326

参考文献

[1] 牛小军, 包兴伟, 郑旭霞, 等. 四川九龙古茶树种质资源农艺性状遗传多样性研究[J]. 植物遗传资源学报, 2024, 25(2): 249-258.
Niu X J, Bao X W, Zheng X X, et al.The phenotypic diversity analysis of ancient tea germplasm resources in Jiulong County, Sichuan Province, China[J]. Journal of Plant Genetic Resources, 2024, 25(2): 249-258.
[2] 余文权, 林郑和, 陈常颂, 等. 19个茶树杂交新品系主要性状比较及其遗传多样性分析[J]. 热带亚热带植物学报, 2021, 29(6): 649-659.
Yu W Q, Lin Z H, Chen C S, et al.Main agronomic characters and genetic diversity of 19 cross new lines of tea cultivars[J]. Journal of Tropical and Subtropical Botany, 2021, 29(6): 649-659.
[3] 刘莹, 郝心愿, 郑梦霞, 等. 茶树成花机理研究进展[J]. 茶叶科学, 2019, 39(1): 1-10.
Liu Y, Hao X Y, Zheng M X, et al.Recent advances on tea flowering mechanisms[J]. Journal of Tea Science, 2019, 39(1): 1-10.
[4] 陈琪予, 马建强, 陈杰丹, 等. 利用图像特征分析茶树成熟叶表型的遗传多样性[J]. 茶叶科学, 2022, 42(5): 649-660.
Chen Q Y, Ma J Q, Chen J D, et al.Genetic diversity of mature leaves of tea germplasms based on image features[J]. Journal of Tea Science, 2022, 42(5): 649-660.
[5] 李红蝶, 肖田, 李亦龙, 等. 茶树花的功能成分及相关产品研究进展[J]. 食品安全质量检测学报, 2024, 15(6): 117-123.
Li H D, Xiao T, Li Y L, et al.Research progress on functional components of Camellia sinensis and related products[J]. Journal of Food Safety & Quality, 2024, 15(6): 117-123.
[6] Xia E H, Tong W, Wu Q, et al. Tea plant genomics: achievements, challenges and perspectives[J]. Horticulture Research, 2020, 7: 7. https://doi.org/10.1038/s41438-019-0225-4.
[7] Sehgal D, Dreisigacker S.GWAS case studies in wheat[M]//Walker J M. Methods in molecular biology. Totowa: Humana Press, 2022: 341-351.
[8] Wang Q, Tang J L, Han B, et al.Advances in genome-wide association studies of complex traits in rice[J]. Theoretical and Applied Genetics, 2020, 133(5): 1415-1425.
[9] 瞿静涛, 胡颖雄, 卫季辉, 等. 鲜食玉米株高和穗位高性状的全基因组关联分析[J/OL]. 分子植物育种, 2025-09-04
[2026-01-23]. https://link.cnki.net/urlid/46.1068.S.20250903.1821.002. Qu J T, Hu Y X, Wei J H, et al. Genome-wide association analysis of plant height and ear height traits in edible maize[J]. Molecular Plant Breeding: 2025-09-04[2026-01-23]. https://link.cnki.net/urlid/46.1068.S.20250903.1821.002.
[10] Yamashita H, Uchida T, Tanaka Y, et al. Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plant[J]. Scientific Reports, 2020, 10(1): 17480. https://doi.org/10.1038/s41598-020-74623-7.
[11] Lei X G, Li H Y, Li P P, et al. Genome-wide association studies of Biluochun tea plant populations in Dongting Mountain and comprehensive identification of candidate genes associated with core agronomic traits by four analysis models[J]. Plants, 2023, 12(21): 3719. https://doi.org/10.3390/plants12213719.
[12] Lu L T, Chen H F, Wang X J, et al. Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits[J]. Horticulture Research, 2021, 8(1): 190. https://doi.org/10.1038/s41438-021-00617-9.
[13] Hazra A, Kumar R, Sengupta C, et al.Genome-wide SNP discovery from Darjeeling tea cultivars: their functional impacts and application toward population structure and trait associations[J]. Genomics, 2021, 113(1): 66-78.
[14] Wang R J, Gao X F, Yang J, et al.Genome-wide association study to identify favorable SNP allelic variations and candidate genes that control the timing of spring bud flush of tea (Camellia sinensis) using SLAF-seq[J]. Journal of Agricultural and Food Chemistry, 2019, 67(37): 10380-10391.
[15] Huang R, Wang J Y, Yao M Z, et al. Quantitative trait loci mapping for free amino acid content using an albino population and SNP markers provides insight into the genetic improvement of tea plants[J]. Horticulture Research, 2022, 9: uhab029. https://doi.org/10.1093/hr/uhab029.
[16] Zhang J, Chen C, Yang Q H, et al.Evolution of HD-ZIP transcription factors and their function in cabbage leafy head formation[J]. Frontiers in Plant Science, 2025, 16: 1583110. https://doi.org/10.3389/fpls.2025.1583110.
[17] 陈亮, 杨亚军, 虞富莲, 等. 茶树种质资源描述规范和数据标准[M]. 北京: 中国农业出版社, 2005: 15-49.
Chen L, Yang Y J, Yu F L, et al.Descriptors and data standard for tea (Camellia spp.)[M]. Beijing: China Agriculture Press, 2005: 15-49.
[18] 郝曦煜, 杨涛, 梁杰, 等. 160份外引鹰嘴豆种质主要农艺性状的遗传多样性分析[J]. 植物遗传资源学报, 2020, 21(4): 875-883.
Hao X Y, Yang T, Liang J, et al.Genetic diversity analysis of major agronomic traits in 160 introduced chickpea(Cicer arietinum L.)germplasm resources[J]. Journal of Plant Genetic Resources, 2020, 21(4): 875-883.
[19] 曹磊, 毛文文, 梁晓雪, 等. 甜瓜叶绿素含量全基因组关联分析及候选基因预测[J]. 河南农业大学学报, 2023, 57(2): 231-240.
Cao L, Mao W W, Liang X X, et al.Genome-wide association analysis of chlorophyll content in melon and prediction of the candidate genes[J]. Journal of Henan Agricultural University, 2023, 57(2): 231-240.
[20] Yang N, Lu Y L, Yang X H, et al. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel[J]. PLoS Genetics, 2014, 10(9): e1004573. https://doi.org/10.1371/journal.pgen.1004573.
[21] Ma L L, Qing C Y, Frei U, et al.Association mapping for root system architecture traits under two nitrogen conditions in germplasm enhancement of maize doubled haploid lines[J]. The Crop Journal, 2020, 8(2): 213-226.
[22] Cardon L R, Palmer L J.Population stratification and spurious allelic association[J]. The Lancet, 2003, 361(9357): 598-604.
[23] Guo J, Zhao C C, Gupta S, et al. Genome-wide association mapping for seedling and adult resistance to powdery mildew in barley[J]. Theoretical and Applied Genetics, 2024, 137(3): 50. https://doi.org/10.1007/s00122-024-04550-y.
[24] Yoosefzadeh-Najafabadi M, Eskandari M, Torabi S, et al. Machine-learning-based genome-wide association studies for uncovering QTL underlying soybean yield and its components[J]. International Journal of Molecular Sciences, 2022, 23(10): 5538. https://doi.org/10.3390/ijms23105538.
[25] 玉山江·麦麦提, 杨渡, 韩盛, 等. 水稻转录因子OsHOX6过量表达及其对水稻根生长作用[J]. 分子植物育种, 2019, 17(19): 6350-6355.
Yushanjiang M, Yang D, Han S, et al.Over expression of rice transcription factor OsHOX6 in rice effect on rice root growth[J]. Molecular Plant Breeding, 2019, 17(19): 6350-6355.
[26] Li J X, Hu N, Sun J, et al. Genome-wide identification and characterization of the homeodomain leucine zipper protein (HD-Zip) gene family in sea buckthorn (Hippophae rhamnoides) under lead stress[J]. Forests, 2025, 16(1): 171. https://doi.org/10.3390/f16010171.
[27] Yousaf S, Rehman T, Tabassum B, et al. Genome scale analysis of 1-aminocyclopropane-1-carboxylate oxidase gene family in G. barbadense and its functions in cotton fiber development[J]. Scientific Reports, 2023, 13(1): 4004. https://doi.org/10.1038/s41598-023-30071-7.
[28] 裴芸, 虞夏清, 赵晓坤, 等. 多倍化与植物新表型关联性的研究进展[J]. 园艺学报, 2023, 50(9): 1854-1866.
Pei Y, Yu X Q, Zhao X K, et al.Progress in the study of the association of polyploidy with new plant phenotypes[J]. Acta Horticulturae Sinica, 2023, 50(9): 1854-1866.
[29] 李洪果, 陈达镇, 许靖诗, 等. 濒危植物格木天然种群的表型多样性及变异[J]. 林业科学, 2019, 55(4): 69-83.
Li H G, Chen D Z, Xu J S, et al.Phenotypic diversity and variation in natural populations of Erythrophleum fordii,an endangered plant species[J]. Scientia Silvae Sinicae, 2019, 55(4): 69-83.
[30] 苏群, 杨亚涵, 田敏, 等. 49份睡莲资源表型多样性分析及综合评价[J]. 西南农业学报, 2019, 32(11): 2670-2681.
Su Q, Yang Y H, Tian M, et al.Phenotypic diversity analysis and comprehensive evaluation of 49 waterlily resources[J]. Southwest China Journal of Agricultural Sciences, 2019, 32(11): 2670-2681.
[31] 董胜君, 王若溪, 张皓凯, 等. 不同种源东北杏果实表型性状多样性分析[J]. 植物资源与环境学报, 2020, 29(6): 42-50.
Dong S J, Wang R X, Zhang H K, et al.Analysis on diversity of fruit phenotypic characters of Armeniaca mandshurica from different provenances[J]. Journal of Plant Resources and Environment, 2020, 29(6): 42-50.
[32] 李长乐, 葛悦, 闫美琳, 等. 32份茶树地方群体种资源的遗传多样性和群体结构分析[J]. 茶叶科学, 2021, 41(5): 619-630.
Li C Y, Ge Y, Yan M L, et al.Analysis of genetic diversity and population structure of 32 tea landraces in China[J]. Journal of Tea Science, 2021, 41(5): 619-630.
[33] 房婉萍, 雷小刚, 杨彬, 等. 全基因组关联分析在茶叶研究中的应用进展[J]. 华中农业大学学报, 2022, 41(5): 33-40.
Fang W P, Lei X G, Yang B, et al.Application of genome-wide association analysis in studying tea[J]. Journal of Huazhong Agricultural University, 2022, 41(5): 33-40.
[34] 江彪, 闫晋强, 晏石娟, 等. 葫芦科作物基因组学研究进展[J]. 广东农业科学, 2023, 50(4): 1-12.
Jiang B, Yan J Q, Yan S J, et al.Research progresses on the genomics of Cucurbitaceae crops[J]. Guangdong Agricultural Sciences, 2023, 50(4): 1-12.
[35] 梅飘, 刘丁丁, 叶圆圆, 等. 基于茶树液相功能芯片的白化茶树资源遗传多样性分析[J]. 作物学报, 2025, 51(9): 2358-2370.
Mei P, Liu D D, Ye Y Y, et al.Genetic diversity analysis of domestic albino tea germplasm resources based onthe tea plant liquid phase functional chip[J]. Acta Agronomica Sinica, 2025, 51(9): 2358-2370.
[36] 郭佳璐, 璩馥榕, 蔡天晨, 等. 基于农艺性状和SNP分子标记的湖南78份茶树种质资源遗传多样性研究[J]. 茶叶科学, 2025, 45(2): 219-233.
Guo J L, Qu F R, Cai T C, et al.Study on the genetic diversity of 78 tea germplasm resources in Hunan based on agronomic traits and SNP molecular markers[J]. Journal of Tea Science, 2025, 45(2): 219-233.
[37] Remington D L, Thornsberry J M, Matsuoka Y, et al.Structure of linkage disequilibrium and phenotypic associations in the maize genome[J]. PNAS, 2001, 98(20): 11479-11484.
[38] Wang A J, Jiang Y Q, Shu X Y, et al.Genome-wide association study-based identification genes influencing agronomic traits in rice (Oryza sativa L.)[J]. Genomics, 2021, 113(3): 1396-1406.
[39] 马超, 原佳乐, 张苏, 等. GRF转录因子对植物生长发育及胁迫响应调控的分子机制[J]. 核农学报, 2017, 31(11): 2145-2153.
Ma C, Yuan J L, Zhang S, et al.The molecular mechanisms of growth-regulating factors (GRFs) in plant growth, development and stress response[J]. Journal of Nuclear Agricultural Sciences, 2017, 31(11): 2145-2153.
[40] Lazzara F E, Rodriguez R E, Palatnik J F.Molecular mechanisms regulating GROWTH-REGULATING FACTORS activity in plant growth, development, and environmental responses[J]. Journal of Experimental Botany, 2024, 75(14): 4360-4372.
[41] Kim J H.Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants[J]. BMB Reports, 2019, 52(4): 227-238.
[42] Sugita M. An overview of pentatricopeptide repeat (PPR) proteins in the moss Physcomitrium patens and their role in organellar gene expression[J]. Plants, 2022, 11(17): 2279. https://doi.org/10.3390/plants11172279.
[43] Shikanai T, Fujii S.Function of PPR proteins in plastid gene expression[J]. RNA Biology, 2013, 10(9): 1446-1456.
[44] Saha D, Prasad A M, Srinivasan R.Pentatricopeptide repeat proteins and their emerging roles in plants[J]. Plant Physiology and Biochemistry, 2007, 45(8): 521-534.
[45] Kobayashi K, Suzuki T, Iwata E, et al.MYB3Rs, plant homologs of Myb oncoproteins, control cell cycle-regulated transcription and form DREAM-like complexes[J]. Transcription, 2015, 6(5): 106-111.
[46] Cominelli E, Tonelli C.A new role for plant R2R3-MYB transcription factors in cell cycle regulation[J]. Cell Research, 2009, 19(11): 1231-1322.
[47] Yang W B, Cortijo S, Korsbo N, et al.Molecular mechanism of cytokinin-activated cell division in Arabidopsis[J]. Science, 2021, 371(6536): 1350-1355.
[48] Noh Y S, Amasino R M.PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis article[J]. The Plant Cell Online, 2003, 15(7): 1671-1682.
[49] Nie W F, Wang J Y. Actin-related protein 4 interacts with PIE1 and regulates gene expression in Arabidopsis[J]. Genes, 2021, 12(4): 520. https://doi.org/10.3390/genes12040520.
[50] Fojtová M, Fajkus J. Chromatin, epigenetics and plant physiology[J]. International Journal of Molecular Sciences, 2020, 21(8): 2763. https://doi.org/10.3390/ijms21082763.
[51] Zhao Y S, Jiang T, Li L, et al.The chromatin remodeling complex imitation of switch controls stamen filament elongation by promoting jasmonic acid biosynthesis in Arabidopsis[J]. Journal of Genetics and Genomics, 2021, 48(2): 123-133.
[52] Wu M L, Bian X X, Huang B B, et al.HD-Zip proteins modify floral structures for self-pollination in tomato[J]. Science, 2024, 384(6691): 124-130.
[53] Lin Z F, Hong Y G, Yin M G, et al.A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening[J]. The Plant Journal, 2008, 55(2): 301-310.
[54] Castricum A, Bakker E H, de Vetten N C M H, et al. HD-ZIP transcription factors and brassinosteroid signaling play a role in capitulum patterning in chrysanthemum[J]. International Journal of Molecular Sciences, 2023, 24(8): 7655. https://doi.org/10.3390/ijms24087655.
[55] 王宏, 李刚波, 张大勇, 等. 植物HD-Zip转录因子的生物学功能[J]. 遗传, 2013, 35(10): 1179-1188.
Wang H, Li G B, Zhang D Y, et al.Biological functions of HD-Zip transcription factors[J]. Hereditas (Beijing), 2013, 35(10): 1179-1188.
[56] Żyła N, Babula-Skowrońska D.Evolutionary consequences of functional and regulatory divergence of HD-Zip Ⅰ transcription factors as a source of diversity in protein interaction networks in plants[J]. Journal of Molecular Evolution, 2023, 91(5): 581-597.
[57] 卢小云, 余礼, 张秀峰, 等. 禾本科植物HD-ZIP转录因子研究进展[J]. 植物生理学报, 2021, 57(4): 727-738.
Lu X Y, Yu L, Zhang X F, et al.Research progress of HD-ZIP transcription factor in gramineae plants[J]. Plant Physiology Journal, 2021, 57(4): 727-738.