基于全基因组重测序的白化茶树mSNP标记开发及验证

doi:10.13305/j.cnki.jts.2023.01.003

茶叶科学 ›› 2023, Vol. 43 ›› Issue (1): 27-39.doi: 10.13305/j.cnki.jts.2023.01.003

基于全基因组重测序的白化茶树mSNP标记开发及验证

刘浩然^1,2, 张晨禹^1,2, 龚洋^1,2, 叶圆圆^1,2, 陈杰丹¹, 陈亮¹, 刘丁丁^1,*, 马春雷^1,*

1.中国农业科学院茶叶研究所/农业农村部特种经济动植物生物学与遗传育种重点实验室,浙江杭州 310008;
2.中国农业科学院研究生院,北京 100081

收稿日期:2022-10-12 修回日期:2022-11-24 出版日期:2023-02-15 发布日期:2023-03-01
通讯作者: * liudingding@tricaas.com;malei220@tricaas.com
作者简介:刘浩然,男,硕士研究生,主要从事茶树资源育种与遗传改良研究。
基金资助:
国家重点研发计划课题（2021YFD1200203）、浙江省农业（茶树）新品种选育重大科技专项子课题（2021C02067-6-1）、中国农业科学院茶叶研究所基本科研业务费（1610212022009）、浙江省自然科学基金（LQ20C160010）

Development and Application of Albinotea Plant mSNP Molecular Markers Based on Genome-wide Resequencing

LIU Haoran^1,2, ZHANG Chenyu^1,2, GONG Yang^1,2, YE Yuanyuan^1,2, CHEN Jiedan¹, CHEN Liang¹, LIU Dingding^1,*, MA Chunlei^1,*

1. Tea Research Institute of the Chinese Academy of Agricultural Science/Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, P. R. China, Hangzhou 310008, China;
2. Graduate School of Chinese Academy of Agriculture Science, Beijing 100081, China

Received:2022-10-12 Revised:2022-11-24 Online:2023-02-15 Published:2023-03-01

摘要/Abstract

摘要： 为探究白化茶树遗传变异信息及mSNP液相芯片在茶树种质资源鉴定中的可行性,利用全基因组重测序对18份白化茶树资源进行遗传多样性分析和突变位点检测。结果表明,基于全基因组水平的SNP标记可将18份白化茶树资源分为3类,且基本呈现出具有亲缘关系或地理位置接近的资源聚在一起的趋势;对重测序数据进行功能注释后发现,在18份白化茶树资源中存在17 056个共有非同义突变基因,其中14个叶绿素合成相关基因中存在98个错义突变位点。随后,基于前期获得的基因组变异信息开发了一套包含59个mSNP、222个SNP位点的液相芯片,利用该液相芯片检测13份茶树资源的基因型信息。结果表明,同一品种两两之间的遗传相似度在92%~98%,不同品种间的遗传相似度则在84%以下,表明该芯片可对18份白化茶树资源进行准确鉴别,研究结果可为mSNP液相芯片在茶树种质资源鉴定、分子标记辅助育种等方面的应用奠定基础。

关键词: 茶树, mSNP分子标记, 靶向测序基因型检测, 遗传多样性, 全基因组重测序

Abstract: To explore the information of genetic variation in albino tea and the feasibility of the mSNP liquid chip in the identification of tea germplasm, we analyzed the genetic diversity and detected the mutation sites of 18 tea resources by genome resequencing. The results indicate that the 18 albino tea accessions could be divided into three groups based on genome-wide SNP markers, and the resources with genetic relationship or close geographical location tended to cluster together. Functional annotation of the resequencing data reveals 17 056 non-synonymous mutated genes in the 18 albino tea resources, of which 98 missense mutations were found in 14 chlorophyll synthesis related genes. Then, based on the genomic variation information obtained in the previous study, we developed a set of liquid chip containing 59 mSNP and 222 SNP sites for the first time, and used the liquid chip to detect the genotype information of 13 tea plants. The results show that the genetic similarity between pairs of the same cultivar was 92%-98%, and the genetic similarity between different cultivar was less than 84%, indicating that the chip could accurately identify 18 albino tea accessions. Our results laid a foundation for the application of mSNP liquid phase chip in the identification of tea germplasm resources and molecular marker-assisted breeding.

Key words: tea plant, mSNP, GBTS, genetic diversity, whole genome resequencing

中图分类号:

S571.1
S326

刘浩然, 张晨禹, 龚洋, 叶圆圆, 陈杰丹, 陈亮, 刘丁丁, 马春雷. 基于全基因组重测序的白化茶树mSNP标记开发及验证[J]. 茶叶科学, 2023, 43(1): 27-39. doi: 10.13305/j.cnki.jts.2023.01.003.

LIU Haoran, ZHANG Chenyu, GONG Yang, YE Yuanyuan, CHEN Jiedan, CHEN Liang, LIU Dingding, MA Chunlei. Development and Application of Albinotea Plant mSNP Molecular Markers Based on Genome-wide Resequencing[J]. Journal of Tea Science, 2023, 43(1): 27-39. doi: 10.13305/j.cnki.jts.2023.01.003.

参考文献

[1] 刘丁丁, 梅菊芬, 王君雅, 等. 茶树白化突变研究进展[J]. 中国茶叶, 2020, 42(4): 24-35.
Liu D D, Mei J F, Wang J Y, et al.Research progress on albino trait of tea plant[J]. China Tea, 2020, 42(4): 24-35.
[2] 王开荣, 李明, 梁月荣, 等. 茶树新品种黄金芽选育研究[J]. 中国茶叶, 2008, 30(4): 21-23.
Wang K R, Li M, Liang Y R, et al.Study on breeding of new tea variety ‘Huangjinya’[J]. China Tea, 2008, 30(4): 21-23.
[3] 虞富莲. 中黄1号、中黄2号的特异性、一致性和稳定性[J]. 中国茶叶, 2016, 38(3): 14-16.
Yu F L.Distinctness uniformity and stability of ‘Zhonghuang 1’ and ‘Zhonghuang 2’[J]. China Tea, 2016, 38(3): 14-16.
[4] 张友炯, 曾建明, 章志芳, 等. 白化茶树新品种“中白1号”选育报告[J]. 中国茶叶, 2016, 38(3): 22-24.
Zhang Y J, Zeng J M, Zhang Z F, et al.Breeding report of a new albino tea variety ‘Zhongbai 1’[J]. China Tea, 2016, 38(3): 22-24.
[5] 陈亮, 杨亚军, 虞富莲, 等. 15个茶树品种遗传多样性的RAPD分析[J]. 茶叶科学, 1998, 18(1): 21-27.
Chen L, Yang Y J, Yu F L, et al.Genetic diversity of 15 tea (Camellia sinensis (L.) O. Kuntze) cultivars using RAPD markrrs[J]. Journal of Tea Science, 1998, 18(1): 21-27.
[6] 黎星辉, 章传政, 刘春林, 等. 中国茶组植物种质资源遗传多样性的RAPD分析[J]. 园艺学报, 2007, 34(2): 507-508.
Li X H, Zhang C Z, Liu C L, et al.RAPD analysis of the genetic diversity in chinese tea germplasm[J]. Acta Horticulturae Sinica, 2007, 34(2): 507-508.
[7] 唐立群, 肖层林, 王伟平. SNP分子标记的研究及其应用进展[J]. 中国农学通报, 2012, 28(12): 154-158.
Tang L Q, Xiao C L, Wang W P.Research and application progress of SNP markers[J]. Chinese Agricultural Science Bulletin, 2012, 28(12): 154-158.
[8] 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 L, 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.
[9] 陈立杰, 张素勤, 尹杰, 等. 贵阳花溪古茶树遗传进化的SNP分析[J]. 西南大学学报(自然科学版), 2019, 41(8): 33-40.
Chen L J, Zhang S Q, Yin J, et al.SNP analysis of the genetic evolution of ancient Camellia sinensis tress from Huaxi, Guiyang[J]. Journal of Southwest University (Natural Science Edition), 2019, 41(8): 33-40.
[10] 樊晓静, 于文涛, 蔡春平, 等. 利用SNP标记构建茶树品种资源分子身份证[J]. 中国农业科学, 2021, 54(8): 1751-1772.
Fan X J, Yu W T, Cai C P, et al.Construction of molecular ID for tea cultivars by using of single-nucleotide polymorphism (SNP) markers[J]. Scientia Agricultura Sinica, 2021, 54(8): 1751-1772.
[11] 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. doi: 10.1093/hr/uhab029.
[12] 方治伟, 周俊飞, 刘致浩, 等. 一种筛选植物高多态性分子标记位点的方法: CN107815489B[P].2021-06-29.
Fang Z W, Zhou J F, Liu Z H, et al. A method for screening highly polymorphic molecular markers in plants: CN107815489B [P].2021-06-29.
[13] 徐云碧, 杨泉女, 郑洪建, 等. 靶向测序基因型检测(GBTS)技术及其应用[J]. 中国农业科学, 2020, 53(15): 2983-3004.
Xu Y B, Yang Q N, Zheng H J, et al.Genotyping by target sequencing (GBTS) and its applications[J]. Scientia Agricultura Sinica, 2020, 53(15): 2983-3004.
[14] Guo Z, Yang Q, Huang F, et al.Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip[J]. Plant Communications, 2021, 2(6): 100230. doi: 10.1016/j.xplc.2021.100230.
[15] 蒋成功, 石慧敏, 王红武, 等. 玉米籽粒突变体smk7的表型分析和基因定位[J]. 作物学报, 2021, 47(2): 285-293.
Jiang C G, Shi H M, Wang H W, et al.Phenotype analysis and gene mapping of small kernel 7 (smk7) mutant in maize[J]. Acta Agronomica Sinica, 2021, 47(2): 285-293.
[16] 陈宇, 邱奥, 张梓鹏, 等. 猪SNP液相芯片10K~50K基因型填充效果研究[J]. 畜牧兽医学报, 2022, 53(10): 3368-3376.
Chen Y, Qiu A, Zhang Z P, et al.Study on the genotype imoutation effect of 10K-50K genotype of pig SNP liquid chip[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(10): 3368-3376.
[17] 邱奥, 王雪, 孟庆利, 等. 3款猪50K SNP芯片基因型填充效果研究[J]. 中国畜牧杂志, 2021, 57(s1): 33-38.
Qiu A, Wang X, Meng Q L, et al.Study on genotype filling effect of three kinds of 50K SNP chips[J]. Chinese Journal of Animal Science, 2021, 57(s1): 33-38.
[18] 王松琳, 马春雷, 黄丹娟, 等. 基于SSR标记的白化和黄化茶树品种遗传多样性分析及指纹图谱构建[J]. 茶叶科学, 2018, 38(1): 58-68.
Wang S L, Ma C L, Huang D J, et al.Analysis of genetic diversity and construction of DNA fingerprints of chorophyll-deficient tea cultivars by SSR markers[J]. Journal of Tea Science, 2018, 38(1): 58-68.
[19] 李佳佳, 于旭东, 蔡泽坪, 等. 高等植物叶绿素生物合成研究进展[J]. 分子植物育种, 2019, 17(18): 6013-6019.
Li J J, Yu X D, Cai Z P, et al.An overview of chlorophyll biosynthesis in higher plants[J]. Molecular Plant Breeding, 2019, 17(18): 6013-6019.
[20] 张彬, 李萌, 刘晶, 等. 绿小米和白小米谷子籽粒叶绿素合成途径结构基因的表达分析[J]. 中国农业科学, 2020, 53(12): 2331-2339.
Zhang B, Li M, Liu J, et al.expression analysis of the chorophyll biosynthesis structural genes in green and white foxtail millet [Setaria italica (L.) Beauv][J]. Scientia Agricultura Sinica, 2020, 53(12): 2331-2339.
[21] 张稳, 孟淑君, 王琪月, 等. 玉米pTAC2影响苗期叶片叶绿素合成的转录组分析[J]. 中国农业科学, 2020, 53(5): 874-889.
Zhang W, Meng S J, Wang Q Y, et al.Transcriptome analysis of maize pTAC2 effects on chlorophyll synthesis in seeding leaves[J]. Scientia Agricultura Sinica, 2020, 53(5): 874-889.
[22] 袁金红, 李俊华, 黄小城, 等. 基于全基因组重测序的SNP分析在作物基因定位中的研究进展[J]. 植物生理学报, 2015, 51(9): 1400-1404.
Yuan J H, Li J H, Huang X C, et al.Advance of SNP analysis based on whole genome resequencing in crop gene mapping[J]. Plant Physiology Journal, 2015, 51(9): 1400-1404.
[23] 李国治, 邓卫东. 基因组测序技术及其应用研究进展[J]. 安徽农业科学, 2018, 46(22): 20-22, 25.
Li G Z, Deng W D.Research progress and application of genome sequencing technology[J]. Journal of Anhui Agricultural Sciences, 2018, 46(22): 20-22, 25.
[24] 马春雷, 姚明哲, 王新超, 等. 茶树叶绿素合成相关基因克隆及在白叶1号不同白化阶段的表达分析[J]. 作物学报, 2015, 41(2): 240-250.
Ma C L, Yao M Z, Wang X C, et al.Cloning and expression of three genes involved in chlorophyll biosynthesis at different albescent stages of tea plant variety ‘Baiye1’[J]. Acta Agronomica Sinica, 2015, 41(2): 240-250.
[25] 曹璐, 于旭东, 蔡泽坪, 等. 植物叶色白化的研究进展[J]. 分子植物育种, 2019, 17(16): 5390-5397.
Cao L, Yu X D, Cai Z P, et al.Research progress of plant leaf albino[J]. Molecular Plant Breeding, 2019, 17(16): 5390-5397.
[26] Li N N, Lu J L, Li Q S, et al.Dissection of chemical composition and associated gene expression in the pigment-deficient tea cultivar ‘Xiaoxueya’ reveals an albino phenotype and metabolite formation[J]. Frontiers in Plant Science, 2019, 10: 1543. doi: 10.3389/fpls.2019.01543.
[27] 王涛, 王艺清, 漆思雨, 等. 茶树CLH基因家族的鉴定与转录调控研究及其在白化茶树中的表达分析[J]. 茶叶科学, 2022, 42(3): 331-346.
Wang T, Wang Y Q, Qi S Y, et al.Identification and transcriptional regulation of CLH gene family and expression analysis in albion tea plants (Camellis sinensis)[J]. Journal of Tea Science, 2022, 42(3): 331-346.
[28] Liu Y C, Liu S L, Zhang Z F, et al.GenoBaits Soy40K: a highly flexible and low-cost SNP array for soybean studies[J]. Science China Life Sciences, 2022, 65(9): 1898-1901.
[29] Lin Y, Jiang X J, Hu H Y, et al.QTL mapping for grain number per spikelet in wheat using a high-density genetic map[J]. The Crop Journal, 2021, 9(5): 1108-1114.
[30] Huang S, Zhang Y, Ren H, et al.Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9[J]. Theoretical and Applied Genetics, 2022, 135(7): 2501-2513.
[31] Li S N, Lin D X, Zhang Y W, et al.Genome-edited powdery mildew resistance in wheat without growth penalties[J]. Nature, 2022, 602(7897): 455-460.
[32] Guo Z F, Wang H W, Tao J J, et al.Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize[J]. Molecular Breeding, 2019, 39(3): 37. doi: 10.1007/s11032-019-0940-4.
[33] 丁向东, 王楚端, 张勤. 基于液相芯片的猪基因组选择实施新策略[J]. 中国畜牧杂志, 2022, 58(4): 65-69.
Ding X D, Wang C D, Zhang Q.New strategy of pig genome selection based on liquid chip[J]. Chinese Journal of Animal Science, 2022, 58(4): 65-69.
[34] 徐云碧, 王冰冰, 张健, 等. 应用分子标记技术改进作物品种保护和监管[J]. 作物学报, 2022, 48(8): 1853-1870.
Xu Y B, Wang B B, Zhang J, et al.Enhancement of plant variety protection and regulation using molecular market technology[J]. Acta Agronomica Sinica, 2022, 48(8): 1853-1870.
[35] Xia E H, Zhang H B, Sheng J, et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J]. Molecular Plant, 2017, 10(6): 866-877.
[36] Chen J D, Zheng C, Ma J Q, et al.The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant[J]. Horticulture Research, 2020, 7: 63. doi: 10.1038/s41438-020-0288-2.
[37] Goodwin S, Mcpherson J D, Mccombie W R.Coming of age: ten years of next-generation sequencing technologies[J]. Nature Reviews Genetics, 2016, 17: 333-351.

基于全基因组重测序的白化茶树mSNP标记开发及验证

Development and Application of Albinotea Plant mSNP Molecular Markers Based on Genome-wide Resequencing

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

Metrics

本文评价

推荐阅读 10

[1]	闫佳伟, 陈宗懋, 李兆群, 罗宗秀, 边磊, 蔡晓明, 金珊. 小贯小绿叶蝉水状唾液蛋白的鉴定及其参与茶树“叶蝉烧”症状形成的初步研究[J]. 茶叶科学, 2023, 43(1): 40-54.
[2]	程开鑫, 杨凯欣, 邓雅元, 黎欣, 刘恩贝, 王玉春, 吕务云. 山茶炭疽菌对茶树的致病性及其对杀菌剂的敏感性研究[J]. 茶叶科学, 2023, 43(1): 55-66.
[3]	邓晓旭, 谢夏, 潘娅梅, 赵丰华, 蒋双丰, 徐文, 张洁, 孙润红, 夏明聪, 杨丽荣. 茶树腐皮镰刀菌拮抗菌株的筛选鉴定及促生防病特性分析[J]. 茶叶科学, 2023, 43(1): 67-77.
[4]	卢丽, 詹冬梅, 周承哲, 朱晨, 谢思艺, 徐凯, 田采云, 赖钟雄, 郭玉琼. 茶树茉莉酸合成与转导途径关键基因在乌龙茶加工过程中对萜类物质的影响[J]. 茶叶科学, 2023, 43(1): 91-108.
[5]	陈一凡, 阚新意, 蒋晓岚, 高丽萍, 夏涛. 茶树单宁酶CsTA的理化性质及其在绿茶饮料中的应用[J]. 茶叶科学, 2023, 43(1): 124-134.
[6]	盖淑杰, 王奕雄, 李兰, 刘硕谦, 李银花, 程孝, 夏茂, 刘仲华, 周智. 茶树生长光调控研究进展[J]. 茶叶科学, 2022, 42(6): 753-767.
[7]	汤榕津, 刘浩然, 刘丁丁, 张晨禹, 龚洋, 叶圆圆, 陈杰丹, 陈亮, 马春雷. 茶树白化果皮超微结构观察及分子机制研究[J]. 茶叶科学, 2022, 42(6): 779-790.
[8]	陈薛, 左欣欣, 徐安安, 徐平, 王岳飞. 不同茶树品种鲜叶多糖的理化性质和抗氧化活性比较研究[J]. 茶叶科学, 2022, 42(6): 806-818.
[9]	周贝妮, 梅慧玲, 李建杰, 陈伶俐, 衷青, 李小倩, 陈暄, 黎星辉. 磷铝互作对茶树根系生长及有机酸分泌的影响[J]. 茶叶科学, 2022, 42(6): 819-827.
[10]	王留彬, 黄丽蕴, 滕翠琴, 吴立赟, 成浩, 于翠平, 王丽鸳. 梧州茶树种质资源的遗传多样性及亲缘关系分析[J]. 茶叶科学, 2022, 42(5): 601-609.
[11]	周汉琛, 杨霁虹, 徐玉婕, 吴琼, 雷攀登. 香叶醇生物合成相关基因NUDX1的进化分析[J]. 茶叶科学, 2022, 42(5): 638-648.
[12]	陈琪予, 马建强, 陈杰丹, 陈亮. 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.
[13]	孙悦, 吴俊, 韦朝领, 刘梦月, 高晨曦, 张灵枝, 曹士先, 余顺甜, 金珊, 孙威江. 抗小贯松村叶蝉和茶棍蓟马的茶树种质筛选及其抗性相关因素分析[J]. 茶叶科学, 2022, 42(5): 689-704.
[14]	王玉源, 刘任坚, 刘少群, 舒灿伟, 孙彬妹, 郑鹏. 茶树R2R3-MYB转录因子CsTT2表达分析及功能初步鉴定[J]. 茶叶科学, 2022, 42(4): 463-476.
[15]	刘建军, 张金玉, 彭叶, 刘晓博, 杨云, 黄涛, 温贝贝, 李美凤. 不同光质摊青对夏秋茶树鲜叶挥发性物质及其绿茶品质影响研究[J]. 茶叶科学, 2022, 42(4): 500-514.