The Development of CAPS Molecular Markers for CsAL1, A Gene Associated with Early and Late Spring Tip Emergence in Tea Plants

HUANG Mengdi; CHEN Lan; SU Qin; HU Jinyu; LIU Guizhi; TAN Yueping; LIU Shuoqian; TIAN Na

doi:10.13305/j.cnki.jts.2024.02.001

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Journal of Tea Science ›› 2024, Vol. 44 ›› Issue (2) : 207-218. DOI: 10.13305/j.cnki.jts.2024.02.001

The Development of CAPS Molecular Markers for CsAL1, A Gene Associated with Early and Late Spring Tip Emergence in Tea Plants

HUANG Mengdi¹, CHEN Lan¹, SU Qin¹, HU Jinyu¹, LIU Guizhi¹, TAN Yueping³, LIU Shuoqian^1,2,*, TIAN Na^1,2,*

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Abstract

Camellia sinensis is an economically important foliar plant. The time of spring sprouting is a crucial biological trait that affects the economic value of tea. Therefore, selecting and breeding early sprouting tea cultivars are of great practical significance for improving the quality and economic benefits of tea. The study used ‘Tieguanyin’ as the reference genome and screened a gene, CsAL1 (Auxilin-like 1, TGY040711), which was highly significantly correlated with the time of spring sprouting based on genome-wide association analysis. SNP calling was used to obtain SNPs of CsAL1 in each sample. Correlation analysis of the SNPs and spring sprouting phenotypes was performed to obtain the key SNP loci that associating with spring sprouting traits. Suitable enzyme cleavage sites were analyzed for each SNP to develop CAPS molecular markers related to early-sprouting traits in tea plants. PCR was used to amplify the CAPS molecular markers, which were then digested in the genomic DNA of 12 tea materials. The markers were further verified in 72 tea materials to provide a reference for the association between single-base mutations in CsAL1 and early sprouting traits using CAPS molecular markers. This study also provided theoretical support for the breeding of early sprouting tea cultivars.

Key words

Camellia sinensis / CAPS molecular marker / early sprouting / molecular marker breeding / SNP

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HUANG Mengdi, CHEN Lan, SU Qin, HU Jinyu, LIU Guizhi, TAN Yueping, LIU Shuoqian, TIAN Na. The Development of CAPS Molecular Markers for CsAL1, A Gene Associated with Early and Late Spring Tip Emergence in Tea Plants[J]. Journal of Tea Science. 2024, 44(2): 207-218 https://doi.org/10.13305/j.cnki.jts.2024.02.001

References

[1] Shen J, Wang Y, Chen C, et al.Metabolite profiling of tea (Camellia sinensis L.) leaves in winter[J]. Scientia Horticulturae, 2015, 192(12): 1-9.
[2] Wu Z, Li X, Liu Z, et al.Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis)[J]. Functional & Integrative Genomics, 2015, 15(6): 741-752.
[3] 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.
[4] 李慧, 熊丙全, 吴庆丽, 等. 影响茶树芽休眠的内部调控因素研究进展[J]. 南方农业, 2019, 13(23): 112-113.
Li H, Xiong B Q, Wu Q L, et al.Research progress on internal regulatory factors affecting bud dormancy in tea tree[J]. Southern Agriculture, 2019, 13(23): 112-113.
[5] Zeng X, Li Y, Ling H, et al.Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodiaelata[J]. Botanical Studies, 2017, 58(1): 1-11.
[6] Lee S K, Hong W, Silva J, et al.Global identification of ANTH genes involved in rice pollen germination and functional characterization of a key member, OsANTH3[J]. Frontiers in Plant Science, 2021, 12: 609473. doi: 10.3389/fpls.2021.609473.
[7] Hou B, Shen Y.A Clathrin-related protein, SCD2/RRP1, participates in abscisic acid signaling in Arabidopsis[J]. Frontiers in Plant Science, 2020, 11: 892. doi: 10.3389/fpls.2020.00892.
[8] Shi L, Luo Y, Wang X, et al.Molecular cloning and expression analysis of auxilin-like gene stal1 in potato (Solanum tuberosum)[J]. Russian Journal of Plant Physiology, 2021, 68(1): 56-65.
[9] Adamowski M, Narasimhan M, Kania U, et al.A functional study of AUXILIN-LIKE1 and 2, two putative clathrin uncoating factors in arabidopsis[J]. The Plant Cell, 2018, 30(3): 700-716.
[10] Suetsugu N, Kagawa T, Wada M.An auxilin-like J-domain protein, JAC1, regulates phototropin-mediated chloroplast movement in Arabidopsis[J]. Plant Physiology, 2005, 139(1): 151-162.
[11] Ezaki B, Kiyohara H, Matsumoto H, et al.Overexpression of an auxilin-like gene (F9E10. 5) can suppress Al uptake in roots of Arabidopsis[J]. Journal of Experimental Botany, 2007, 58(3): 497-506.
[12] 王彩芬, 刘冬成, 马晓玲, 等. 水稻耐盐基因SKC1特异性CAPS标记的开发与验证[J]. 分子植物育种, 2015, 13(11): 2437-2440.
Wang C F, Liu D C, Ma X L, et al.Development and validation of a CAPS marker specific for the salt tolerance gene SKC1 in rice[J]. Molecular Plant Breeding, 2015, 13(11): 2437-2440.
[13] 王军, 赵婕宇, 许扬, 等. 水稻稻瘟病抗性基因Bsr-d1功能标记的开发和利用[J]. 作物学报, 2018, 44(11): 1612-1620.
Wang J, Zhao J Y, Xu Y, et al.Development and utilisation of functional markers for rice rice blast resistance gene Bsr-d1[J]. Journal of Crops, 2018, 44(11): 1612-1620.
[14] 吴林楠, 司文洁, 郭利建, 等. 小麦粒重相关基因TaCYP78A16的克隆和CAPS标记开发[J]. 农业生物技术学报, 2018, 26(10): 1659-1669.
Wu L N, Si W J, Guo L J, et al.Cloning and CAPS marker development of wheat grain weight-related gene TaCYP78A16[J]. Journal of Agricultural Biotechnology, 2018, 26(10): 1659-1669.
[15] 艾子凌, 高鹏, 杜黎黎, 等. 利用CAPS初步定位甜瓜MR-1白粉病抗性基因[J]. 江苏农业科学, 2016, 44(6): 66-70.
Ai Z L, Gao P, Du L L, et al.Preliminary localisation of MR-1 powdery mildew resistance gene in melon using CAPS[J]. Jiangsu Agricultural Science, 2016, 44(6): 66-70.
[16] Seçgin Z, Arvas Y E, Ssendawula S P, et al.Selection of root-knot nematod resistance in inbred tomato lines using CAPS molecular markers[J]. International Journal of Life Sciences and Biotechnology, 2018, 1(1): 10-16.
[17] 郝耀港, 宋建军, 李珂, 等. 与番茄灰叶斑病抗病基因Sm连锁的CAPS标记开发[J]. 中国瓜菜, 2023, 36(4): 47-55.
Hao Y G, Song J J, Li K, et al.Development of CAPS markers linked to the Sm gene for grey leaf spot resistance in tomato[J]. China Cucurbit, 2023, 36(4): 47-55.
[18] 陶爱芬, 游梓翊, 徐建堂, 等. 基于黄麻转录组序列SNP位点的CAPS标记开发与验证[J]. 作物学报, 2020, 46(7): 987-996.
Tao A F, Yu Z Y, Xu J T, et al.Development and validation of CAPS markers based on SNP sites in jute transcriptome[J]. Journal of Crops, 2020, 46(7): 987-996.
[19] Lopez-pardo R, Barandalla L, Ritter E, et al. Validation of molecular markers for pathogen resistance in potato[J]. Plant Breeding, 2013, 132(3): 246-251.
[20] 李佳奇. 四倍体马铃薯块茎淀粉候选基因的挖掘及分子标记辅助育种[D]. 呼和浩特: 内蒙古农业大学, 2022.
Li J Q.Mining of tetraploid potato tuber starch candidate genes and molecular marker-assisted breeding [D]. Huhhot: Inner Mongolia Agricultural University, 2022.
[21] 张丹丹, 周延清, 杨珂. 基因特异性分子标记在植物育种中的研究进展[J]. 湖北农业科学, 2018, 57(11): 5-9.
Zhang D D, Zhou Y Q, Yang K.Research progress of gene-specific molecular markers in plant breeding[J]. Hubei Agricultural Science, 2018, 57(11): 5-9.
[22] 毛润锦, 王留彬, 崔懂, 等. 茶树休眠相关基因连锁SSR标记开发及萌发性状关联分析[J/OL]. 分子植物育种, 2022: 1-10[2024-03-25]. http://kns.cnki.net/kcms/detail/46.1068.S.20221101.1325.002.html.
Mao R J, Wang L B, Cui D, et al. Development of SSR markers for dormancy-associated gene sequences and correlation analysis of germination traits in tea tree [J/OL]. Molecular Plant Breeding, 2022: 1-10[2024-03-25]. http://kns.cnki.net/kcms/detail/46.1068.S.20221101.1325.002.html.
[23] 王新超, 王璐, 郝心愿, 等. 中国茶树遗传育种发展、创新之回顾与展望[J]. 华中农业大学学报, 2022, 41(5): 1-8.
Wang X C, Wang L, Hao X Y, et al.Review and prospect of genetic breeding development and innovation of tea tree in China[J]. Journal of Huazhong Agricultural University, 2022, 41(5): 1-8.
[24] Li L, Liu J J, Xue X, et al.CAPS/dCAPS Designer: a web-based high-throughput dCAPS marker design tool[J]. Science China Life Sciences, 2018, 61(8): 992-995.
[25] 邢冉冉, 王佳雯, 张九凯, 等. SNP检测技术在动植物源性成分鉴定中的应用[J]. 质量安全与检验检测, 2023, 33(1): 58-63.
Xing R R, Wang J W, Zhang J K, et al.Application of SNP detection technology in the identification of plant and animal source components[J]. Quality Safety and Inspection, 2023, 33(1): 58-63.
[26] Wang L B, Xun H S, Aktar S, et al.Development of SNP markers for original analysis and germplasm identification in Camellia sinensis[J]. Plants, 2022, 12(1): 162. doi: 10.3390/plants12010162.
[27] 张璨. 小麦抗寒性相关位点的鉴定及CAPS标记开发[D]. 合肥: 安徽农业大学, 2018.
Zhang C.Identification of cold resistance related loci and development of CAPS markers in wheat [D]. Hefei: Anhui Agricultural University, 2018.
[28] 王泽涵, 于文涛, 樊晓静, 等. 利用SNP标记构建漳州南部茶树种质资源的分子身份证[J]. 江苏农业科学, 2022, 50(18): 284-289.
Wang Z H, Yu W T, Fan X J, et al.Construction of a molecular identity card for tea germplasm resources in southern Zhangzhou using SNP markers[J]. Jiangsu Agricultural Science, 2022, 50(18): 284-289.
[29] 罗祥宗, 胡云飞, 吴淋慧, 等. 茶树叶绿体基因组SNP分子标记的初步研究[J]. 茶叶科学, 2022, 42(6): 768-778.
Luo X Z, Hu Y F, Wu L H, et al.A preliminary study on SNP molecular markers in the chloroplast genome of tea[J]. Journal of Tea Science, 2022, 42(6): 768-778.
[30] 顾渝娟, 郭建英, 程红梅, 等. 单核苷酸多态性的检测及应用[J]. 中国农学通报, 2007, 24(4): 38-41.
Gu Y J, Guo J Y, Cheng H M, et al.Detection and application of single nucleotide polymorphisms[J]. Chinese Agronomy Bulletin, 2007, 24(4): 38-41.
[31] 张成才, 王丽鸳, 韦康, 等. 基于茶树EST-SNP的CAPS标记开发[J]. 分子植物育种, 2013, 11(6): 8-11.
Zhang C C, Wang L Y, Wei K, et al.Development of CAPS markers based on EST-SNP in tea tree[J]. Molecular Plant Breeding, 2013, 11(6): 8-11.
[32] 刘声传, 鄢东海, 周雪, 等. 茶树CsSMT基因的单核苷酸多态性及其表达[J]. 西南农业学报, 2016, 29(8): 1793-1797.
Liu S C, Yan D H, Zhou X, et al.Single nucleotide polymorphism of CsSMT gene and its expression in tea tree[J]. Southwest Journal of Agriculture, 2016, 29(8): 1793-1797.
[33] 张丽群, 韦康, 王丽鸳, 等. 茶树CHS基因结构及编码区单核苷酸多态性分析[J]. 中国农业科学, 2014, 47(1): 133-144.
Zhang L Q, Wei K, Wang L Y, et al.Analysis of single nucleotide polymorphisms in the structure and coding region of the CHS gene of tea tree[J]. Chinese Agricultural Science, 2014, 47(1): 133-144.
[34] 刘硕谦, 叶洁连. 茶树咖啡碱合成酶基因分子变异检测及其关联分析[J]. 茶叶通讯, 2023, 50(3): 279-287.
Liu S Q, Ye J L.Detection of molecular variation in caffeine synthase gene of tea tree and its association analysis[J]. Journal of Tea Communication, 2023, 50(3): 279-287.
[35] An Y L, Mi X Z, Zhao S Q, et al.Revealing distinctions in genetic diversity and adaptive evolution between two varieties of Camellia sinensis by whole-genome resequencing[J]. Frontiers in Plant Science, 2020, 11: 603819. doi: 10.3389/fpls.2020.603819.
[36] Fang K X, Xia Z Q, Li H J, et al.Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites[J]. Horticulture Research, 2021, 8(1): 42. doi: 10.1038/s41438-021-00477-3.
[37] 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. doi: 10.1038/s41438-021-00617-9.
[38] Liu Y J, Chen S, Jiang C K, et al. Combined QTL mapping, GWAS and transcriptomic analysis revealed a candidate gene associated with the timing of spring bud flush in tea plant (Camellia sinensis) [J]. Horticulture Research, 2023, 10(9): uhad149. doi: 10.1093/hr/uhad149.