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SSR Identification of Transcriptome and Fingerprint Construction in Color-leafed Cinnamomum camphora |
KONG Lin-Lin1, MENG Xian-Dong2, WANG Jian-Jun3, YU Jin-Jian1, HU Xian-Ge1, LIN Er-Pei1, HUANG Hua-Hong1,* |
1 The State Key Laboratory of Subtropical Silviculture, Zhengjiang Agricultural and Forestry University, Hangzhou 311300, China; 2 Forestry Seed and Seedling Management Station of Zhejiang Province, Hangzhou 311300, China; 3 Ningbo Agricultural Technology Extension Station , Ningbo 315012, China |
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Abstract Color-leafed Cinnamomum camphora is an ornamental plant variety with colored leaves in spring. Although these varieties have broad market prospects, a technology system for distinguishing them effectively has not yet been established, which affects the protection of new variety rights and market circulation. In this study, in order to rapidly identify 3 color-leafed varieties, their fingerprints were constructed using SSR markers derived from the transcriptome of C. camphora. The transcriptome of C. camphora 'Yongjin' was sequenced using the Illumina high-throughput sequencing platform, and a total of 129 175 Unigenes were obtained, with a total length of 92 429 171 bp. The SSR search of the transcriptome sequences by MIcroSAtellite identification tool (MISA) revealed that 28 895 sequences contained 36 430 SSR sites, with an average of 1 SSR per 2 537.2 bp and a frequency of 22.37%. Mononucleotide repeats (accounting for 49.74%) were the most abundant, followed by dinucleotide (29.12%) and trinucleotide (19.93%). Fifty-four primer pairs were randomly selected for PCR amplification, and 39 of them were successfully amplified. In total, 32 primer pairs were polymorphic in 23 C. camphora germplasms. In addition, unweighted pair-group method with arithmetic means (UPGMA) cluster analysis showed that the similarity coefficients of 23 germplasms ranged from 0.69 to 0.88. At the similarity coefficient of 0.70, these germplasms could be classified into 3 major groups. Finally, 6 primer pairs (c117334, c90845, c108367, c115142, c49114 and c101928) were selected to construct the fingerprints, which could effectively distinguish the 3 new varieties from their offsprings and other germplasms from different geographical sources. The results could provide technical support and theoretical basis for new variety identification, intellectual property protection and molecular assisted breeding of C. camphora.
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Received: 28 November 2022
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Corresponding Authors:
*huanghh@zafu.edu.cn
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[1] 蔡金峰, 杨晓明, 郁万文, 等. 2021. 基于苦楝转录组测序的SSR分子标记开发[J]. 林业科学, 57(6): 85-92. (Cai J F, Yang X M, Yu W W, et al.2021. Development of SSR molecular markers based on transcriptome sequencing of Melia azedarach[J]. Scientia Silvae Sinicae, 57(6): 85-92.) [2] 查美琴, 赵玉玲, 李疆, 等. 2016. 新疆枸杞种质资源遗传多样性分析及DNA指纹图谱构建[J]. 植物遗传资源学报, 17(06): 1065-1071. (Zha M Q, Zhao Y L, Li J, et al.2016. Analysis of genetic diversity and construction of DNA fingerprint of germplasm resources of wolfberry(Lycium barbarum L.) revealed by SCoT in Xinjiang of China[J] Journal of Plant Genetic Resources, 17(06): 1065-1071.) [3] 郭俊, 朱婕, 谢尚潜, 等. 2020. 油梨转录组SSR分子标记开发与种质资源亲缘关系分析[J]. 园艺学报, 47(8): 1552-1564. (Guo J, Zhu J, Xie S Q, et al.2020. Development of SSR molecular markers based on transcriptome and analysis of genetic relationship of germplasm resources in Avocado[J]. Acta Horticulturae Sinica, 47(8): 1552-1564.) [4] 郭艳春, 张力岚, 陈思远, 等. 2021. 黄麻应用核心种质的DNA分子身份证构建[J]. 作物学报, 47(1): 80-93. (Guo Y C, Zhang L L, Chen S Y, et al.2021. Establishment of DNA molecular fingerprint of applied core germplasm in jute (Corchorus spp.)[J]. Acta Agronomica Sinica, 47(1): 80-93.) [5] 郝晨阳, 王兰芬, 贾继增, 等. 2005. SSR荧光标记和银染技术的比较分析[J]. 作物学报, 31(2): 144-149. (Hao C Y, Wang L F, Jia J Z, et al.2005. Comparisonof fluorescence and silver-staining detection systems of microsatellite markers[J]. Acta Agronomica Sinica, 31(2): 144-149.) [6] 李超, 杨英, 陈伟, 等. 2022. 西州密系列甜瓜SSR指纹图谱构建及聚类分析[J]. 园艺学报, 49(03): 622-632. (Li C, Yang Y, Chen W, et al.2022. Construction of DNA fingerprinting and clustering analysis with SSR markers for the muskmelon of Xizhoumi series[J] Acta Horticulturae Sinica, 49(03): 622-632.) [7] 李清莹, 仲崇禄, 姜清彬, 等. 2019. 珍贵树种火力楠转录组SSR特征分析[J]. 基因组学与应用生物学, 38(4): 1674-1682. (Li Q Y, Zhong C L, Jiang Q B, et al.2019. Characteristic analysis of microsatellites in the transcriptome of Michelia macclurei of rare tree species[J]. Genomics and Applied Biology, 38(4): 1674-1682.) [8] 刘果, 张党权, 谢耀坚, 等. 2013. 桉树Genomic-SSR和EST-SSR引物的快速筛选与通用性研究[J]. 林业科学, 49(02): 127-133. (Liu G, Zhang D Q, Xie Y J, et al.2013. Rapid Screening screening and transferability analysis of genomic-SSR and EST-SSR primers in Eucalypt[J]. Scientia Silvae Sinicae, 49(02): 127-133.) [9] 聂兴华, 刘松, 王碧瑶, 等. 2022. 基于SSR标记的我国主栽日本栗品种(系)遗传结构分析和指纹图谱构建[J]. 核农学报, 36(11): 2104-2114. (Nie X H, Liu S, Wang B Y, et al.2022. Genetic structure analysis and fingerprinting construction of the mian Japanese chestnut cultivars (Lineslines) using SSR markers in China[J]. Journal of Nuclear Agricultural Sciences, 36(11): 2104-2114.) [10] 石艳, 童再康, 高燕会. 2018. 换锦花EST-SSR标记开发及遗传多样性分析[J]. 核农学报, 32(6): 1089-1096. (Shi Y, Tong Z K, Gao Y H2018. Development of EST-SSR markers and genetic diversity analysis in Lycoris sprengeri[J]. Journal of Nuclear Agricultural Sciences, 32(6): 1089-1096.) [11] 时小东, 朱学慧, 盛玉珍, 等. 2016. 基于转录组序列的楠木SSR分子标记开发[J]. 林业科学, 52(11): 71-78. (Shi X D, Zhu X H, Sheng Y Z, et al.2016. Development of SSR markers based on transcriptome sequence of Phoebe zhennan[J]. Scientia Silvae Sinicae, 52(11): 71-78.) [12] 唐梅, 孙富, 何聪, 等. 2023. SSR荧光标记毛细管电泳分析24个广西常规香稻品种的遗传多样性[J]. 热带作物学报: 44(3): 506-515. (Tang M, Sun F, He C, et al.2023. Genetic diversity analysis of 24 Guangxi common aromatic rice varieties by fluorescent SSR marker capillary electrophoresis[J]. Chinese Journal of Tropical Crops, 44(3): 506-515.) [13] 王豪, 张波, 陆云峰, 等. 2019. 香樟新品种'御黄'[J]. 园艺学报, 46(S2): 2924-2925. (Wang H, Zhang B, Lu Y F, et al.2019. A new Cinnamomum camphora cultivar 'Yuhuang'[J]. Acta Horticulturae Sinica, 46(S2): 2924-2925.) [14] 王建军. 2010. 香樟新品种'涌金'[J]. 林业科学, 46(8): 181. (Wang J J.2010. A new variety Cinnamomum camphora 'Yongjin'[J]. Scientia Silvae Sinicae, 46(8): 181.) [15] 王建军. 2015. 香樟新品种'霞光'[J]. 林业科学, 51(6): 163. (Wang J J.2015. A new variety of Cinnamomum camphora 'Xiaguang'[J]. Scientia Silvae Sinicae, 51(6): 163.) [16] 叶兴状, 杨先吉, 王妙青, 等. 2020. 濒危珍稀植物半枫荷转录组中SSR位点分析[J]. 分子植物育种, 18(5): 1585-1592. (Ye X Z, Yang X J, Wang M Q, et al.2020. Analysis of SSR loci in transcriptome of rare and endangered plants of Semiliquidambar cathayensis[J]. Molecular Plant Breeding, 18(5): 1585-1592.) [17] 俞金健, 王建军, 尹雨钦, 等. 2019. 彩叶香樟叶片色素含量及其合成相关基因表达的变化[J]. 农业生物技术学报, 27(11): 1962-1972. (Yu J J, Wang J J, Yin Y Q, et al.2019. Changes of pigment content and expressions of the synthetic related genes in leaves of color-leafed Cinnamomum camphora[J]. Journal of Agricultural Biotechnology, 27(11): 1962-1972.) [18] 张守锋. 2012. 上海地区不同表型香樟的遗传多样性分析[J]. 上海交通大学学报(农业科学版), 30(05): 1-4. (Zhang S F.2012.Analysis of genetic diversity of different phenotypes Cinnamomum camphora in Shanghai[J] Journal of Shanghai Jiaotong University (Agricultural Science), 30(05): 1-4.) [19] Bali S, Patel G, Novy R, et al.2018. Evaluation of genetic diversity among Russet potato clones and varieties from breeding programs across the United States[J]. PLOS ONE, 13(8): e0201415. [20] Bazzo B R, De Carvalho L M, Carazzolle M F, et al.2018. Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species[J]. BMC plant biology, 18(1): 1-10. [21] Gao L, Tang J, Li H, et al.2003. Analysis of microsatellites in major crops assessed by computational and experimental approaches[J]. Molecular Breeding, 12(3): 245-261. [22] Guo Q, Wang J X, Su L Z, et al.2017. Development and evaluation of a novel set of EST-SSR markers based on transcriptome sequences of black locust (Robinia pseudoacacia L.)[J]. Genes, 8(7): 177. [23] Humberto R V M, Amalio S V, OctaviO M, et al.2013. Analysis and optimization of bulk DNA sampling with binary scoring for germplasm characterization[J]. PLOS ONE, 8(11): e79936. [24] Li Z, Zhong Y, Yu F, et al.2018. Novel SSR marker development and genetic diversity analysis of Cinnamomum camphora based on transcriptome sequencing[J]. Plant Genetic Resources Characterization & Utilization, 16(6): 568-571. [25] Lin E, Zhuang H, Yu J, et al.2020. Genome survey of Chinese fir (Cunninghamia lanceolata): Identification of genomic SSRs and demonstration of their utility in genetic diversity analysis[J]. Scientific Reports, 10(1): 1-12. [26] Ma S, Han C, Zhou J, et al.2020. Fingerprint identification of white clover cultivars based on SSR molecular markers[J]. Molecular Biology Reports, 47(11): 8513-8521. [27] Porebski S, Bailey L G, Baum B R, 1997. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components[J]. Plant Molecular Biology Reporter, 15(1): 8-15. [28] Powell W, Machray G C, Provan.1996. Polymorphism revealed by simple sequence repeats[J]. Trends in Plant Science, 1(7): 215-222. [29] Yang Q W, Jiang Y J, Wang Y P, et al.2022. SSR loci analysis in transcriptome and molecular marker development in Polygonatum sibiricum[J]. Biomed Research International, 2022: 4237913. [30] Zhang J, Liang S, Duan J, et al.2012. De novo assembly and characterization of the transcriptome during seed development, and generation of Genicgenic-SSR markers in Pomegranate (Punica granatum L.)[J]. BMC Genomics, 13(1): 90. [31] Tian L, Gao Y, Cao Y, et al.2012. Identification of chinese white pear cultivars using SSR markers[J]. Genetic Resources, 59(3): 317-326. [32] Wang N C, Dan X, Liu T, et al.2022. Genetic relationships of 24 Pennisetum cultivars and construction of DNA fingerprints based on SSR markers[J]. Plant Biochemistry Biotechnology, 31(3): 545-553. [33] Wang J, Zhang W, Huang H2015. 'Yongjin', 'Xiaguang' and 'Yuhuang': Three ornamental cultivars of Cinnamomum camphora[J]. Hortscience, 50(5): 762-764. [34] Wu Q, Liang X, Dai X, et al.2018. Molecular discrimination and ploidy level determination for elite willow cultivars[J]. Tree Genetics & Genomes, 14(5): 1-11. [35] Zhong Y, Yang A, Li Z, et al.2019. Genetic diversity and population genetic structure of Cinnamomum camphora in South China evealed by EST-SSR markers[J]. Forests, 10(11): 1019. [36] Zhou Q, Zhou P Y, Zou W T, et al.2021. EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)[J]. Molecular Biology Reports, 48(3): 2201-2208. |
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