Analysis of Canarium album Transcriptome SSR Information and Molecular Marker Development and Application

doi:10.16420/j.issn.0513-353x.2023-0355

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (11): 2350-2364.doi: 10.16420/j.issn.0513-353x.2023-0355

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Analysis of Canarium album Transcriptome SSR Information and Molecular Marker Development and Application

XIE Qian¹, ZHANG Shiyan¹, JIANG Lai¹, DING Mingyue¹, LIU Lingling¹, WU Rujian², CHEN Qingxi¹^,^*()

¹ College of Horticulture，Fujian Agricultural and Forest University，Fuzhou 350002，China
² Fruit Research Institute，Fujian Academy of Agricultural Sciences，Fuzhou 350013，China

Received:2023-05-22 Revised:2023-07-02 Online:2023-11-25 Published:2023-11-28
Contact: CHEN Qingxi

Abstract

Abstract:

The mature fruits of different varieties（lines）of Canarium album L. were selected for transcriptome sequencing，and 296 314 sequences were obtained. MISA software was used to analyze SSR loci，and 86 084 SSR loci were obtained，distributed in 70 686 sequences. The frequency of SSR in the detected sequences was 23.86%，of which 54 735 sequences contained two or more SSR loci，accounting for 68.4%. The SSR sequences in the Chinese olive transcriptome were mainly composed of compound nucleotide，single nucleotide and dinucleotide repeats，accounting for 88.88% of the total SSRs. The dominant motifs in mononucleotide and dinucleotide repeat types were A/T and AG/CT/TC/GA，respectively. The effectiveness and polymorphism of 99 pairs of SSR primers randomly selected from six different Chinese olive lines（species）were screened. Finally，53 effective SSR molecular markers and 12 polymorphic SSR molecular markers were developed. The polymorphism evaluation and population structure analysis of 59 Chinese olive germplasm were carried out by using 12 polymorphic EST-SSR markers. A total of 48 polymorphic loci were detected. The average Shannon diversity index was 0.876，and the average polymorphic information content was 0.426. The population structure of 59 Chinese olive germplasms was analyzed by three methods of mixed group model grouping，UPGMA clustering and PCA. The results of mixed group model analysis were crossed with those of UPGMA clustering and principal component analysis，but the number of groups was different. The mixed group model was divided into three groups. UPGMA cluster analysis was divided into two populations at the genetic similarity coefficient of 0.68，which was the same as the PCA method. The results of the study concluded that the 12 pairs of SSR markers developed were genetically diverse and valid，and provided a reliable basic tool for Chinese olive germplasm resource identification.

Key words: Canarium album, transcriptome, SSR, polymorphic primer, genetic diversity, population structure

XIE Qian, ZHANG Shiyan, JIANG Lai, DING Mingyue, LIU Lingling, WU Rujian, CHEN Qingxi. Analysis of Canarium album Transcriptome SSR Information and Molecular Marker Development and Application[J]. Acta Horticulturae Sinica, 2023, 50(11): 2350-2364.

Figures/Tables 11

References 40

[1]	Botstein D, White R L, Skolnick M, Davis R W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32 (3):314-331. pmid: 6247908
[2]	Chen Jie-zhong. 2011. Canarium album Raeusch. Various Treatises on Fruit Tree Cultivation:Southern Text(4th ed). Beijing: China Agriculture Press. (in Chinese)
	陈杰忠. 2011. 橄榄. 果树栽培学各论:南方本(第四版). 北京: 中国农业出版社.
[3]	Chen Mingkun, Chen Lu, Sun Weihong, Ma Shanhu, Lan Siren, Peng Donghui, Liu Zhongjian, Ai Ye. 2022. Genetic diversity analysis and core collection of Cymbidium ensifolium germplasm resources. Acta Horticulturae Sinica, 49 (1):175-186. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-0312 URL
	陈明堃, 陈璐, 孙维红, 马山虎, 兰思仁, 彭东辉, 刘仲健, 艾叶. 2022. 建兰种质资源遗传多样性分析及核心种质构建. 园艺学报, 49 (1):175-186. doi: 10.16420/j.issn.0513-353x.2021-0312 URL
[4]	Chi Yu-bin, Xie Qian, Chen Qing-xi. 2016. Introduction to several fresh olive varieties(lines)and good breeding methods. South China Fruits, 45 (3):154-156,166. (in Chinese)
	池毓斌, 谢倩, 陈清西. 2016. 几个鲜食橄榄品种(系)及良种繁育方法简介. 中国南方果树, 45 (3):154-156,166.
[5]	Chinese Pharmacopoeia Commission. 2020. Canarii fructus. Pharmacopoeia of the people's republic of China:2020 ed. Beijing: The Medicine Science and Technology Press of China. (in Chinese)
	国家药典委员会. 2020. 青果. 中华人民共和国药典: 2020年版. 北京: 中国医药科技出版社.
[6]	Ding J Q, Ali F, Chen G S, Li H H, Mahuku G, Yang N, Narro L, Magorokosho C, Makumbi D, Yan J B. 2015. Genome-wide association mapping reveals novel sources of resistance to northern corn leaf blight in maize. BMC Plant Biology, 15 (1):206. doi: 10.1186/s12870-015-0589-z URL
[7]	Du Qing-zhang. 2014. Dissection of allelic variation underlying important traits in Populus tomentosa Carr. by using joint linkage and linkage disequilibrium mapping[Ph. D. Dissertation]. Beijing: Beijing Forestry University. (in Chinese)
	杜庆章. 2014. 利用连锁与连锁不平衡联合作图解析毛白杨重要性状的等位遗传变异[博士论文]. 北京: 北京林业大学.
[8]	Editorial Committee of flora of China,Chinese Academy of Sciences. 1997. Burseraceae. Flora of China. Vol. 43. Beijing: Science Press. (in Chinese)
	中国科学院中国植物志编辑委员会. 1997. 橄榄科. 中国植物志:第四十三卷. 北京: 科学出版社.
[9]	Eujayl I, Sledge M K, Wang L, May G D, Chekhovskiy K, Zwonitzer J C, Mian M A R. 2004. Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theoretical and Applied Genetics, 108 (3):414-422. pmid: 13679975
[10]	Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study. Molecular Ecology, 14 (8):2611-2620. doi: 10.1111/j.1365-294X.2005.02553.x pmid: 15969739
[11]	Gu Zhen-jun, Yang Chun-xia, Ding Wei, Li Kang-qin, Huang Bao-xiang. 2019. Characterization analysis of SSR sequences in the transcriptome of Choerospondias axillaris and its molecular marker development. South China Forestry Science, 47 (3):12-15. (in Chinese)
	谷振军, 杨春霞, 丁伟, 李康琴, 黄宝祥. 2019. 南酸枣转录组SSR序列特征分析及其分子标记开发. 南方林业科学, 47 (3):12-15.
[12]	Guo Jun, Zhu Jie, Xie Shangqian, Zhang Ye, Ye Beilei, Zheng Liyan, Ling Peng. 2020. Development of SSR molecular markers based on transcriptome and analysis of genetic relationship of germplasm resources in avocado. Acta Horticulturae Sinica, 47 (8):1552-1564. (in Chinese) doi: 10.16420/j.issn.0513-353x.2019-0840 URL
	郭俊, 朱婕, 谢尚潜, 张叶, 叶蓓蕾, 郑丽燕, 凌鹏. 2020. 油梨转录组SSR分子标记开发与种质资源亲缘关系分析. 园艺学报, 47 (8):1552-1564. doi: 10.16420/j.issn.0513-353x.2019-0840 URL
[13]	Hu Wenshun, Chen Xiuping, Zheng Shaoquan. 2019. EST-SSR markers developed from Dimocarpus longan and their application in genetic diversity analysis of five genera of sapindaceae. Acta Horticulturae Sinica, 46 (7):1359-1372. (in Chinese) doi: 10.16420/j.issn.0513-353x.2018-0753 URL
	胡文舜, 陈秀萍, 郑少泉. 2019. 龙眼EST-SSR标记开发及无患子科5个属种质遗传多样性分析. 园艺学报, 46 (7):1359-1372. doi: 10.16420/j.issn.0513-353x.2018-0753 URL
[14]	Jiang Shuang, Zhang Xueying, An Haishan, Xu Fangjie, Zhang Jiaying. 2021. Development and analysis of polymorphism of SSR markers in the whole genome of loquat. Acta Horticulturae Sinica, 48 (5):1013-1022. (in Chinese) doi: 10.16420/j.issn.0513-353x.2020-0497 URL
	蒋爽, 张学英, 安海山, 徐芳杰, 章加应. 2021. 枇杷全基因组SSR标记开发及其多态性研究. 园艺学报, 48 (5):1013-1022. doi: 10.16420/j.issn.0513-353x.2020-0497 URL
[15]	Lai Rui-lian, Shen Chao-gui, Feng Xin, Chen Yi-ting, Wei Xiao-xia, Wu Ru-jian. 2023. SSR and SNP/InDel characteristics of fruit transcriptomic data of Canarium album. Chinese Journal of Tropical Crops, 44 (4):681-688. (in Chinese)
	赖瑞联, 沈朝贵, 冯新, 陈义挺, 韦晓霞, 吴如健. 2023. 橄榄果实转录组SSR和SNP/InDel位点特征. 热带作物学报, 44 (4):681-688.
[16]	Li He-rong. 2012. Devei opment of est-derived ssr markers and construction of digital northern platform for apple[M. D. Dissertation]. Nanjing: Nanjing Agricultural University. (in Chinese)
	李荷蓉. 2012. 苹果EST-SSR标记的开发与电子表达平台建立[硕士论文]. 南京: 南京农业大学.
[17]	Li Y C, Korol A B, Fahima T, Nevo E. 2004. Microsatellites within genes:structure,function,and evolution. Molecular Biology and Evolution, 21 (6):991-1007. doi: 10.1093/molbev/msh073 URL
[18]	Lou W R, Lyu Y Z, Hu L J, Yang X F, Zhai M, Xuan J P, Mo Z H. 2022. Development and characterization of EST-SSR markers in pecan(Carya illinoinensis). Trees,Doi:10.1007/s00468-022-02347-4.
[19]	Ma S N, Han C Y, Zhou J, Hu R C, Jiang X, Wu F F, Tian K, Nie G, Zhang X Q. 2020. Fingerprint identification of white clover cultivars based on SSR molecular markers. Molecular Biology Reports, 47 (11):8513-8521. doi: 10.1007/s11033-020-05893-7 pmid: 33040266
[20]	Mao Juan, Liang Guo-ping, Lu Shi-xiong, Ma Zong-huan, Wang Ping, Chen Bai-hong. 2019. Development of the EST-SSRs marker and application on genetic diversity analysis from grapevine. Sino-Overseas Grapevine & Wine,(6):12-19. (in Chinese)
	毛娟, 梁国平, 卢世雄, 马宗桓, 王萍, 陈佰鸿. 2019. 葡萄EST-SSR标记的开发及其在遗传多样性分析中的应用. 中外葡萄与葡萄酒,(6):12-19.
[21]	Peakall R, Smouse P E. 2006. GENALEX 6:genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6:288-295. doi: 10.1111/men.2006.6.issue-1 URL
[22]	Peakall R, Smouse P E. 2012. GenAlEx 6.5:genetic analysis in Excel. Population genetic software for teaching and research-an update. Molecular Ecology Notes, 28 (19):2537-2539.
[23]	Peringottillam M, Vasumathy S K, Selvakumar H K K, Alagu M. 2022. Genetic diversity and population structure of rice(Oryza sativa L.) landraces from Kerala,India analyzed through genotyping-by-sequencing. Molecular Genetics and Genomics, 297 (1):169-182. doi: 10.1007/s00438-021-01844-4 pmid: 35039933
[24]	Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155 (2):945-959. doi: 10.1093/genetics/155.2.945 pmid: 10835412
[25]	Sun J J, Zhou T, Zhang R T, Jia Y, Zhao Y M, Yang J, Zhao G F. 2019. Comparative transcriptomes and development of expressed sequence tag-simple sequence repeat markers for two closely related oak species. Journal of Systematics and Evolution, 57 (5):440-450. doi: 10.1111/jse.v57.5 URL
[26]	Temnykh S, de Clerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. 2001. Computational and experimental analysis of microsatellites in rice(Oryza sativa L.):frequency,length variation,transposon associations,and genetic marker potential. Genome Research, 11 (8):1441-1452. doi: 10.1101/gr.184001 pmid: 11483586
[27]	Tuskan G A, Gunter L E, Yang Z M K, Yin T M, Sewell M M, DiFazio S P. 2004. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Canadian Journal of Forest Research, 34 (1):85-93. doi: 10.1139/x03-283 URL
[28]	Vilayheuang K, Machida-Hirano R, Bounphanousay C, Watanabe K N. 2016. Genetic diversity and population structure of‘Khao Kai Noi’,a lao rice(Oryza sativa L.) landrace,revealed by microsatellite DNA markers. Breeding Science, 66 (2):204-212. doi: 10.1270/jsbbs.66.204 pmid: 27162492
[29]	Wang L Y, Li S S, Wang T Y, He C Y, Luo H M, Zhang J G, Zeng Y F. 2021. Genomic SSR and EST-SSR markers for phylogenetic and pedigree reconstructions-A comparison in sea buckthorn. Plant Breeding, 140 (1):167-183. doi: 10.1111/pbr.v140.1 URL
[30]	Wang Xiao-min, Zhang Chun-hong, Hu Li-chao, Wu Wen-Long, Li Wei-lin. 2022. SSR information analysis of blueberry fruit transcriptome based on high-throughput sequencing. Northern Horticulture,(13):49-54. (in Chinese)
	王小敏, 张春红, 胡丽超, 吴文龙, 李维林. 2022. 基于高通量测序的蓝莓果实转录组SSR信息分析. 北方园艺,(13):49-54.
[31]	Wang Z, Yan H W, Fu X N, Li X H, Gao H W. 2013. Development of simple sequence repeat markers and diversity analysis in alfalfa(Medicago sativa L.). Molecular Biology Reports, 40 (4):3291-3298. doi: 10.1007/s11033-012-2404-3 pmid: 23275197
[32]	Wei W L, Qi X Q, Wang L H, Zhang Y X, Hua W, Li D H, Lv H X, Zhang X R. 2011. Characterization of the sesame(Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12:451. doi: 10.1186/1471-2164-12-451
[33]	Wei Zun-zheng. 2010. Evaluation of genetic resouces and identification of SSRs associated with important traits in Populus simonii[Ph. D. Dissertation]. Beijing: Beijing Forestry University. (in Chinese)
	卫尊征. 2010. 小叶杨遗传资源评价及重要性状的SSRs关联分析[博士论文]. 北京: 北京林业大学.
[34]	Xie Qian, Li Yi-yi, Zhang Shi-yan, Shu Yan-ping, Wang Wei, Chen Qing-xi. 2023. Quality analysis of table Cauarium album L. based on fuzzy mathematics sensory evaluation,physicochemical properties and electronic tongue. Food Science, 44 (3):69-78. (in Chinese) doi: 10.1111/jfds.1979.44.issue-1 URL
	谢倩, 李易易, 张诗艳, 束燕萍, 王威, 陈清西. 2023. 基于模糊数学感官评价、理化特性与电子舌的橄榄鲜食品质分析. 食品科学, 44 (3):69-78.
[35]	Xu Wan, Lin Yajun, Zhao Zhuang, Zhou Zhuang. 2022. Advances in genetic resources and breeding research of Cymbidium. Acta Horticulturae Sinica, 49 (12):2722-2742. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-0943 URL
	徐婉, 林雅君, 赵荘, 周庄. 2022. 兰属植物资源与育种研究进展. 园艺学报, 49 (12):2722-2742. doi: 10.16420/j.issn.0513-353x.2021-0943 URL
[36]	Yu H P, Cheng F Y, Zhong Y, Cai C F, Wu J, Cui H L. 2013. Development of simple sequence repeat(SSR)markers from Paeonia ostii to study the genetic relationships among tree peonies(Paeoniaceae). Scientia Horticulturae, 164:58-64. doi: 10.1016/j.scienta.2013.06.043 URL
[37]	Zeng S H, Xiao G, Guo J, Fei Z J, Xu Y Q, Roe B A, Wang Y. 2010. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant,Epimedium sagittatum(Sieb. Et Zucc.)Maxim. BMC Genomics, 11:94. doi: 10.1186/1471-2164-11-94
[38]	Zhao Qing, Du Zhenzhen, Li Xixiang, Song Jiangping, Zhang Xiaohui, Yang Wenlong, Jia Huixia, Wang Haiping. 2021. Genetic diversity of garlic germplasm resources based on SSRseq molecular markers. Acta Horticulturae Sinica, 48 (7):1397-1408. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-0203 URL
	赵青, 都真真, 李锡香, 宋江萍, 张晓辉, 阳文龙, 贾会霞, 王海平. 2021. 利用SSRseq分子标记的大蒜种质资源遗传多样性研究. 园艺学报, 48 (7):1397-1408. doi: 10.16420/j.issn.0513-353x.2021-0203 URL
[39]	Zheng Shi-mao, Zhou Xi-xi, He Qiao-qiao, Zhang Yu. 2022. The SSR characteristics of Actinidia chinensis var. deliciosa based on transcriptome. Molecular Plant Breeding, http://kns.cnki.net/kcms/detail/46.1068.S.20221129.1037.012.html:2023-05-19in Chinese)
	郑世茂, 周希希, 贺乔乔, 张羽. 2022. 基于美味猕猴桃转录组的SSR特征分析. 分子植物育种, http://kns.cnki.net/kcms/detail/46.1068.S.20221129.1037.012.html:2023-05-19
[40]	Zhou C P, He X D, Li F G, Weng Q J, Yu X L, Wang Y, Li M, Shi J S, Gan S M. 2014. Development of 240 novel EST-SSRs in Eucalyptus L'herit. Molecular Breeding, 33 (1):221-225. doi: 10.1007/s11032-013-9923-z URL

种质来源 Germplasm source	编号 Number	代号 Code	种质名称 Germplasm name
福建福州闽侯 Minhou，Fuzhou，Fujian	1	MA1	福榄1号 Fulan 1
	2	MA2	惠圆 Huiyuan
	3	MA3	青皮长营 Qingpi Changying
	4	MA4	大长营 Dachangying
	5	MA5	黄皮长营 Huangpi Changying
	6	MA6	长营 Changying
	7	MA7	檀头 Tantou
	8	MA8	甜榄1号 Tianlan 1
	9	MA9	自来圆1号 Zilaiyuan 1
	10	MA10	自来圆2号 Zilaiyuan 2
福建福州闽清 Minqing，Fuzhou，Fujian	11	MA11	福榄2号 Fulan 2
	12	MA12	灵峰Lingfeng
	13	MA13	闽清1号 Minqing 1
	14	MA14	清榄1号 Qinglan 1
福建福州晋安 Jin’an，Fuzhou，Fujian	15	MA15	实生1 Shisheng 1
	16	MA16	实生2 Shisheng 2
	17	MA17	实生3 Shisheng 3
	18	MA18	实生4 Shisheng 4
福建莆田 Putian，Fujian	19	MB1	庄边1号 Zhuangbian 1
福建泉州南安 Nan’an，Quanzhou，Fujian	20	MC1	南安1号 Nan’an 1
	21	MC2	南安2号 Nan’an 2
福建漳州云霄 Yunxiao，Zhangzhou，Fujian	22	ME1	穗橄榄 Suiganlan
福建漳州漳浦 Zhangpu，Zhangzhou，Fujian	23	ME2	漳浦11号Zhangpu 11
	24	ME3	漳浦7号 Zhangpu 7
福建龙岩永定 Yongding，Longyan，Fujian	25	MF1	永定1号Yongding 1
	26	MF2	永定2号Yongding 2
福建龙岩长汀 Changting，Longyan，Fujian	27	MF3	长汀1号Changting 1
福建南平延平 Yanping，Nanping，Fujian	28	MH1	埔头1号 Putou 1
	29	MH2	剑州榄 Jianzhoulan
福建宁德福安 Fu’an，Ningde，Fujian	30	MJ1	葡萄橄榄 Grape Chinese Olive
	31	MJ2	四季榄1号 Sijilan 1
	32	MJ3	四季榄2号 Sijilan 2
	33	MJ4	子弹橄榄 Bullet Chinese Olive
	34	MJ5	子阳1号 Ziyang 1
广东茂名电白 Dianbai，Maoming，Guangdong	35	YK1	青皮榄 Green-Rind Chinese Olive
广东茂名高州 Gaozhou，Maoming，Guangdong	36	YK2	高州1号 Gaozhou 1
	37	YK3	高州2号 Gaozhou 2
	38	YK4	香榄 Xianglan
广东潮州饶平 Raoping，Chaozhou，Guangdong	39	YU1	棱尖 Lengjian
广东揭阳揭西 Jiexi，Jieyang，Guangdong	40	YV1	大白榄 Dabailan
	41	YV2	东山长穗 Dongshan Changsui
	42	YV3	三棱榄 Sanlenglan
广西钦州浦北 Pubei，Qinzhou，Guangxi	43	GN1	猪腰榄 Zhuyaolan
四川泸州合江 Hejiang，Luzhou，Sichuan	44	CE1	大梭子Dasuozi
	45	CE2	丁香榄 Dingxianglan
	46	CE3	青果Chinese White Olive
	47	CE4	三白圆 Sanbaiyuan
浙江温州平阳 Pingyang，Wenzhou，Zhejiang	48	ZC1	平阳1号 Pingyang 1
	49	ZC2	平阳2号 Pingyang 2
	50	ZC3	平阳3号 Pingyang 3
	51	ZC4	平阳4号 Pingyang 4
	52	ZC5	平阳5号 Pingyang 5
	53	ZC6	平阳6号 Pingyang 6
	54	ZC7	平阳7号 Pingyang 7
	55	ZC8	平阳8号 Pingyang 8
浙江温州瑞安 Rui’an，Wenzhou，Zhejiang	56	ZC9	瑞安1号 Rui’an 1
	57	ZC10	瑞安2号Rui’an 2
	58	ZC11	瑞安3号Rui’an 3
	59	ZC12	瑞安4号Rui’an 4

种质来源 Germplasm source	编号 Number	代号 Code	种质名称 Germplasm name
福建福州闽侯 Minhou，Fuzhou，Fujian	1	MA1	福榄1号 Fulan 1
	2	MA2	惠圆 Huiyuan
	3	MA3	青皮长营 Qingpi Changying
	4	MA4	大长营 Dachangying
	5	MA5	黄皮长营 Huangpi Changying
	6	MA6	长营 Changying
	7	MA7	檀头 Tantou
	8	MA8	甜榄1号 Tianlan 1
	9	MA9	自来圆1号 Zilaiyuan 1
	10	MA10	自来圆2号 Zilaiyuan 2
福建福州闽清 Minqing，Fuzhou，Fujian	11	MA11	福榄2号 Fulan 2
	12	MA12	灵峰Lingfeng
	13	MA13	闽清1号 Minqing 1
	14	MA14	清榄1号 Qinglan 1
福建福州晋安 Jin’an，Fuzhou，Fujian	15	MA15	实生1 Shisheng 1
	16	MA16	实生2 Shisheng 2
	17	MA17	实生3 Shisheng 3
	18	MA18	实生4 Shisheng 4
福建莆田 Putian，Fujian	19	MB1	庄边1号 Zhuangbian 1
福建泉州南安 Nan’an，Quanzhou，Fujian	20	MC1	南安1号 Nan’an 1
	21	MC2	南安2号 Nan’an 2
福建漳州云霄 Yunxiao，Zhangzhou，Fujian	22	ME1	穗橄榄 Suiganlan
福建漳州漳浦 Zhangpu，Zhangzhou，Fujian	23	ME2	漳浦11号Zhangpu 11
	24	ME3	漳浦7号 Zhangpu 7
福建龙岩永定 Yongding，Longyan，Fujian	25	MF1	永定1号Yongding 1
	26	MF2	永定2号Yongding 2
福建龙岩长汀 Changting，Longyan，Fujian	27	MF3	长汀1号Changting 1
福建南平延平 Yanping，Nanping，Fujian	28	MH1	埔头1号 Putou 1
	29	MH2	剑州榄 Jianzhoulan
福建宁德福安 Fu’an，Ningde，Fujian	30	MJ1	葡萄橄榄 Grape Chinese Olive
	31	MJ2	四季榄1号 Sijilan 1
	32	MJ3	四季榄2号 Sijilan 2
	33	MJ4	子弹橄榄 Bullet Chinese Olive
	34	MJ5	子阳1号 Ziyang 1
广东茂名电白 Dianbai，Maoming，Guangdong	35	YK1	青皮榄 Green-Rind Chinese Olive
广东茂名高州 Gaozhou，Maoming，Guangdong	36	YK2	高州1号 Gaozhou 1
	37	YK3	高州2号 Gaozhou 2
	38	YK4	香榄 Xianglan
广东潮州饶平 Raoping，Chaozhou，Guangdong	39	YU1	棱尖 Lengjian
广东揭阳揭西 Jiexi，Jieyang，Guangdong	40	YV1	大白榄 Dabailan
	41	YV2	东山长穗 Dongshan Changsui
	42	YV3	三棱榄 Sanlenglan
广西钦州浦北 Pubei，Qinzhou，Guangxi	43	GN1	猪腰榄 Zhuyaolan
四川泸州合江 Hejiang，Luzhou，Sichuan	44	CE1	大梭子Dasuozi
	45	CE2	丁香榄 Dingxianglan
	46	CE3	青果Chinese White Olive
	47	CE4	三白圆 Sanbaiyuan
浙江温州平阳 Pingyang，Wenzhou，Zhejiang	48	ZC1	平阳1号 Pingyang 1
	49	ZC2	平阳2号 Pingyang 2
	50	ZC3	平阳3号 Pingyang 3
	51	ZC4	平阳4号 Pingyang 4
	52	ZC5	平阳5号 Pingyang 5
	53	ZC6	平阳6号 Pingyang 6
	54	ZC7	平阳7号 Pingyang 7
	55	ZC8	平阳8号 Pingyang 8
浙江温州瑞安 Rui’an，Wenzhou，Zhejiang	56	ZC9	瑞安1号 Rui’an 1
	57	ZC10	瑞安2号Rui’an 2
	58	ZC11	瑞安3号Rui’an 3
	59	ZC12	瑞安4号Rui’an 4

重复类型 Repeat types	序列数量 Number of sequences	位点数量 Number of loci	占全部SSR/% Proportion of all SSRs	EST中出现频率/% Frequency in EST	平均距离/ kb Average distance	平均长度/ bp Average length
单核苷酸Single nucleotide	25 262	27 390	31.82	8.53	12.59	10.34
二核苷酸Dinucleotide	9 370	9 742	11.32	3.16	35.39	13.97
三核苷酸Trinucleotide	7 773	8 114	9.43	2.62	42.48	16.88
四核苷酸Tetranucleotide	954	961	1.12	0.32	358.71	21.91
五核苷酸Pentanucleotide	269	269	0.31	0.09	1 281.50	26.43
六核苷酸Hexanucleotide	234	234	0.27	0.08	1 473.17	37.10
复合型核苷酸Compound nucleotides	36 135	39 374	45.74	12.19	8.76	24.45

重复类型 Repeat types	序列数量 Number of sequences	位点数量 Number of loci	占全部SSR/% Proportion of all SSRs	EST中出现频率/% Frequency in EST	平均距离/ kb Average distance	平均长度/ bp Average length
单核苷酸Single nucleotide	25 262	27 390	31.82	8.53	12.59	10.34
二核苷酸Dinucleotide	9 370	9 742	11.32	3.16	35.39	13.97
三核苷酸Trinucleotide	7 773	8 114	9.43	2.62	42.48	16.88
四核苷酸Tetranucleotide	954	961	1.12	0.32	358.71	21.91
五核苷酸Pentanucleotide	269	269	0.31	0.09	1 281.50	26.43
六核苷酸Hexanucleotide	234	234	0.27	0.08	1 473.17	37.10
复合型核苷酸Compound nucleotides	36 135	39 374	45.74	12.19	8.76	24.45

引物代号 Primer code	正向引物序列 Forward primer sequence	反向引物序列 Reverse primer sequence	产物大小/bp Product size	退火温度（正/反）/℃ Annealing temperature (F/R)	重复基元 Repeat primitive	等位位点数 Number of alleles
1	CTCCAAGGGGCAAGACAGAG	TCACTGTCGCCGTCGTTAAA	174 ~ 178	60.04/59.97	(A)10；(GA)6	2
8	GCCAACAGGACGATTCTCCA	AGCTAGGAGGTGAGACAGGG	119 ~ 125	60.04/60.03	(A)10；(TT)6(T)13*	2
15	AGCTTCCCCACACATGTCAG	ACTGGTATGCCCTTCACGTG	221 ~ 226	59.96/60.04	(TA)6	2
38	TCATGCTCCTCCTCTCTGCT	CAGTGCACTTGTTCAGCCAC	291 ~ 294	60.03/59.97	(AAA)5(A)17(AA)8	3
49	GGAGACTCAAGGTCACTGCC	TTTGCTCTCCAGTGACGGTC	290 ~ 305	60.04/59.97	(GAGA)5(GA)10*	2
53	AATCTCCCAAGCAGATGGCC	ATCAGGCCACATCACTTGGG	147 ~ 153	60.11/60.03	(A)10；(TT)8(TTT)5(T)17	2
59	CTCCCACCCACAACCACTAC	GCCGCAAATCTCGCAGAAAT	156 ~ 159	59.96/59.90	(TGGAGA)13	2
63	ACACCACCAAGCTTGTCACA	ACATTCCAGTCAGCAGCTCC	205 ~ 215	60.04/60.04	(A)10；(TT)6(T)12*	3
64	GGCAGATACGGGGCTCTTAC	CCATTCTCGTCCGCTGATGA	293 ~ 326	59.97/59.90	(CCT)6；(T)12(TT)6*	6
69	TCCGGGTATTGGAAGGCAAC	GGCTCTCTGCAAGGCGATAT	180 ~ 183	60.04/59.97	(AGG)5；(AA)6(A)12ttcatctag aagg(A)10gtattagaataacaaaaagctgagctagccaatcctagatgaagatgtgtacagaatagtgtgtga(T)12(TT)6	2
72	GGTCCAAAGAATCCGGGTGT	TGCTTTGATGGCAACGTGTG	209 ~ 216	59.96/59.97	(T)10	3
77	GCCCCTTCCTGTTCTTCCTC	GGAACCGGAGTTTGGGCTAA	177 ~ 194	60.04/59.96	(CT)7	2

Analysis of Canarium album Transcriptome SSR Information and Molecular Marker Development and Application

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SSR位点代号 SSR locus code	N_a 等位基因数 Allele number	N_e 有效等位基因数 Effective allele number	H_o 观测杂合度 Observed heterozygosity	H_e 期望杂合度 Expected heterozygosity	I 香农多样性指数 Shannon’s diversity index	PIC 多态性信息含量 Polymorphism information content
1	3	2.068	0.390	0.521	0.767	0.399
8	4	2.487	1.000	0.603	1.040	0.515
15	2	2.000	1.000	0.504	0.693	0.375
38	3	2.636	1.000	0.626	1.031	0.549
49	4	2.208	1.000	0.552	0.881	0.444
53	4	1.932	0.458	0.487	0.901	0.438
59	4	2.446	0.102	0.589	1.022	0.496
63	6	3.118	1.000	0.685	1.359	0.633
64	10	4.497	0.661	0.784	1.766	0.748
69	3	2.068	1.000	0.521	0.767	0.399
72	3	1.108	0.102	0.099	0.233	0.095
77	2	1.017	0.017	0.017	0.049	0.017
平均值Average	4	2.299	0.644	0.499	0.876	0.426

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