基于重测序的中国李基因组InDel标记的开发及应用

doi:10.16420/j.issn.0513-353x.2024-0066

园艺学报 ›› 2024, Vol. 51 ›› Issue (11): 2510-2522.doi: 10.16420/j.issn.0513-353x.2024-0066

• 遗传育种·种质资源·分子生物学 • 上一篇下一篇

基于重测序的中国李基因组InDel标记的开发及应用

陈方策¹, 胡平正², 解为玮¹, 王钲彭¹, 钟创南¹, 李海炎³, 何业华¹, 彭泽¹, 万保雄³^,^*(), 刘朝阳¹^,^*()

¹ 农业农村部华南地区园艺作物生物学与种质创制重点实验室，华南农业大学园艺学院，广州 510642
² 重庆果派园艺有限公司，重庆 402560
³ 广西特色作物研究院，广西桂林 541004

收稿日期:2024-04-02 修回日期:2024-09-03 出版日期:2024-12-12 发布日期:2024-11-25
通讯作者:
^* E-mail：wan77118@163.com，
liuchaoyang@scau.edu.cn
基金资助:
广州市科技计划项目(202206010038); 省级乡村振兴战略专项资金种业振兴项目(2022-NPY-00-029); 省级乡村振兴战略专项资金种业振兴项目(2023-NBH-00-026)

Development and Application of Prunus salicina InDel Markers Based on Genome Re-sequencing

CHEN Fangce¹, HU Pingzheng², XIE Weiwei¹, WANG Zhengpeng¹, ZHONG Chuangnan¹, LI Haiyan³, HE Yehua¹, PENG Ze¹, WAN Baoxiong³^,^*(), LIU Chaoyang¹^,^*()

¹ Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China，Ministry of Agriculture and Rural Affairs，Colleage of Horticulture，South China Agricultural University，Guangzhou 510642，China
² Chongqing Guopai Horticulture Co.，Ltd.，Chongqing 402560，China
³ Guangxi Academy of Special Crops，Guilin，Guangxi 541004，China

Received:2024-04-02 Revised:2024-09-03 Published:2024-12-12 Online:2024-11-25

摘要/Abstract

摘要：

基于部分中国李种质资源的基因组重测序结果，挖掘出一系列候选InDel位点，并从中筛选出分布在8条染色体上且表现出稳定多态性的53个InDel标记。利用开发的53个InDel标记对79份李种质资源进行遗传多样性评价，主要等位基因频率平均为0.6593，平均基因多样性指数（H_s）为0.4304，多态性信息含量（PIC）为0.3489，其中45个标记多态性信息含量较大（PIC > 0.25），多态性较好。UPGMA聚类分析在遗传相似系数为0.623和0.666处，将79份材料划分为2个类群和10个亚群，分类结果与种质的地理分布有一定关联。利用其中的13个InDel 标记将79份李种质进行区分，并构建了各种质13位的分子身份证。选择在亲本间具有多态性的 InDel 标记，对2个华南地区李品种正反杂交组合F₁代杂种的真伪进行了鉴定。

关键词: 李, InDel标记, 遗传多样性, 分子身份证, F₁真实性鉴定

Abstract:

Based on the genome re-sequencing results of several Chinese plum（Prunus salicina）germplasm resources，a series of candidate indel loci were mined，and 53 InDel markers which were distributed on different chromosomes and exhibited stable polymorphism，were screened out. The genetic diversity of 79 plum germplasm resources was evaluated by using 53 InDel markers. The average frequency of major alleles was 0.6593，the genetic diversity index（H_s）was 0.4304，and the polymorphism information content（PIC）was 0.3489. Among them，45 markers had high polymorphism information content（PIC > 0.25）. Based on UPGMA cluster analysis，79 accessions were divided into 2 groups and 10 subgroups with genetic similarity coefficients of 0.623 and 0.666，respectively. The classification results were related to the geographical distribution of germplasm resources. The plum germplasms were distinguished by 13 InDel markers，and the germplasm specific molecular identity cards were constructed. By selecting InDel markers with polymorphism among parents，the F₁ hybrid authenticity of positive and negative cross combinations of two plum cultivars in South China was identified.

Key words: plum, InDel marker, genetic diversity, molecular identity card, F₁identification

陈方策, 胡平正, 解为玮, 王钲彭, 钟创南, 李海炎, 何业华, 彭泽, 万保雄, 刘朝阳. 基于重测序的中国李基因组InDel标记的开发及应用[J]. 园艺学报, 2024, 51(11): 2510-2522.

CHEN Fangce, HU Pingzheng, XIE Weiwei, WANG Zhengpeng, ZHONG Chuangnan, LI Haiyan, HE Yehua, PENG Ze, WAN Baoxiong, LIU Chaoyang. Development and Application of Prunus salicina InDel Markers Based on Genome Re-sequencing[J]. Acta Horticulturae Sinica, 2024, 51(11): 2510-2522.

图/表 8

参考文献 26

[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. pmid: 6247908
[2]	Chen Hong, Yang Yiran. 2014. Genetic diversity and relationship of plum resources in Guizhou analyzed by ISSR markers. Journal of Fruit Science, 31 (2):175-180. (in Chinese)
	陈红, 杨迤然. 2014. 贵州李资源遗传多样性及亲缘关系的ISSR分析. 果树学报, 31 (2):175-180.
[3]	Fernandez I Marti A, Saski C A, Manganaris G A, Gasic K, Crisosto C H. 2018. Genomic sequencing of Japanese plum(Prunus salicina Lindl.) mutants provides a new model for Rosaceae fruit ripening studies. Frontiers in Plant Science, 9:21. doi: 10.3389/fpls.2018.00021 pmid: 29515596
[4]	Fiol A, García S, Dujak C, Pacheco I, Infante R, Aranzana M J. 2022. An LTR retrotransposon in the promoter of a PsMYB10. 2 gene associated with the regulation of fruit flesh color in Japanese plum. Horticulture Research, 9:uhac206.
[5]	García-Lor A, Luro F, Navarro L, Ollitrault P. 2012. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Molecular Genetics & Genomics, 287 (1):77-94.
[6]	Guo Cuihong, He Yehua, Feng Junting, Chen Chengjie, Lin Wenqiu, Luan Aiping, Zhang Yafen. 2015. Investigation of plum industry development in Guangdong Province. Nonwood Forest Research, 33 (1):141-146. (in Chinese)
	郭翠红, 何业华, 冯筠庭, 陈程杰, 林文秋, 栾爱萍, 张雅芬. 2015. 广东省李产业发展现状调查. 经济林研究, 33 (1):141-146.
[7]	He Yehua, Pan Jianjun, Yang Xianghui, Liu Chaoyang, Li Chuhao, Xia Jingxian, Zhang Wei, Peng Weizhuo, Hao Jingjing, Xu Rongbo, Kong Wenhui, Zhong Yizhong. 2023. A new plum cultivar‘Congzao 1 Zaoli’. Acta Horticulturae Sinica, 50 (12):2765-2766. (in Chinese)
	何业华, 潘建君, 杨向晖, 刘朝阳, 李楚豪, 夏靖娴, 张伟, 彭伟卓, 郝静静, 徐荣波, 孔文辉, 钟乙中. 2023. 李新品种‘从早1号早李’. 园艺学报, 50 (12):2765-2766. doi: 10.16420/j.issn.0513-353x.2021-0317
[8]	He Yehua, Yang Xianghui, Luan Aiping, Liu Chengming, Hu Guibing, Lin Shunquan, Qin Yonghua, Xia Jingxian, Fu Jiaxin, Zhao Jietang, Gao Yongshun, Zhang Zhike, Wen Ruiming, Chen Shikai, Luo Xueyou, Chi Qiongyun, Lu Shiwei. 2020. A new plum cultivar‘Yunkai 1’. Acta Horticulturae Sinica, 47 (S2):2891-2892. (in Chinese) doi: 10.16420/j.issn.0513-353x.2020-0067
	何业华, 杨向晖, 栾爱萍, 刘成明, 胡桂兵, 林顺权, 秦永华, 夏靖娴, 傅嘉欣, 赵杰堂, 高用顺, 张志珂, 温瑞明, 陈世凯, 罗学优, 池琼云, 卢仕威. 2020. 华南李新品种‘云开1号’. 园艺学报, 47 (S2):2891-2892.
[9]	Hu Zhenbang, Gao Yunlai, Qi Zhaoming, Jiang Hongwei, Liu Chunyan, Xin Dawei, Hu Guohua, Pan Xiaocheng, Chen Qingshan. 2016. Software development of ID analysis for crop molecular identity construction. Scientia Agricultura Sinica, 49 (12):2255-2266. (in Chinese) doi: 10.3864/j.issn.0578-1752.2016.12.002
	胡振帮, 高运来, 齐照明, 蒋洪蔚, 刘春燕, 辛大伟, 胡国华, 潘校成, 陈庆山. 2016. 作物分子身份证构建软件ID analysis的编制. 中国农业科学, 49 (12):2255-2266.
[10]	Lin Cunxue, Yang Xiaohua, Liu Hairong. 2020. Genetic diversity analysis of 96 plum germplasm resources by phenotypic traits in northeast cold area. Acta Horticulturae Sinica, 47 (10):1917-1929. (in Chinese) doi: 10.16420/j.issn.0513-353x.2019-0982
	林存学, 杨晓华, 刘海荣. 2020. 东北寒地96份李种质资源表型性状遗传多样性分析. 园艺学报, 47 (10):1917-1929.
[11]	Liu Jun. 2017. Genetic variation analysis of mutagenic grafted plum lines based on SRAP and IRAP markers[M. D. Dissertation]. Chengdu: Sichuan Agricultural University. (in Chinese)
	刘均. 2017. 基于SRAP和IRAP标记的诱变李嫁接株系遗传变异分析[硕士论文]. 成都: 四川农业大学.
[12]	Liu K, Muse S V. 2005. PowerMarker:an integrated analysis environment for genetic marker analysis. Bioinformatics, 21 (9):2128-2129.
[13]	Liu Shuantao, Zhang Zhigang, Wang Ronghua, Wang Lihua, Li Qiaoyun, Zhao Zhizhong. 2019. Construction of molecular identity card for Chinese cabbage breeding materials based on InDel markers. China Vegetables,(2):34-41. (in Chinese)
	刘栓桃, 张志刚, 王荣花, 王立华, 李巧云, 赵智中. 2019. 基于InDel标记的大白菜育种材料分子身份证构建. 中国蔬菜,(2):34-41.
[14]	Liu Weisheng, Zhang Qiuping, Ma Xiaoxue, Zhang Yuping, Liu Jiacheng, Zhang Yujun, Liu Shuo, Liu Ning, Xu Ming. 2019. Fruit scientific research in New China in the past 70 years:plum. Journal of Fruit Science, 36 (10):1320-1338. (in Chinese)
	刘威生, 章秋平, 马小雪, 张玉萍, 刘家成, 张玉君, 刘硕, 刘宁, 徐铭. 2019. 新中国果树科学研究70年——李. 果树学报, 36 (10):1320-1338.
[15]	Liu Yuanxia, Lan Jinhao, Bai Suhua, Sun Xiaohong, Liu Chunxiao, Zhang Yugang, Dai Hongyi. 2017. Screening of SNP and InDel markers to glomerella leaf spot resistance gene locus in apple using HRM technology. Acta Horticulturae Sinica, 44 (2):215-222. (in Chinese) doi: 10.16420/j.issn.0513-353x.2016-0519
	刘源霞, 兰进好, 柏素花, 孙晓红, 刘春晓, 张玉刚, 戴洪义. 2017. 苹果抗炭疽菌叶枯病基因SNP和InDel标记的HRM筛选. 园艺学报, 44 (2):215-222. doi: 10.16420/j.issn.0513-353x.2016-0519
[16]	Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M A. 2010. The genome analysis toolkit:a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20 (9):1297-1303.
[17]	Rohlf F J. 1993. NTSYS-pc:numerical taxonomy and multivariate analysis system:version1.7. Exeter Software,Setauket.
[18]	Shedlock A M, Okada N. 2000. Sine insertions:powerful tools for molecular systematics. Bioessays, 22 (2):148-160. doi: 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z pmid: 10655034
[19]	Song Haiyan, Xun Shuxia, Li Jing, Tu Meiyan, Wang Lingli, Xu Zihong, Chen Dong, Jiang Guoliang. 2023. Identification and genetic background analysis of three plum varieties based on SSR marker detection and resequencing technology. South China Fruits, 52 (3):94-101. (in Chinese)
	宋海岩, 孙淑霞, 李靖, 涂美艳, 王玲利, 徐子鸿, 陈栋, 江国良. 2023. 基于SSR标记检测与重测序技术的3个李品种鉴定与遗传背景简析. 中国南方果树, 52 (3):94-101.
[20]	Tang Yuqing, Yang Huidong, Yan Chengpu, Wang Siyu, Wang Yuting, Hu Zhongdong, Zhu Fanghong. 2023. Development and application of Jinlan pummelo(Citrus maxima)InDel markers based on genome re-sequencing. Acta Horticulturae Sinica, 50 (1):15-26. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-0935
	汤雨晴, 杨惠栋, 闫承璞, 王斯妤, 王雨亭, 胡钟东, 朱方红. 2023. 基于重测序的‘金兰柚’基因组InDel标记的开发及应用. 园艺学报, 50 (1):15-26. doi: 10.16420/j.issn.0513-353x.2021-0935
[21]	Wang Jue, Wang Yan, Zhang Jing, Chen Tao, Wang Lei,Chen Qing,Tang Hao-ru,Wang Xiaorong. 2020. Development of Insertion-Deletion(InDel)markers based on wholegenome sequencing data in Chinese cherry and their transferability in Rosaceae fruit trees. Acta Horticulturae Sinica, 47 (1):98-110. (in Chinese)
	王珏, 王燕, 张静, 陈涛, 王磊, 陈清, 汤浩茹, 王小蓉. 2020. 中国樱桃InDel标记开发及其在蔷薇科果树中通用性评价. 园艺学报, 47 (1):98-110. doi: 10.16420/j.issn.0513-353x.2019-0062
[22]	Wei Xiao, Zhang Qiuping, Liu Ning, Zhang Yuping, Xu Ming, Liu Shuo, Zhang Yujun, Ma Xiaoxue, Liu Weisheng. 2019. Genetic diversity of the Prunus salicina L. from different sources and their related species. Scientia Agricultura Sinica, 52 (3):568-578. (in Chinese) doi: 10.3864/j.issn.0578-1752.2019.03.017
	魏潇, 章秋平, 刘宁, 张玉萍, 徐铭, 刘硕, 张玉君, 马小雪, 刘威生. 2019. 不同来源中国李(Prunus salicina L.) 的多样性与近缘种关系. 中国农业科学, 52 (3):568-578. doi: 10.3864/j.issn.0578-1752.2019.03.017
[23]	Xu Yicen. 2022. Analysis of chloroplast genome sequences and molecular identification of Prunus[M. D. Dissertation]. Chongqing: Southwest University. (in Chinese)
	徐溢岑. 2022. 李属植物资源叶绿体基因组序列分析与分子鉴定[硕士论文]. 重庆: 西南大学.
[24]	Zhang Jiayan, Zhou En. 1998. Chinese fruit trees · Prunus. Bejing: China Forestry Publishing House. (in Chinese)
	张加延, 周恩. 1998. 中国果树志 · 李卷. 北京: 中国林业出版社.
[25]	Zhang Shuwen, Yu Zheping, Sun Li, Liang Senmiao, Zheng Xiliang, Yan Lijü, Huang Yinghong, Qi Xingjiang. 2024. Genetic diversity analysis and DNA fingerprint construction of Chinese bayberry germplasm resources. Molecular Plant Breeding, 22 (5):1488-1500. (in Chinese)
	张淑文, 俞浙萍, 孙鹂, 梁森苗, 郑锡良, 颜丽菊, 黄颖宏, 戚行江. 2024. 杨梅种质资源遗传多样性分析与DNA指纹图谱构建. 分子植物育种, 22 (5):1488-1500.
[26]	Zuo Lihui, Han Zhixiao, Liang Haiyong, Yang Minsheng. 2015. Analysis of genetic diversity of Prunus salicina from different producing areas by SSR markers. Acta Horticulturae Sinica, 42 (1):111-118. (in Chinese) doi: 10.16420/j.issn.0513-353x.2014-0679
	左力辉, 韩志校, 梁海永, 杨敏生. 2015. 不同产地中国李资源遗传多样性SSR分析. 园艺学报, 42 (1):111-118. doi: 10.16420/j.issn.0513-353x.2014-0679

类群 Group	编号 Code	样品名称 Sample name	来源 Login	果肉颜色 Flesh color
华南品种	GD01	灌村三华李Guancun Sanhuali	广东Guangdong	红色Red
Southern cultivar	GD02	上罗三华李Shangluo Sanhuali	广东Guangdong	红色Red
	GD03	大蜜李Damili	广东Guangdong	红色Red
	GD04	华蜜大蜜李Huami Damili	广东Guangdong	红色Red
	GD05	白脆鸡麻李实生Baicuijimali Shisheng	广东Guangdong	黄色Yellow
	GD06	白脆鸡麻李Baicuijimali	广东Guangdong	红色Red
	GD07	竹丝李Zhusili	广东Guangdong	黄色Yellow
	GD08	硬枝李Yingzhili	广东Guangdong	黄色Yellow
	GD09	连麻三月李Lianma Sanyueli	广东Guangdong	黄色Yellow
	GD10	桂峰三月李Guifeng Sanyueli	广东Guangdong	黄色Yellow
	GD11	三月李实生Sanyueli Shisheng	广东Guangdong	黄色Yellow
	GD12	岭溪李实生Lingxili Shisheng	广东Guangdong	黄色Yellow
	GD13	乳源岭溪李Ruyuan Lingxili	广东Guangdong	黄色Yellow
	GD14	乳源大黄李Ruyuan Dahuangli	广东Guangdong	黄色Yellow
	GD15	乳源1号Ruyuan 1	广东Guangdong	黄色Yellow
	GD16	早竹李Zaozhuli	广东Guangdong	黄色Yellow
	GD17	香蜜李Xiangmili	广东Guangdong	红色Red
	GD18	学佬李Xuelaoli	广东Guangdong	黄色Yellow
	GD19	瑶山李Yaoshanli	广东Guangdong	红色Red
	GD20	韶关4号野李Shaoguan 4 Yeli	广东Guangdong	黄色Yellow
	GD21	韶关6号野李Shaoguan 6 Yeli	广东Guangdong	黄色Yellow
	GD22	猪血李Zhuxueli	广东Guangdong	红色Red
	GD23	从早1号Congzao 1	广东Guangdong	黄色Yellow
	GD24	云开1号Yunkai 1	广东Guangdong	红色Red
	GD25	早禾李Zaoheli	广东Guangdong	黄色Yellow
	GD26	串珠李Chuanzhuli	广东Guangdong	黄色Yellow
	GD27	黄金㮈李Huangjin Naili	广东Guangdong	黄色Yellow
	GX01	乐业早熟李Leye Zaoshuli	广西Guangxi	黄色Yellow
	GX02	广西大水李Guangxi Dashuili	广西Guangxi	黄色Yellow
	GX03	胭脂李Yanzhili	广西Guangxi	红色Red
	GX04	苞谷李Baoguli	广西Guangxi	黄色Yellow
	GX05	凌云鸡血李Lingyun Jixueli	广西Guangxi	红色Red
	GX06	凌云桐壳李Lingyun Tongkeli	广西Guangxi	黄色Yellow
	GX07	乐业黄壳李Leye Huangkeli	广西Guangxi	黄色Yellow
	GX08	乐业小栽秧李Leye Xiaozaiyangli	广西Guangxi	黄色Yellow
	GX09	乐业红牛心李Leye Hongniuxinli	广西Guangxi	黄色Yellow
	GX10	化峒镇血红李Huadongzhen Xuehongli	广西Guangxi	红色Red
	GX11	乐业黄皮李Leye Huangpili	广西Guangxi	黄色Yellow
	GX12	乐业牛鸡心李Leye Niujixinli	广西Guangxi	黄色Yellow
西南品种	GZ01	蜂糖李Fengtangli	贵州Guizhou	黄色Yellow
Southwest cultivar	GZ02	一点红蜂糖李Yidianhong Fengtangli	贵州Guizhou	黄色Yellow
	GZ03	蜜李1号Mili 1	贵州Guizhou	黄色Yellow
	GZ04	安顺本地晚熟李Anshun Bendi Wanshuli	贵州Guizhou	黄色Yellow
	GZ05	四月李Siyueli	贵州Guizhou	黄色Yellow
	GZ06	打帮李Dabangli	贵州Guizhou	黄色Yellow
	GZ07	冰脆李Bingcuili	贵州Guizhou	黄色Yellow
	GZ08	棉花李Mianhuali	贵州Guizhou	黄色Yellow
	GZ09	紫云本地红李Ziyun Bendi Hongli	贵州Guizhou	黄色Yellow
	GZ10	脆红李Cuihongli	贵州Guizhou	黄色Yellow
	GZ11	沿河空心李Yanhe Kongxinli	贵州Guizhou	黄色Yellow
	GZ12	黄蜡李Huanglali	贵州Guizhou	黄色Yellow
	GZ13	九阡李Jiuqianli	贵州Guizhou	黄绿色Chartreuse
	SC01	晚熟青脆李Wanshu Qingcuili	四川Sichuan	黄色Yellow
	SC02	五月脆Wuyuecui	四川Sichuan	黄绿色Chartreuse
	SC03	苍溪早青脆Cangxi Zaoqingcui	四川Sichuan	黄色Yellow
	SC04	江安李Jianganli	四川Sichuan	黄绿色Chartreuse
	CQ01	铜梁龙李Tongliang Longli	重庆Chongqing	黄色Yellow
	CQ02	粉黛脆李Fendai Cuili	重庆Chongqing	黄色Yellow
	YN01	云南黄李Yunnan Huangli	云南Yunnan	黄色Yellow
南方其他地区品种	HB01	五峰翰林空心李Wufeng Hanlin Kongxinli	湖北Hubei	黄色Yellow
Other southern cultivar	HB02	油头青Youtouqing	湖北Hubei	黄色Yellow
	ZJ01	桃形李Taoxingli	浙江Zhejiang	黄色Yellow
	ZJ02	檇李Zuili	浙江Zhejiang	黄色yellow
	ZJ03	金塘李Jintangli	浙江Zhejiang	红色Red
	FJ01	芙蓉李Furongli	福建Fujian	红色Red
	FJ02	油奈Younai	福建Fujian	黄色Yellow
	FJ03	鹅黄李Ehuangli	福建Fujian	黄色Yellow
北方品种	SD01	山东早红Shandong Zaohong	山东Shandong	黄色Yellow
Northern cultivar	SD02	玉皇李Yuhuangli	山东Shandong	黄色Yellow
	HN01	灰子李Huizili	河南Henan	黄色Yellow
	XJ01	新疆黄李Xinjiang Huangli	新疆Xinjiang	黄色Yellow
	SX01	商县梅李Shangxian Meili	陕西Shaanxi	黄色Yellow
	LN01	大红袍Dahongpao	辽宁Liaoning	黄色Yellow
	LN02	国峰7号Guofeng 7	辽宁Liaoning	黄色Yellow
	JL01	晚金玉Wanjinyu	吉林Jinlin	黄色Yellow
	JL02	松祥桃李Songxiang Taoli	吉林Jinlin	黄色Yellow
	HLJ01	龙园蜜李Longyuan Mili	黑龙江Heilongjiang	黄色Yellow
	HLJ02	秋甜李Qiutianli	黑龙江Heilongjiang	黄色Yellow
杏李品种P. simonii	XL01	味帝Weidi	国外Foreign	红色Red

类群 Group	编号 Code	样品名称 Sample name	来源 Login	果肉颜色 Flesh color
华南品种	GD01	灌村三华李Guancun Sanhuali	广东Guangdong	红色Red
Southern cultivar	GD02	上罗三华李Shangluo Sanhuali	广东Guangdong	红色Red
	GD03	大蜜李Damili	广东Guangdong	红色Red
	GD04	华蜜大蜜李Huami Damili	广东Guangdong	红色Red
	GD05	白脆鸡麻李实生Baicuijimali Shisheng	广东Guangdong	黄色Yellow
	GD06	白脆鸡麻李Baicuijimali	广东Guangdong	红色Red
	GD07	竹丝李Zhusili	广东Guangdong	黄色Yellow
	GD08	硬枝李Yingzhili	广东Guangdong	黄色Yellow
	GD09	连麻三月李Lianma Sanyueli	广东Guangdong	黄色Yellow
	GD10	桂峰三月李Guifeng Sanyueli	广东Guangdong	黄色Yellow
	GD11	三月李实生Sanyueli Shisheng	广东Guangdong	黄色Yellow
	GD12	岭溪李实生Lingxili Shisheng	广东Guangdong	黄色Yellow
	GD13	乳源岭溪李Ruyuan Lingxili	广东Guangdong	黄色Yellow
	GD14	乳源大黄李Ruyuan Dahuangli	广东Guangdong	黄色Yellow
	GD15	乳源1号Ruyuan 1	广东Guangdong	黄色Yellow
	GD16	早竹李Zaozhuli	广东Guangdong	黄色Yellow
	GD17	香蜜李Xiangmili	广东Guangdong	红色Red
	GD18	学佬李Xuelaoli	广东Guangdong	黄色Yellow
	GD19	瑶山李Yaoshanli	广东Guangdong	红色Red
	GD20	韶关4号野李Shaoguan 4 Yeli	广东Guangdong	黄色Yellow
	GD21	韶关6号野李Shaoguan 6 Yeli	广东Guangdong	黄色Yellow
	GD22	猪血李Zhuxueli	广东Guangdong	红色Red
	GD23	从早1号Congzao 1	广东Guangdong	黄色Yellow
	GD24	云开1号Yunkai 1	广东Guangdong	红色Red
	GD25	早禾李Zaoheli	广东Guangdong	黄色Yellow
	GD26	串珠李Chuanzhuli	广东Guangdong	黄色Yellow
	GD27	黄金㮈李Huangjin Naili	广东Guangdong	黄色Yellow
	GX01	乐业早熟李Leye Zaoshuli	广西Guangxi	黄色Yellow
	GX02	广西大水李Guangxi Dashuili	广西Guangxi	黄色Yellow
	GX03	胭脂李Yanzhili	广西Guangxi	红色Red
	GX04	苞谷李Baoguli	广西Guangxi	黄色Yellow
	GX05	凌云鸡血李Lingyun Jixueli	广西Guangxi	红色Red
	GX06	凌云桐壳李Lingyun Tongkeli	广西Guangxi	黄色Yellow
	GX07	乐业黄壳李Leye Huangkeli	广西Guangxi	黄色Yellow
	GX08	乐业小栽秧李Leye Xiaozaiyangli	广西Guangxi	黄色Yellow
	GX09	乐业红牛心李Leye Hongniuxinli	广西Guangxi	黄色Yellow
	GX10	化峒镇血红李Huadongzhen Xuehongli	广西Guangxi	红色Red
	GX11	乐业黄皮李Leye Huangpili	广西Guangxi	黄色Yellow
	GX12	乐业牛鸡心李Leye Niujixinli	广西Guangxi	黄色Yellow
西南品种	GZ01	蜂糖李Fengtangli	贵州Guizhou	黄色Yellow
Southwest cultivar	GZ02	一点红蜂糖李Yidianhong Fengtangli	贵州Guizhou	黄色Yellow
	GZ03	蜜李1号Mili 1	贵州Guizhou	黄色Yellow
	GZ04	安顺本地晚熟李Anshun Bendi Wanshuli	贵州Guizhou	黄色Yellow
	GZ05	四月李Siyueli	贵州Guizhou	黄色Yellow
	GZ06	打帮李Dabangli	贵州Guizhou	黄色Yellow
	GZ07	冰脆李Bingcuili	贵州Guizhou	黄色Yellow
	GZ08	棉花李Mianhuali	贵州Guizhou	黄色Yellow
	GZ09	紫云本地红李Ziyun Bendi Hongli	贵州Guizhou	黄色Yellow
	GZ10	脆红李Cuihongli	贵州Guizhou	黄色Yellow
	GZ11	沿河空心李Yanhe Kongxinli	贵州Guizhou	黄色Yellow
	GZ12	黄蜡李Huanglali	贵州Guizhou	黄色Yellow
	GZ13	九阡李Jiuqianli	贵州Guizhou	黄绿色Chartreuse
	SC01	晚熟青脆李Wanshu Qingcuili	四川Sichuan	黄色Yellow
	SC02	五月脆Wuyuecui	四川Sichuan	黄绿色Chartreuse
	SC03	苍溪早青脆Cangxi Zaoqingcui	四川Sichuan	黄色Yellow
	SC04	江安李Jianganli	四川Sichuan	黄绿色Chartreuse
	CQ01	铜梁龙李Tongliang Longli	重庆Chongqing	黄色Yellow
	CQ02	粉黛脆李Fendai Cuili	重庆Chongqing	黄色Yellow
	YN01	云南黄李Yunnan Huangli	云南Yunnan	黄色Yellow
南方其他地区品种	HB01	五峰翰林空心李Wufeng Hanlin Kongxinli	湖北Hubei	黄色Yellow
Other southern cultivar	HB02	油头青Youtouqing	湖北Hubei	黄色Yellow
	ZJ01	桃形李Taoxingli	浙江Zhejiang	黄色Yellow
	ZJ02	檇李Zuili	浙江Zhejiang	黄色yellow
	ZJ03	金塘李Jintangli	浙江Zhejiang	红色Red
	FJ01	芙蓉李Furongli	福建Fujian	红色Red
	FJ02	油奈Younai	福建Fujian	黄色Yellow
	FJ03	鹅黄李Ehuangli	福建Fujian	黄色Yellow
北方品种	SD01	山东早红Shandong Zaohong	山东Shandong	黄色Yellow
Northern cultivar	SD02	玉皇李Yuhuangli	山东Shandong	黄色Yellow
	HN01	灰子李Huizili	河南Henan	黄色Yellow
	XJ01	新疆黄李Xinjiang Huangli	新疆Xinjiang	黄色Yellow
	SX01	商县梅李Shangxian Meili	陕西Shaanxi	黄色Yellow
	LN01	大红袍Dahongpao	辽宁Liaoning	黄色Yellow
	LN02	国峰7号Guofeng 7	辽宁Liaoning	黄色Yellow
	JL01	晚金玉Wanjinyu	吉林Jinlin	黄色Yellow
	JL02	松祥桃李Songxiang Taoli	吉林Jinlin	黄色Yellow
	HLJ01	龙园蜜李Longyuan Mili	黑龙江Heilongjiang	黄色Yellow
	HLJ02	秋甜李Qiutianli	黑龙江Heilongjiang	黄色Yellow
杏李品种P. simonii	XL01	味帝Weidi	国外Foreign	红色Red

染色体Chromosome	插入Insertion	缺失Deletion	总计Total	InDel/%
Chr1	14 749	28 997	43 746	20.79
Chr2	10 058	18 077	28 135	13.37
Chr3	8 631	16 786	25 417	12.08
Chr4	8 632	16 391	25 023	11.89
Chr5	5 972	11 660	17 632	8.38
Chr6	9 103	17 140	26 243	12.47
Chr7	6 909	14 076	20 985	9.97
Chr8	7 302	14 492	21 794	10.36
染色体支架Scaffolds	526	931	1 457	0.69
总计Total	71 882	138 550	210 432	100.00

染色体Chromosome	插入Insertion	缺失Deletion	总计Total	InDel/%
Chr1	14 749	28 997	43 746	20.79
Chr2	10 058	18 077	28 135	13.37
Chr3	8 631	16 786	25 417	12.08
Chr4	8 632	16 391	25 023	11.89
Chr5	5 972	11 660	17 632	8.38
Chr6	9 103	17 140	26 243	12.47
Chr7	6 909	14 076	20 985	9.97
Chr8	7 302	14 492	21 794	10.36
染色体支架Scaffolds	526	931	1 457	0.69
总计Total	71 882	138 550	210 432	100.00

染色体 Chromosome	引物名 Primer name	物理位置 Physical location	正向引物（5′-3′） Forward primer sequence	反向引物（5′-3′） Reverse primer sequence
Chr1	M1	38894318	GGGGAGATGGAAAGTTAA	GTATTGCTCTTGGGCTGA
	M2	47980202	GGTTTTCTCGAAGTCGGTGAT	GGCTTGTGATATATTAGAACCCATG
	M3	48304762	GGACCCCATGCTGAAGAAAA	CAAATCTAAGGGCAAGTCCAAT
	M4	48570078	AGAAACCCACTATGTCACTG	AGACGGAGCATCAAATCA
	M5	49049772	ATCCCGTCAAACTCACTA	TGGATTGAACCCATACAC
	M6	50387422	CCACTTGGTCAAGGTTAAATGTC	GCAAATTGTAAGGGGTATGGTG
	M7	52179403	TGAAGTAGTCAGGACCTCTGGC	GGTCAGAGGTGAGAGCGATGA
	M8	52719011	TGGCTTCCAAACATCCTC	GTAGAGGCATCCAGCACA
Chr2	M9	12500445	CAGGAGTAGGCTCAAGAT	TTATGATGGATGGGTATG
	M10	31689717	CGTCGTTAGCGAGTGAGT	TGGCACGAAACAAGCAGT
	M11	31757195	GAGGCTCAATCGTAGACA	GATTCACGTTTGGGTTGT
	M12	33259045	CCTGGAACCCACGAATTTCT	CTTTCCTGACCAAGACAGTGTGA
	M13	33866248	CTCTAGGGTTCTTCTCTGCTATCTTC	GCTCGTTTGGTACGTTGGACT
Chr3	M14	1698465	CACCCACTAAGACTGACG	CCTTTGCGGAACACTTTA
	M15	6074639	TAGAAACGCTACGAAGGC	AATGGCTAAATGCTTGGTT
	M16	6079326	TTTGGGAAGTTAGTGGGA	TGCGGTCTTTCTCAACTCG
	M17	6982515	TCTGGGAACCTGGTGTTA	AATGTGCCTTTCTGTCCC
	M18	27839434	GGGTGGTCTGGTTCCCATAA	CATCGGCACAATAGTAGAGAAGC
	M19	28695379	ACAACGAAGCCTCCTCTTGAG	CACCTTTCCCCACAAATTTTG
	M20	29098986	ACCTTCCTCCTCATCATTGGA	ATAGTCGGGCTTTGCTGCTT
	M21	29210781	TGATCCACACTTCCCTATGACAG	GCCACGTGCATTATTTCTAAGAG
	M22	29355454	GCACGCACCCTTTCTTTTCT	CAGGGGCTTAGACAACCATCA
	M23	31644114	CTTACTGCAGAAGTTCGTGAGAAA	CACGCCTTTTCTGTTTCTTCTT
Chr4	M24	7678285	AGCCTGGTTGATTGTTGG	CAAACGCACTACGCAAAC
	M25	7903736	ACATCATCACGACCAGTA	CATCCACCAACAGCAACA
	M26	8483245	CTGTCTTCCTCTGCCATTT	GAATCTGCTCGGTCAAAG
	M27	11530071	ACCACCATTTTGCCAAGAGG	CCCAATCTTAGACTGGCCGTA
	M28	18058101	CGCGCGGCTATACTATTTTT	GATTTGGGCAACCTCTACCC
	M29	19467756	GGAGACCTTGCGACTGAT	AAGAGGTGGCTTGGTCAG
	M30	22025126	CCAGCTCACATGCTCTTTTCC	GATGCCTCTCATATGCCACTTG
	M31	23776947	AGATGTTGCCGAGAAAGG	CTCTATTTGCACCCACCC
	M32	24553291	ACATAGGTGGCTGTGATTACGC	CATGTGATGGAGGAAGTCTTGC
	M33	31285226	TGGCACACTACAATAGCACAATG	CCCAGGTCCCTCAACAGAAT
Chr5	M34	330880	TTTAGCCAAGTGGTGTTT	GATGGCTACTGAGGAAGG
	M35	7534231	AAAGAACTTACTTGGGAGAT	CAGAATCCACCAAGAAGA
	M36	12530378	GCAGTGGCGGAGCTAGAGT	TTTGCTAAGATACGATTAC
	M37	12533577	GTATCAATACCCTTTGGC	GGCACATTTTGTCTCGGT
	M38	14348889	CATTCCGTGAACCAAACAGG	CAATGCTGCCCAAATTGCTA
	M39	15641569	CAACAGTCACCCCGCAATTA	GTCAGCATCCCATCCCAAAT
	M40	22769129	CCAAAACTTTTCCCCAGAAAAC	GAGCTTGAGCAAGCATCGAG
Chr6	M41	3392066	AAACTGACTCGGAAAGGT	TGCCATTGGTTCCCTACT
	M42	3650929	AATGAGCACGGGCAGATA	GATTGATAGCCTCGGTTG
	M43	8649659	TATAGGGCACCTTCATCG	ACTGCTTTCAACTGTGGG
	M44	34659045	TGCGACTCATCAGTTTGT	CCTTTCCCGTTCTACCAT
Chr7	M45	2356604	CAAGGAGAAATAGAAGCGAAGA	CCCAAAGCACTCCGAAAG
	M46	8337435	CGGAAGAGGAGATGGTGGAA	GAGACTCTCACAGAGGCATTTCA
	M47	9880809	ATGTTCCCTCCACTCCTT	AAGCCTTGTTGAGGTGAT
	M48	9973675	CCTTGAAAAGACAGTGAACAGCA	TCCAAAGCCACCATTGTAACC
	M49	12448075	CCATGAGGAGGGAAAACAAAA	AATGAGCGTGAGTATACAATTAGGC
Chr8	M50	5495485	AAACTGACTCGGAAAGGT	ATTGCCATTGGTTCCCTA
	M51	13608340	TTCAGTGCCACAACAATAGGG	CGACGTACCCTTGTATCCCTTA
	M52	19291686	ACATTGTTTGCTGGGCTAT	TCCCGTTTGACAACCATT
	M53	19739188	AAACGCAAAGGACAAGAT	CGGGCAGTTCAAGGATTA

基于重测序的中国李基因组InDel标记的开发及应用

Development and Application of Prunus salicina InDel Markers Based on Genome Re-sequencing

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

图/表 8

参考文献 26

相关文章 15

编辑推荐

Metrics

本文评价

访问总数:　当日访问总数:　当前在线人数:

标记名称Marker name	主等位基因频率Major allele frquency	基因型数Genotype number	N_a 等位基因数 Number of allele	H_s 基因多样性指数 Gene diversity index	H_e 期望杂合度 Expected heterozygosity	PIC 多态性信息含量 Polymorphic information content
M1	0.8101	3	2	0.3076	0.3038	0.2603
M2	0.8734	3	2	0.2211	0.1013	0.1967
M3	0.7278	3	2	0.3962	0.1646	0.3177
M4	0.8354	2	2	0.2750	0.3291	0.2372
M5	0.6519	3	2	0.4539	0.443	0.3509
M6	0.6582	3	2	0.4499	0.5063	0.3487
M7	0.6282	3	2	0.4671	0.3333	0.3580
M8	0.7025	3	2	0.4180	0.5190	0.3306
M9	0.4808	6	3	0.6335	0.5513	0.5620
M10	0.4286	3	3	0.6208	0	0.5404
M11	0.5321	3	2	0.4979	0.5769	0.3740
M12	0.6329	3	2	0.4647	0.5316	0.3567
M13	0.5506	3	2	0.4949	0.7215	0.3724
M14	0.5886	3	2	0.4843	0.6456	0.3670
M15	0.6042	3	2	0.4783	0.2639	0.3639
M16	0.4464	6	3	0.6435	0.2679	0.5697
M17	0.3667	8	4	0.7212	0.4889	0.6703
M18	0.5506	3	2	0.4949	0.2405	0.3724
M19	0.5000	3	2	0.5000	0.3333	0.3750
M20	0.8671	2	2	0.2305	0.2658	0.2039
M21	0.8101	2	2	0.3076	0.3797	0.2603
M22	0.5513	3	2	0.4947	0.2564	0.3724
M23	0.9679	3	2	0.0620	0.0385	0.0601
M24	0.6456	5	4	0.5042	0.5696	0.4375
M25	0.5064	3	2	0.4999	0.8077	0.3750
M26	0.5949	2	2	0.4820	0.8101	0.3658
M27	0.5506	3	2	0.4949	0.5696	0.3724
M28	0.5972	3	2	0.4811	0.4167	0.3654
M29	0.7500	3	2	0.3750	0.2917	0.3047
M30	0.7278	3	2	0.3962	0.2911	0.3177
M31	0.5789	3	2	0.4875	0.1579	0.3687
M32	0.6753	3	2	0.4385	0.2078	0.3424
M33	0.7756	3	2	0.3480	0.3974	0.2875
M34	0.6731	3	2	0.4401	0.2949	0.3432
M35	0.4333	4	3	0.6516	0.0222	0.5784
M36	0.8924	3	2	0.1920	0.1139	0.1736
M37	0.9026	3	2	0.1758	0.1429	0.1604
M38	0.6899	4	3	0.4423	0.3671	0.3644
M39	0.8103	3	2	0.3074	0.1034	0.2601
M40	0.8291	3	2	0.2834	0.3165	0.2432
M41	0.6218	3	2	0.4703	0.5513	0.3597
M42	0.6866	4	3	0.4740	0.0896	0.4216
M43	0.6014	3	2	0.4794	0.1014	0.3645
M44	0.7722	3	2	0.3519	0.3797	0.2900
M45	0.8734	3	2	0.2211	0.2025	0.1967
M46	0.7975	3	2	0.3230	0.3797	0.2709
M47	0.6392	2	2	0.4612	0.7215	0.3549
M48	0.5294	3	2	0.4983	0.1569	0.3741
M49	0.6582	3	2	0.4499	0.3797	0.3487
M50	0.5779	3	2	0.4879	0.5065	0.3689
M51	0.5833	6	3	0.5195	0.3462	0.4235
M52	0.8176	3	2	0.2983	0.0135	0.2538
M53	0.3851	5	3	0.6599	0.4730	0.5856
平均Mean	0.6593	3.3019	2.2264	0.4304	0.3480	0.3489

编号 Code	分子身份证 Molecular ID	编号 Code	分子身份证 Molecular ID	编号 Code	分子身份证 Molecular ID	编号 Code	分子身份证 Molecular ID
GD01	0A40012232122	GD21	0A20811132122	GZ02	1111121111221	HB02	1327812242222
GD02	3610811121152	GD22	3514411121122	GZ03	2222212142331	ZJ01	8814421121142
GD03	5A69822122112	GD23	7653412332322	GZ04	3222312112321	ZJ02	6912731151151
GD04	6A14811531252	GD24	2514411121242	GZ05	5223213212231	ZJ03	B528811224156
GD05	8A20011231252	GD25	4A14811531202	GZ06	5223212112331	FJ01	3529811264156
GD06	1A14811131152	GD26	4340721122201	GZ07	3223212112301	FJ02	2A02221723112
GD07	2261211332242	GD27	6513211132102	GZ08	4331211122102	FJ03	6630215142302
GD08	0940012232222	GX01	8A20811252451	GZ09	1411412222121	SD01	4640321153102
GD09	7A50812322352	GX02	3660811142252	GZ10	3713312225256	SD02	3212514123102
GD10	7A50012322352	GX03	0650312142341	GZ11	3681011205305	HN01	9940717153102
GD11	C690611321262	GX04	6A40312242344	GZ12	BA93011125305	XJ01	3660351143102
GD12	8A24611321152	GX05	3650811152131	GZ13	BA33312725303	SX01	4330312153402
GD13	2A14611321112	GX06	6370811242141	SC01	4220312112001	LN01	6770725131202
GD14	AA20811623122	GX07	0619811422152	SC02	1230211132121	LN02	4900326130102
GD15	9970811131152	GX08	4635825242354	SC03	9320312142331	JL01	3AA2311126506
GD16	7660812232152	GX09	6615812222151	SC04	B617221424255	JL02	36A2321226506
GD17	1A10812132212	GX10	4619812422112	CQ01	4320315142301	HLJ01	3AA0372126606
GD18	4A10812232222	GX11	8630962541252	CQ02	8620312142331	HLJ02	3AA2321126506
GD19	6A14811531222	GX12	6615812242111	YN01	4344612123102	XL01	2223121121242
GD20	8B52311231152	GZ01	1111121111211	HB01	6325715242222

[1]	钟乙中, 汪州, 谢静瑶, 王钲彭, 郝静静, 刘朝阳, 张伟, 吴竞, 钟紫琴, 陈程杰, 何业华, . 2个熟期不同的华南李品种在热带北界线附近地区的开花结果行为[J]. 园艺学报, 2024, 51(9): 2105-2119.
[2]	秦子璐, 徐正康, 戴晓港, 陈赢男. 望春玉兰种质资源遗传多样性分析与核心种质构建[J]. 园艺学报, 2024, 51(8): 1823-1832.
[3]	秦宇, 郭荣琨, 农惠兰, 王燕, 崔凯, 董宁光. 利用SSR荧光标记构建山楂种质分子身份证[J]. 园艺学报, 2024, 51(6): 1227-1240.
[4]	袁娜, 徐勤圆, 徐照龙, 周玲, 刘晓庆, 陈新, 杜建厂. 基于靶向测序技术的菜豆SNP液相芯片开发及验证[J]. 园艺学报, 2024, 51(5): 1017-1032.
[5]	游平, 杨进, 周俊, 黄爱军, 鲍敏丽, 易龙, . 柑橘黄龙病菌原噬菌体的遗传多样性分析[J]. 园艺学报, 2024, 51(4): 727-736.
[6]	尤园园, 王帅, 方莹莹, 齐诚, 李淑培, 张映, 陈钰辉, 刘伟, 刘富中, 舒金帅. 茄子全基因组InDel变异特征及分子标记开发和应用[J]. 园艺学报, 2024, 51(3): 520-532.
[7]	岳林清, 吴怡超, 何星星, 向明燕, 王进, 武峥, 朱世国, 丁梦琦, 张建, 方小梅, 易泽林. 李资源果实主要性状的SSR标记关联分析及指纹图谱构建[J]. 园艺学报, 2024, 51(11): 2495-2509.
[8]	王荣波, 王海云, 张前荣, 蔡松龄, 李本金, 张美祥, 刘裴清. 福建省番茄青枯病菌遗传多样性分析及其抗性砧木的筛选[J]. 园艺学报, 2024, 51(11): 2540-2554.
[9]	姚远, 邓利君, 胡娟, 唐晓雨, 王铁, 李航, 孙国超, 熊博, 廖玲, 汪志辉, . ‘脆红李’及其早熟芽变全基因组重测序分析[J]. 园艺学报, 2024, 51(10): 2255-2266.
[10]	李春牛, 苏群, 李先民, 黄展文, 孙明艳, 卢家仕, 王虹妍, 卜朝阳. 茉莉花全基因组SSR标记开发及其亲缘关系鉴定[J]. 园艺学报, 2024, 51(10): 2343-2357.
[11]	关夏玉, 陈细红, 郭菁, 吕浩阳, 梁晨媛, 高芳銮. 建兰花叶病毒的遗传变异及其寄主适应性[J]. 园艺学报, 2024, 51(1): 203-212.
[12]	潘佳佳, 张东梅, 孟建, 高苏南, 朱凯杰, 刘军伟, 李国怀. 李坏死环斑病毒诱导的桃PpPDS沉默体系的优化及验证[J]. 园艺学报, 2023, 50(7): 1587-1600.
[13]	王瑞, 洪文娟, 罗华, 赵丽娜, 陈颖, 王君. 石榴品种SSR指纹图谱构建及杂种父本鉴定[J]. 园艺学报, 2023, 50(2): 265-278.
[14]	王梦梦, 孙德岭, 陈锐, 杨迎霞, 张冠, 吕明杰, 王倩, 谢添羽, 牛国保, 单晓政, 谭津, 姚星伟. 花椰菜核心种质的构建与评价[J]. 园艺学报, 2023, 50(2): 421-431.
[15]	段开行, 王晓玲, 毛永民, 王瑶, 任勇响, 任柳柳, 申连英. 酸枣种质资源果实数量性状遗传多样性分析[J]. 园艺学报, 2023, 50(12): 2568-2576.

基于重测序的中国李基因组InDel标记的开发及应用

Development and Application of Prunus salicina InDel Markers Based on Genome Re-sequencing

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

图/表 8

参考文献 26

相关文章 15

编辑推荐

Metrics

本文评价

访问总数: 当日访问总数: 当前在线人数:

访问总数:　当日访问总数:　当前在线人数: