Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data

doi:10.16420/j.issn.0513-353x.2022-1176

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (3): 520-532.doi: 10.16420/j.issn.0513-353x.2022-1176

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

Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data

YOU Yuanyuan¹^,², WANG Shuai², FANG Yingying¹, QI Cheng¹, LI Shupei¹, ZHANG Ying¹, CHEN Yuhui¹, LIU Wei³, LIU Fuzhong¹^,^**(), SHU Jinshuai¹^,^**()

¹ State Key Laboratory of Vegetable Biobreeding，Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China
² College of Horticultural Science and Technology，Hebei Normal University of Science and Technology，Qinhuangdao，Hebei 066004，China
³ Shouguang Vegetable Research and Development Center，Chinese Academy of Agricultural Sciences，Shouguang，Shandong 262704，China

Received:2023-07-05 Revised:2023-08-23 Online:2024-03-25 Published:2024-03-22
Contact: LIU Fuzhong, SHU Jinshuai

Abstract

Abstract:

Four high generation inbred lines of eggplant（Solanum melongena L.）were selected for whole genome re-sequencing，and 145 407 InDels were identified. The number of InDel on chromosome 12 was the least（7 752）and on chromosome 1 was the most（19 738）. There were 7 959 InDel with a length greater than 10 bp，and 144 InDels loci uniformly distributed on the genome were selected to be designed as InDel primers and verified. A total of 144 InDel primers were screened using 26 eggplant samples，63 primers showed stable polymorphism，and the polymorphism ratio was 43.75%. The main allele frequencies ranged from 0.4038 to 0.9808，with an average of 0.7659. Genetic diversity index（H_s）ranged from 0.0377 to 0.6501，with an average of 0.3217. The polymorphism information content（PIC）ranged from 0.0370 to 0.5750，with an average of 0.2663，and the PIC of 43 markers was greater than 0.200，indicating good polymorphism. When the genetic distance was 0.235，26 different types of eggplant materials were divided into two groups. The DNA fingerprints of 26 eggplant materials were constructed using the first ten InDel markers with high polymorphism information content. In addition，InDel markers with polymorphism among parents were selected for F₁ generation authenticity identification of four hybrid combinations，and three real hybrids were identified. The results from purity test of four hybrid combinations from InDel markers matched well with those from field experiments.

Key words: eggplant, Insertion-Deletion（InDel）marker, genetic diversity, fingerprint, F₁ identification

YOU Yuanyuan, WANG Shuai, FANG Yingying, QI Cheng, LI Shupei, ZHANG Ying, CHEN Yuhui, LIU Wei, LIU Fuzhong, SHU Jinshuai. Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data[J]. Acta Horticulturae Sinica, 2024, 51(3): 520-532.

Figures/Tables 8

References 38

[1]	Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, Andolfo G, Aprea G, Avanzato C, Bassolino L, Comino C, Dal Molin A, Ferrarini A, Maor L C, Portis E, Reyes-Chin-Wo S, Rinaldi R, Sala T, Scaglione D, Sonawane P, Tononi P, Almekias-Siegl E, Zago E, Ercolano M R, Aharoni A, Delledonne M, Giuliano G, Lanteri S, Rotino G L. 2019. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Scientific Reports,9:11769.
[2]	Cao Bihao, Lei Jianjun, Sun Xiudong, Chen Guoju, Meng Chengmin. 2006. Construction of RAPD markers linkage map for eggplant. Acta Horticulturae Sinica, 33 (5):1092. (in Chinese)
	曹必好, 雷建军, 孙秀东, 陈国菊, 孟成民. 2006. 茄子RAPD分子标记图谱的构建. 园艺学报, 33 (5):1092.
[3]	Chen R, Chang L C, Cai X, Wu J, Liang J L, Lin R M, Song Y, Wang X W. 2021. Development of InDel markers for Brassica rapa based on a high-resolution melting curve. Horticultural Plant Journal, 7 (1):31-37.
[4]	Da S C, Matos S, Costa H A, Morais P, Santos R M, Espinheira R. 2013. Genetic portrait of south Portugal population with InDel markers. Forensic Science International:Genetics,7:e101-e103.
[5]	Datta D R, Yusop M R, Misran A, Jusoh M, Oladosu Y, Arolu F, Haque A, Sulaiman N M. 2021. Genetic diversity in eggplant(Solanum melongena L.) germplasm from three secondary geographical origins of diversity using SSR markers. Biocell, 45 (5):1393-1401.
[6]	Feng Fangjun, Luo Lijun, Li Ying, Zhou Liguo, Xu Xiaoyan, Wu Jinhong, Chen Hongwei, Chen Liang, Mei Hanwei. 2005. Comparative analysis of polymorphism of InDel and SSR markers in rice. Molecular Plant Breeding, 3 (5):725-730. (in Chinese)
	冯芳君, 罗利军, 李荧, 周立国, 徐小艳, 吴金红, 陈宏伟, 陈亮, 梅捍卫. 2005. 水稻InDel和SSR标记多态性的比较分析. 分子植物育种, 3 (5):725-730.
[7]	Ge Haiyan, Liu Yang, Chen Huoying. 2015. QTL analysis of fruit-associated traits in eggplant. Acta Horticulturae Sinica, 42 (11):2197-2205. (in Chinese) doi: 10.16420/j.issn.0513-353x.2015-0492
	葛海燕, 刘扬, 陈火英. 2015. 茄子果实性状相关基因的QTL定位. 园艺学报, 42 (11):2197-2205. doi: 10.16420/j.issn.0513-353x.2015-0492
[8]	He Y J, Li S H, Dong Y X, Zhang X T, Li D L, Liu Y, Chen H Y. 2022. Fine mapping and characterization of the dominant gene SmFTSH10 conferring non‑photosensitivity in eggplant(Solanum melongena L.). Theoretical and Applied Genetics, 135 (7):2187-2196.
[9]	Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H. 2014. Draft genome sequence of eggplant(Solanum melongena L.):the representative Solanum species indigenous to the old world. DNA Research,21:649-660.
[10]	Hu Taozhu, Lin Li, Hu Jijun, Tai Liansai, Wang Shengjie, Liu Yang. 2019. Construction of fingerprints of tomato varieties by InDel markers. Journal of Shanghai Jiaotong University(Agricultural Science), 37 (2):24-29. (in Chinese)
	胡陶铸, 林丽, 胡继军, 邰连赛, 王圣洁, 刘杨. 2019. 利用InDel标记构建番茄新品种指纹图谱. 上海交通大学学报(农业科学版), 37 (2):24-29.
[11]	Hu Yang, Song Liping, Wang Aihua, Liang Hongyan, Qiu Wenbing, Cai Meizhong, Cui Xiaopei, Gao Changbin, Zhou Guolin, Li Ping. 2021. Genetic research and gene mapping of the stalk glossy trait in pakchoi. China Vegetables,(8):39-45. (in Chinese)
	胡阳, 宋莉萍, 汪爱华, 梁红艳, 邱文兵, 蔡美仲, 崔晓培, 高长斌, 周国林, 李平. 2021. 普通白菜薹茎亮绿性状遗传规律研究及基因定位. 中国蔬菜,(8):39-45.
[12]	Ji Kangna, Zhi Junjie, Lin Danni, Yan Shuangshuang, Tian Shibing, Cao Bihao, Qiu Zhengkun. 2019. Development and application of eggplant InDel markers based on whole genome re-sequencing datasets. Journal of Plant Genetic Resources, 20 (5):1278-1288. (in Chinese) doi: 10.13430/j.cnki.jpgr.20190130001
	吉康娜, 郅俊杰, 林丹妮, 颜爽爽, 田时炳, 曹必好, 邱正坤. 2019. 基于茄子基因组重测序的InDel标记开发及应用. 植物遗传资源学报, 20 (5):1278-1288. doi: 10.13430/j.cnki.jpgr.20190130001
[13]	Lebeau A, Gouy M, Daunay M C, Wicker E, Chiroleu F, Prior P, Frary A, Dintinger J. 2013. Genetic mapping of a major dominant gene for resistance to Ralstonia solanacearum in eggplant. Theoretical and Applied Genetics,126:143-158.
[14]	Li D D, Qian J, Li W L, Yu N, Gan G Y, Jiang Y Q, Li W J, Liang X Y, Chen R Y, Mo Y C, Lian J M, Niu Y C, Wang Y K. 2021. A high-quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis. Molecular Ecology Resources, 21 (4):1274-1286. doi: 10.1111/1755-0998.13321 pmid: 33445226
[15]	Li Sigeng, Shen Di, Liu Bo, Qiu Yang, Zhang Xiaohui, Zhang Zhonghua, Wang Haiping, Li Xixiang. 2013. Development and application of cucumber InDel markers based on genome re-sequencing. Journal of Plant Genetic Resources, 14 (2):278-283. (in Chinese) doi: 10.13430/j.cnki.jpgr.2013.02.013
	李斯更, 沈镝, 刘博, 邱杨, 张晓辉, 张忠华, 王海平, 李锡香. 2013. 基于黄瓜基因组重测序的InDel标记开发及其应用. 植物遗传资源学报, 14 (2):278-283. doi: 10.13430/j.cnki.jpgr.2013.02.013
[16]	Li Tao, Li Zhenxing, Luo Shaobo, Li Zhiliang, Xu Xiaowan. 2014. ISSR analysis of genetic diversity of eggplant(Solanum melongena L.) in Southeast Asia. Chinese Agricultural Science Bulletin, 30 (25):104-110. (in Chinese)
	李涛, 黎振兴, 罗少波, 李植良, 徐小万. 2014. 东南亚茄子种质资源ISSR遗传多样性分析. 中国农学通报, 30 (25):104-110.
[17]	Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui Y, Cheng F, Wang X W, Wu J. 2013. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theoretical and Applied Genetics, 126 (1):231-239. doi: 10.1007/s00122-012-1976-6 pmid: 22972202
[18]	Liu Fuzhong, Shu Jinshuai, Zhang Ying, Chen Yuhui, Lian Yong, Tian Shibing. 2021. Research progress on eggplant genetic breeding during‘The 13th Five-Year Plan’period. China Vegetables,(3):17-27. (in Chinese)
	刘富中, 舒金帅, 张映, 陈钰辉, 连勇, 田时炳. 2021. “十三五”我国茄子遗传育种研究进展. 中国蔬菜,(3):17-27.
[19]	Liu K J, Muse S V. 2005. PowerMarker:an integrated analysis environment for genetic marker analysis. Bioinformatics, 21 (9):2128-2129.
[20]	Manta F, Caiafa A, Pereira R, Silva D, Amorim A, Carvalho E F, Gusmão L. 2012. Indel markers:genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material. Forensic Science International:Genetics,6:658-661.
[21]	Miyatake K, Saito T, Negoro S, Yamaguchi H, Nunome T, Ohyama A, Fukuoka H. 2012. Development of selective markers linked to a major QTL for parthenocarpy in eggplant(Solanum melongena L.). Theoretical and Applied Genetics,124:1403-1413.
[22]	Miyatake K, Saito T, Negoro S, Yamaguchi H, Nunome T, Ohyama A, Fukuoka H. 2016. Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant(Solanum melongena). Theoretical and Applied Genetics,129:357-367.
[23]	Qi Dongxia, Zhang Ying, Liu Fuzhong, Artemyeva A, Gashkova I. 2017. Genetic diversity among Chinese and Russian eggplant(Solanum melongena)germplasm resources. Journal of Plant Genetic Resources, 18 (3):404-412. (in Chinese) doi: 10.13430/j.cnki.jpgr.2017.03.004
	齐东霞, 张映, 刘富中, Artemyeva A, Gashkova I. 2017. 中俄茄子种质资源遗传多样性研究. 植物遗传资源学报, 18 (3):404-412.
[24]	Ren Wei, Ren Jie, Wang Jianjiang, Yang Xiangkun, Zhang Zhanqin, Xie Jianhui, Li Yan, Yang Wencai. 2023. Genetic variation in main inbred lines of processing tomato. China Vegetables,(3):37-46. (in Chinese)
	任唯, 任杰, 王建江, 杨相昆, 张占琴, 颉健辉, 李艳, 杨文才. 2023. 加工番茄骨干自交系的遗传变异. 中国蔬菜,(3):37-46.
[25]	Salimizand H, Menbari S, Ramazanzadeh R, Khonsha M, Saleh Vahedi M. 2016. DNA fingerprinting and antimicrobial susceptibility pattern of clinical and environmental Acinetobacter baumannii isolates:a multicentre study. Journal of Chemotherapy, 28 (4):277-283. doi: 10.1080/1120009X.2016.1175706 pmid: 27461478
[26]	Shu J S, Liu Y M, Zhang L L, Li Z S, Fang Z Y, Yang L M, Zhuang M, Zhang Y Y, Lv H H. 2018. QTL-seq for rapid identification of candidate genes for flowering time in broccoli × cabbage. Theoretical and Applied Genetics,131:917-928.
[27]	Song B, Song Y, Fu Y, Kizito E B, Kamenya S N, Kabod P N, Liu H, Muthemba S, Kariba R, Njuguna J, Maina S, Stomeo F, Djikeng A, Hendre P S, Chen X L, Chen W B, Li X L, Sun W J, Wang S B, Cheng S F, Muchugi A, Jamnadass R, Shapiro H Y, van Deynze A, Yang H M, Wang J, Xu X, Odeny D A, Liu X. 2019. Draft genome sequence of Solanum aethiopicum provides insights into disease resistance,drought tolerance,and the evolution of the genome. GigaScience,8:1-16.
[28]	Sulu G, Polat I, Boyaci H F, Yildirim A, Gumrukcu E. 2022. Screening and validation of three molecular markers for disease resistance in eggplant. Czech Journal of Genetics and Plant Breeding, 58 (2):83-92.
[29]	van Berloo R. 2008. GGT 2.0:versatile software for visualization and analysis of genetic data. Journal of Heredity, 99 (2):232-236. doi: 10.1093/jhered/esm109 pmid: 18222930
[30]	Wei Q Z, Wang J L, Wang W H, Hu T H, Hu H J, Bao C L. 2020. A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. Horticulture Research,7:153.
[31]	Xiang Congchao, Zhang Weiwei, Luo Shuangxia, Zhao Jianjun, Zhang Tingting, Shen Shuxing, Chen Xueping. 2015. Genetic analysis on fruit color under calyx and correlation analysis of SSR markers in eggplant. Journal of Agricultural University of Hebei, 38 (4):50-55. (in Chinese) doi: 10.13320/j.cnki.jauh.2015.0083
	相丛超, 张巍巍, 罗双霞, 赵建军, 张婷婷, 申书兴, 陈雪平. 2015. 茄子果萼下颜色的遗传分析和SSR标记的相关性分析. 河北农业大学学报, 38 (4):50-55.
[32]	Xiao Xi’ou, Lin Bihua, Lin Wenqiu, Li Wei, Gao Xiaomin, Lü Lingling. 2016. Analysis of eggplant genetic diversity by SRAP maker. Chinese Journal of Tropical Agriculture, 36 (3):19-23. (in Chinese)
	肖熙鸥, 林碧桦, 林文秋, 李威, 高晓敏, 吕玲玲. 2016. 利用SRAP分子标记技术分析茄子遗传多样性. 热带农业科学, 36 (3):19-23.
[33]	Yang J, Wang Y, Shen H, Yang W. 2014. In silico identification and experimental validation of Insertion-Deletion polymorphisms in tomato genome. DNA Research,21:429.
[34]	Yang Yi, Li Tingyao, Li Guojing, Chen Hancai, Shen Zhuo, Zhou Xuan, Wu Zengxiang, Wu Xinyi, Zhang Yan. 2022. Development and application of Insertion-Deletion(InDel)markers in asparagus bean based on whole genome re-sequencing data. Acta Horticulturae Sinica, 49 (4):778-790. (in Chinese)
	杨易, 黎庭耀, 李国景, 陈汉才, 沈卓, 周轩, 吴增祥, 吴新义, 张艳. 2022. 基于重测序的长豇豆基因组InDel标记开发及应用. 园艺学报, 49 (4):778-790. doi: 10.16420/j.issn.0513-353x.2021-0347
[35]	Zhang Xu, Xu Jian, Li Ji, Lou Qunfeng, Chen Jinfeng. 2018. QTL mapping and identification of candidate gene for resistance to gummy stem blight in Cucumis sativus/hystrix introgression line‘IL77’. Acta Horticulturae Sinica, 45 (11):2141-2152. (in Chinese)
	张旭, 徐建, 李季, 娄群峰, 陈劲枫. 2018. 黄瓜/酸黄瓜渐渗系‘IL77’抗蔓枯病主效QTL定位及候选基因鉴定. 园艺学报, 45 (11):2141-2152. doi: 10.16420/j.issn.0513-353x.2018-0269
[36]	Zhang Zhigang, Zhao Zhizhong, Li Qiaoyun, Wang Xiao, Liu Shuantao, Wang Shufen, Xu Wenling, Liu Xianxian, Liu Chen. 2016. Development of InDels markers and their usage in detection of residual heterozygous lines in Chinese cabbage(Brassica rapa ssp. pekinensis). Journal of Agricultural Biotechnology, 24 (4):510-518. (in Chinese)
	张志刚, 赵智中, 李巧云, 王晓, 刘栓桃, 王淑芬, 徐文玲, 刘贤娴, 刘辰. 2016. 大白菜InDels标记开发及其在剩余杂合体鉴定中的应用. 农业生物技术学报, 24 (4):510-518.
[37]	Zhao Yujing, Lu Yin, Feng Daling, Luo Lei, Wu Fang, Yang Rui, Chen Yueqi, Sun Xiaoxue, Wang Yanhua, Chen Xueping, Shen Shuxing, Luo Shuangxia, Zhao Jianjun. 2021. Association analysis between background selection InDel markers and important agronomic traits in inbred lines of Chinese cabbage. Acta Horticulturae Sinica, 48 (7):1282-1294. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-0242
	赵玉靖, 卢银, 冯大领, 罗蕾, 吴芳, 杨锐, 陈悦琦, 孙晓雪, 王彦华, 陈雪平, 申书兴, 罗双霞, 赵建军. 2021. 大白菜自交系背景选择InDel标记与重要农艺性状的关联分析. 园艺学报, 48 (7):1282-1294. doi: 10.16420/j.issn.0513-353x.2021-0242
[38]	Zhi X N, Shu J S, Zheng Z, Li T, Sun X R, Bai J R, Cui Y N, Wang X X, Huang Z J, Guo Y M, Du Y C, Yang Y H, Liu L, Li J M. 2021. Fine mapping of the Ph-2 gene conferring resistance to late blight(Phytophthora infestans)in tomato. Plant Disease,105:851-858.

类型 Type	编号 Code	果色 Fruit color	萼片颜色 Sepal color	果形 Fruit shape	来源 Origin
自交系 Inbred line	21CNW1	紫黑 Purple black	紫Purple	圆Round	中国农业科学院蔬菜花卉研究所 Institute of Vegetables and Flowers，Chinese Academy of
	21CNW2	紫黑 Purple black	紫Purple	圆Round	Agricultural Sciences
	21CNW13	紫Purple	紫Purple	长Long
	21CNW14	紫Purple	紫Purple	长Long
	21CNW32	绿Green	绿Green	椭圆Oval
	21CNW33	绿Green	绿Green	椭圆Oval
F₁	21CNL764	紫Purple	紫Purple	长棒Long bar
F₁	21CNL770	紫色条纹 Purple stripe	绿Green	椭圆Oval
	21CNL743	紫黑 Purple black	紫Purple	圆Round	河北惠优特种业有限公司 Hebei Huiyoute Seed Industry Co.，LTD
	21CNL775	绿Green	绿Green	椭圆Oval	济南天瑞种子销售有限公司Jinan Tianrui Seed Sales Co.，LTD
	21CJD164	紫黑 Purple black	绿Green	短棒Short bar	山东省济南市Jinan，Shandong
	21CJD168	紫Purple	紫Purple	长Long	北京井田农业科技有限公司 Beijing Jingtian Agricultural Technology Co.，LTD
	21CJD170	绿Green	绿Green	椭圆Oval	辽宁园艺种苗有限公司 Liaoning Horticultural Seedling Co.，LTD
	21CJD171	绿Green	绿Green	椭圆Oval
	21CJD173	绿Green	绿Green	椭圆Oval	辽宁省鞍山市Anshan，Liaoning
	21CJD174	绿Green	绿Green	椭圆Oval
	21CJD175	绿Green	绿Green	椭圆Oval
	21CJD177	绿Green	绿Green	椭圆Oval
	21CJD179	绿Green	绿Green	椭圆Oval
	21CJD183	紫黑 Purple black	绿Green	短棒Short bar
	21CJD185	紫黑 Purple black	绿Green	短棒Short bar
	21CJD194	紫Purple	紫Purple	长Long
	21CJD184	紫Purple	绿Green	长棒Long bar	山东省潍坊市Weifang，Shandong
	21CJD195	紫Purple	紫Purple	长Long	四川广汉龙盛种业有限公司 Sichuan Guanghan Longsheng Seed Industry Co.，LTD
	21CJD196	紫黑 Purple black	紫Purple	长Long	辽宁省沈阳市Shenyang，Liaoning
自交系 Inbred line	21CJD197	紫红 Purple red	紫绿Purple green	线Line	浙江省杭州市Hangzhou，Zhejiang

类型 Type	编号 Code	果色 Fruit color	萼片颜色 Sepal color	果形 Fruit shape	来源 Origin
自交系 Inbred line	21CNW1	紫黑 Purple black	紫Purple	圆Round	中国农业科学院蔬菜花卉研究所 Institute of Vegetables and Flowers，Chinese Academy of
	21CNW2	紫黑 Purple black	紫Purple	圆Round	Agricultural Sciences
	21CNW13	紫Purple	紫Purple	长Long
	21CNW14	紫Purple	紫Purple	长Long
	21CNW32	绿Green	绿Green	椭圆Oval
	21CNW33	绿Green	绿Green	椭圆Oval
F₁	21CNL764	紫Purple	紫Purple	长棒Long bar
F₁	21CNL770	紫色条纹 Purple stripe	绿Green	椭圆Oval
	21CNL743	紫黑 Purple black	紫Purple	圆Round	河北惠优特种业有限公司 Hebei Huiyoute Seed Industry Co.，LTD
	21CNL775	绿Green	绿Green	椭圆Oval	济南天瑞种子销售有限公司Jinan Tianrui Seed Sales Co.，LTD
	21CJD164	紫黑 Purple black	绿Green	短棒Short bar	山东省济南市Jinan，Shandong
	21CJD168	紫Purple	紫Purple	长Long	北京井田农业科技有限公司 Beijing Jingtian Agricultural Technology Co.，LTD
	21CJD170	绿Green	绿Green	椭圆Oval	辽宁园艺种苗有限公司 Liaoning Horticultural Seedling Co.，LTD
	21CJD171	绿Green	绿Green	椭圆Oval
	21CJD173	绿Green	绿Green	椭圆Oval	辽宁省鞍山市Anshan，Liaoning
	21CJD174	绿Green	绿Green	椭圆Oval
	21CJD175	绿Green	绿Green	椭圆Oval
	21CJD177	绿Green	绿Green	椭圆Oval
	21CJD179	绿Green	绿Green	椭圆Oval
	21CJD183	紫黑 Purple black	绿Green	短棒Short bar
	21CJD185	紫黑 Purple black	绿Green	短棒Short bar
	21CJD194	紫Purple	紫Purple	长Long
	21CJD184	紫Purple	绿Green	长棒Long bar	山东省潍坊市Weifang，Shandong
	21CJD195	紫Purple	紫Purple	长Long	四川广汉龙盛种业有限公司 Sichuan Guanghan Longsheng Seed Industry Co.，LTD
	21CJD196	紫黑 Purple black	紫Purple	长Long	辽宁省沈阳市Shenyang，Liaoning
自交系 Inbred line	21CJD197	紫红 Purple red	紫绿Purple green	线Line	浙江省杭州市Hangzhou，Zhejiang

染色体 Chromosome	插入 Insertion	缺失 Deletion	总计 Total	InDel/%
E01	9 366	10 372	19 738	13.57
E02	4 164	4 737	8 901	6.12
E03	5 236	5 858	11 094	7.63
E04	4 855	5 320	10 175	7.00
E05	4 505	5 042	9 547	6.57
E06	6 132	6 879	13 011	8.95
E07	7 837	8 912	16 749	11.52
E08	5 734	6 468	12 202	8.39
E09	5 538	6 129	11 667	8.02
E10	4 394	5 091	9 485	6.52
E11	7 162	7 831	14 993	10.31
E12	3 640	4 112	7 752	5.33
染色体支架 Scaffold	42	51	93	0.06
总计 Total	68 605	76 802	145 407	100.00

染色体 Chromosome	插入 Insertion	缺失 Deletion	总计 Total	InDel/%
E01	9 366	10 372	19 738	13.57
E02	4 164	4 737	8 901	6.12
E03	5 236	5 858	11 094	7.63
E04	4 855	5 320	10 175	7.00
E05	4 505	5 042	9 547	6.57
E06	6 132	6 879	13 011	8.95
E07	7 837	8 912	16 749	11.52
E08	5 734	6 468	12 202	8.39
E09	5 538	6 129	11 667	8.02
E10	4 394	5 091	9 485	6.52
E11	7 162	7 831	14 993	10.31
E12	3 640	4 112	7 752	5.33
染色体支架 Scaffold	42	51	93	0.06
总计 Total	68 605	76 802	145 407	100.00

染色体Chromo-some	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
E01	EP01-1	7 915 894	CCCCAAGTGACCATTGGATTAG	AGATAGCTAGTTATTATCAACTTGGTGATTATATT
	EP01-2	23 527 396	CTTTAGTCAGGCTCAGGCTTATTC	GGTGACACTCGTAAGAACGCCTG
	EP01-8	64 525 306	GATAATTATCCAGTCGTCCACTTCA	CCCTTTGGGAGCAACTGAAAAATAAAATG
	EP01-3	100 413 397	CAAAAGAGATAATATGTGATTTGTTGCAAAT	TGTTCAGATACATCAATAATGTGCAAGATAC
	EP01-10	82 891 881	CCCTAAAACAAATGATGCATGAGGA	GGAATTTGAATTTTGAATTTTGAATTCAAACCCTAA
	EP01-12	105 994 712	GTTAAGACTGATTATTCTTCCCAAAAGAA	CCTCTGTTTATGACTTGTTTTAGAATATAAATTTCA
E02	EP02-1	1 654 359	GTGGGGGAGCATTGATTTAGTTAGA	TCCTTAAAGAATTCTAACTATCTACTTGTTATCTT
	EP02-9	54 917 742	AGAGAACAGATATAGGCACCCC	TATGGCTGCATAAACTTTTACTTCTATTCAC
	EP02-10	60 002 669	GACAATTGATGGTCCACGTGCT	GGAGAAACCAGCGTCTATGAGAATTATTT
	EP02-11	68 280 945	GGAACTGGAAAACAAAATGTGCAAC	GATGATTGTGAAAAGTTTAAGAATTGCAAGTAC
	EP02-12	74 262 259	ATTAGGGGAAGCGCTCCCTC	TTCTCCCTTAATTAGATATCTCGGCTAG
E03	EP03-1	6 139 884	GGTGGGGAGATTAGGATTTCTTC	CGTTAGGGTTTAACTAAATTTAGTTTCGTAC
	EP03-2	84 066 039	CTAACACATGACACATACCATAAGGT	GTACCTTGAACAAATCATGATCTGTTACTTTTAAA
	EP03-7	46 352 738	GACTAGACATGGACATGTGTAATTTC	GTTCTAGAGTTTAAAAATGGCTAAGTATGAAAG
	EP03-8	56 559 091	ATGAGACCCCGATTATGGGTCA	GAAGATTGGAAAAGAAAAATAGAACGACAAG
	EP03-11	77 552 027	CACCGAATTAGTAATACCTGCATTG	GCAATTTGGACGAATTAATTGACTTACTTCTAAA
	EP03-12	88 470 166	TTGGACTAATAGTACCACCCAAGAA	CTCATTTGGGTGAAATACTTCCTATTGATAATTT
E04	EP04-1	5 445 165	CTAGTGCCTAAGAAGGACGGAAA	CTTGGCATAATTGTCGATGAAAATATGAATG
	EP04-9	41 157 634	GGGTGTGTAATGCCAGTGTAAAAC	CTTTAGGGTGTTGCAAGGTGTTGATTG
	EP04-10	53 164 819	GGTGGATGAAGGACATTTTTGTACTA	CAGTTTTTGCTAGGATATGTAACTTAGTTATTC
	EP04-11	75 729 039	CTTTTAATCAAATGTTATGAGTTTGCATGT	CATCTATCGTTCAATATCGTATTGAAATTTGAC
	EP04-12	78 538 303	GAGTGATTACTTTTCTTTTATCATGTGTTC	TGTTACACTCATTGTTGACCTAGTTTTCTTT
E05	EP05-4	577 619	GATGTGTAGGCCATGAGCCC	CATGGAAAATGGCCGAAATCGCTTG
	EP05-7	43 441 050	AACAAATGAAAGAATGTACATTCTTCCAAT	AAGCTTTAGTACTTTCTTTTCAAACATTCTTTAAG
	EP05-9	60 366 228	CTCTTGACATCTTAGTTGCAAAAGC	GACTCCTTCACTTTGCCGCTTCTTC
	EP05-10	68 771 642	CAACATACCCTTACATAACTTGGCA	GTCTAGTCTAGCTAATGTTGGTTACTATC
	EP05-3	80 781 008	CTTTCGATTGACTAACTCGAGTGAAA	CAGAATGTAATGAACAACAAATCTTAGTTTGC
E06	EP06-4	884 474	CTTATTATGCTTGGCTTCAGCTTATATT	ATTTGTCTCCATGCCAACAATATTGTTTTTC
	EP06-1	9 494 444	CGTGGATAATCCTAATGAGAATCTGT	CTAACAAAAGCGTTCCTAAATTATTTCATAGC
	EP06-2	54 653 085	GTCAAAAATAGAGTCCTGTCTGGC	CATTGTTCCTGCTTTTAAAAAGAGGCAAC
	EP06-11	84 360 559	AAGATGCTTAAAGGTGTAACAGTCTAT	AAAGGTTGATAAATATTTGACAGAACACCAC
E07	EP07-1	4 004 708	CTATTATACTGCCTTTTGGTTGTCATTTT	GGTTAGAATCCACAAATTTCAAATCTTGAATTC
	EP07-4	14 816 419	CCGTCAACCAGAACATGTCGTTA	CTGTAGGAAGGTACAATATCTACATGTG
	EP07-6	46 991 068	CCTAAGGTATGTGGGTTTCTTTCC	CATGCAATTTGAGTAAAAGGAGGTCTGG
	EP07-7	56 540 678	GAAAGTCCCGAATGATATCATTGTC	GAAAATGATAGACATAAAATACTCATATTTTGCCC
	EP07-8	65 335 992	GGTCCCCTCTCGTTTAATATTTAGA	AACCATAACAACCAAGAGTCAAGAACAC
	EP07-3	94 455 988	GACAATGAATAAACAGAGACAGGGC	CAATTATATGTTTTACATATGAAAATCAGGCACATT
E08	EP08-1	4 461 068	CAAAGACAGACCCTAAATTTTTAGAATCAA	GATTGCTTAACTTGTGCTCAATTTGCAG
	EP08-7	39 745 348	ACTCAGACAACTGATTAAGAAGTGAAT	GAATCATGTTCAGGGTGATGTTGTTTTATG
	EP08-9	53 352 594	CCAAGACTTCATCAAATCTCTTATTCAT	GGAACCTTGAAGCTTGAGATGAGTTC
	EP08-10	66 951 767	GTCTCTCCGTCAATTTAAGTCCTAG	GTCTTTGCTTCATCACTTCGGATCAAC
	EP08-12	86 112 573	GAACCATTTTCTTTTCTTGGTTGTGAC	CAAATTGTCAACATAGTGTAAAGAAATTAGATGAAA
E09	EP09-8	41 897 213	AGTTAAATATTTGGAGGAAGTGAAGAC	GTAAAAGGAAAGCAAATAGCCTTACATACC
	EP09-10	56 706 456	TACAAGTTGGGTTCACCCCATATTT	ACTTCATAACTTGTAATGCAGGGATAATAAC
	EP09-2	66 581 625	GATTGATTTGCAACTTTCAAATCGATG	CTCAATTCCTTCGTCAAATTAATTCCCTC
	EP09-3	84 540 296	TAAAGAGGGTCCCGATCAACTTTTT	AGTAATTTACCATTTTAATTAGGCACAAGGC
E10	EP10-4	640 499	GGGGAAACGACGGTAGGAGATT	CTCAGCGGGTGACTAACTAAACTTTTAC
	EP10-5	22 305 109	GTCGTGCGTAACACACTATATATATATATA	AAACTGACCCACCGTACCCAGC
	EP10-6	32 848 394	CATCTTGAGTACCTCCTTGATCG	CCTTATGTCTGGTACAAGGGTAAGG
	EP10-7	36 204 090	TGAAAAGAACTACCCTACCAGTGAA	CCATACAAATAATGACGCCAAATCTTTAATG
	EP10-8	41 868 664	GCAAACCATGAAGAACTAACAAGGT	CCCTTGAAAACATGCAAAAAGAAGAGAG
	EP10-9	56 305 390	ATTCGTGTTGTTTGCTCATTCATCC	GTCCAAATGGTATTCATAAAAGGTCTTCTTG
	EP10-10	63 994 673	TTGAATGCTTATTTGAGTGTTTTATGGATT	CAACTCACATTCTTGATCTTAGCTATTCAAG
	EP10-3	80 974 089	TCATGTTATATGATTATGGCACATTCC	GCCTCTATAGTTGATGTTTTAGAGTTAATTTAG
E11	EP11-5	30 941 193	TGCCATTATAGTAACTGCTATGTATTC	CACCCTCAACTTAGAACTGTTGCTTG
	EP11-6	44 604 118	GGTATGTACCTCAATCACCTTGTC	TTGAGATATCTAACCCTCAACATGGTAG
	EP11-8	62 505 321	CCCTTCGAAATCGAGCAAGCAA	TTACTGAATGATCGATTCGGCCGAG
	EP11-9	71 529 170	CACCATGTCAGAGAAGATGGACA	CACCTTCGCATTTAAGAGGATATCATTC
	EP11-3	98 055 442	TGAAATGGAATTTTCCCCACATTGG	CAGAGACCTTACATTTATCTCTTTATAAGAG
E12	EP12-4	12 541 476	TGTTTAAGTCTTTACATGATGAGATTTGAA	CATTATCTCACATTCAAGTCATATGAAAAATTTTAC
	EP12-5	18 519 761	TAGAACCCGTATTGGGGTGTAG	GAAAAATTCTACTTAAGTCCCTAACCTTCAAA
	EP12-11	64 229 774	GCCTTGAATTTGGAGAAGCTGGA	GTAATGTATGCCACTGCACTATCCAAAC
	EP12-3	70 590 237	AAACAAACAACAATAATATATCTAGTGAAATC	CCCTTGCAATAGCTTTTTGGAAAAAGAATC

Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data

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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
EP01-1	0.5192	3	2	0.4993	0.1923	0.3746
EP01-2	0.5192	3	2	0.4993	0.1923	0.3746
EP01-3	0.5192	3	2	0.4993	0.1923	0.3746
EP01-8	0.7115	4	3	0.4297	0.2692	0.3648
EP01-10	0.8462	3	2	0.2604	0.0769	0.2265
EP01-12	0.7308	3	2	0.3935	0.1538	0.3161
EP02-1	0.5962	3	2	0.4815	0.1923	0.3656
EP02-9	0.5769	4	3	0.5178	0.4615	0.4179
EP02-10	0.9423	2	2	0.1087	0.1154	0.1028
EP02-11	0.6923	3	2	0.4260	0.0769	0.3353
EP02-12	0.6923	3	2	0.4260	0.3077	0.3353
EP03-1	0.6923	3	2	0.4260	0.1538	0.3353
EP03-2	0.5962	3	2	0.4815	0.1154	0.3656
EP03-7	0.7500	3	2	0.3750	0.1923	0.3047
EP03-8	0.8462	3	2	0.2604	0.1538	0.2265
EP03-11	0.6731	3	2	0.4401	0.1923	0.3432
EP03-12	0.8462	3	3	0.2692	0.2308	0.2480
EP04-1	0.9423	2	2	0.1087	0.1154	0.1028
EP04-9	0.9038	4	3	0.1783	0.0385	0.1704
EP04-10	0.7308	4	3	0.4231	0.0769	0.3768
EP04-11	0.6346	4	3	0.5288	0.1154	0.4716
EP04-12	0.9231	2	2	0.1420	0	0.1319
EP05-3	0.7115	3	2	0.4105	0.2692	0.3262
EP05-4	0.8846	3	2	0.2041	0.1538	0.1833
EP05-7	0.7692	3	2	0.3550	0.3077	0.2920
EP05-9	0.9038	4	3	0.1783	0.0385	0.1704
EP05-10	0.8846	3	2	0.2041	0.0769	0.1833
EP06-1	0.7308	3	3	0.4231	0.3846	0.3768
EP06-2	0.9615	2	2	0.0740	0	0.0712
EP06-4	0.6154	4	3	0.5000	0.0769	0.4078
EP06-11	0.7692	3	2	0.3550	0.0769	0.2920
EP07-1	0.8077	3	2	0.3107	0.1538	0.2624
EP07-3	0.5962	3	2	0.4815	0.1154	0.3656
EP07-4	0.5192	3	2	0.4993	0.8077	0.3746
EP07-6	0.9615	2	2	0.0740	0.0769	0.0712
EP07-7	0.8077	3	2	0.3107	0.3077	0.2624
EP07-8	0.9423	3	2	0.1087	0.0385	0.1028
EP08-1	0.5192	3	2	0.4993	0.6538	0.3746
EP08-7	0.9808	2	2	0.0377	0.0385	0.0370
EP08-9	0.9423	3	2	0.1087	0.0385	0.1028
EP08-10	0.7115	3	2	0.4105	0.3462	0.3262
EP08-12	0.8269	3	2	0.2862	0.1923	0.2453
EP09-2	0.6923	4	3	0.4467	0.3077	0.3756
EP09-3	0.7500	4	3	0.3913	0.1923	0.3391
EP09-8	0.9231	3	2	0.1420	0.0769	0.1319
EP09-10	0.8462	3	2	0.2604	0.1538	0.2265
EP10-3	0.4038	6	3	0.6501	0.2692	0.5750
EP10-4	0.5192	3	2	0.4993	0.1923	0.3746
EP10-5	0.7885	2	2	0.3336	0.4231	0.2779
EP10-6	0.8462	3	2	0.2604	0.2308	0.2265
EP10-7	0.9231	2	2	0.1420	0	0.1319
EP10-8	0.9808	2	2	0.0377	0.0385	0.0370
EP10-9	0.7500	4	3	0.3913	0.1923	0.3391
EP10-10	0.9231	2	2	0.1420	0	0.1319
EP11-3	0.5769	3	2	0.4882	0.2308	0.3690
EP11-5	0.8846	3	2	0.2041	0.1538	0.1833
EP11-6	0.9231	3	2	0.1420	0.0769	0.1319
EP11-8	0.9231	3	2	0.1420	0.0769	0.1319
EP11-9	0.9231	2	2	0.1420	0.1538	0.1319
EP12-3	0.7308	4	3	0.4112	0.1538	0.3526
EP12-4	0.9423	2	2	0.1087	0.1154	0.1028
EP12-5	0.6346	3	2	0.4638	0.3462	0.3562
EP12-11	0.6346	3	2	0.4638	0.6538	0.3562
平均值Mean	0.7659	3.03	2.22	0.3217	0.1874	0.2663

编号Code	分子编码Molecular ID	编号Code	分子编码Molecular ID
21CNW1	1111111113	21CJD171	1223131112
21CNW2	1112111132	21CJD173	1213131112
21CNW13	2111132112	21CJD174	3332111113
21CNW14	3212121131	21CJD175	1233221113
21CNW32	1211131312	21CJD177	1223111323
21CNW33	1223111112	21CJD179	1233311133
21CNL743	1111111313	21CJD183	2122312231
21CNL764	2312332113	21CJD184	2232112231
21CNL770	3323122213	21CJD185	2323113221
21CNL775	1233211132	21CJD194	2123232231
21CJD164	2123113213	21CJD195	3112222221
21CJD168	2122332113	21CJD196	2112112133
21CJD170	3323111112	21CJD197	2213112231

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