Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

文献类型： 外文期刊

第一作者： Xu, Pei

作者： Xu, Pei;Wu, Xiaohua;Wang, Baogen;Wang, Sha;Lu, Zhongfu;Li, Guojing;Xu, Shizhong;Tao, Ye;Qin, Dehui

作者机构：

关键词： RAD-Seq;population genomics;shotgun sequencing;Lagenaria siceraria;cucurbit;comparative genomics;fruit shape

期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）

ISSN： 0960-7412

年卷期： 2014 年 77 卷 3 期

页码：

收录情况： SCI

摘要： Restriction site-associated DNA sequencing (RAD-Seq), a next-generation sequencing-based genome complexity reduction' protocol, has been useful in population genomics in species with a reference genome. However, the application of this protocol to natural populations of genomically underinvestigated species, particularly under low-to-medium sequencing depth, has not been well justified. In this study, a Bayesian method was developed for calling genotypes from an F-2 population of bottle gourd [Lagenaria siceraria (Mol.) Standl.] to construct a high-density genetic map. Low-depth genome shotgun sequencing allowed the assembly of scaffolds/contigs comprising approximately 50% of the estimated genome, of which 922 were anchored for identifying syntenic regions between species. RAD-Seq genotyping of a natural population comprising 80 accessions identified 3226 single nuclear polymorphisms (SNPs), based on which two sub-gene pools were suggested for association with fruit shape. The two sub-gene pools were moderately differentiated, as reflected by the Hudson's F-ST value of 0.14, and they represent regions on LG7 with strikingly elevated F-ST values. Seven-fold reduction in heterozygosity and two times increase in LD (r(2)) were observed in the same region for the round-fruited sub-gene pool. Outlier test suggested the locus LX3405 on LG7 to be a candidate site under selection. Comparative genomic analysis revealed that the cucumber genome region syntenic to the high F-ST island on LG7 harbors an ortholog of the tomato fruit shape gene OVATE. Our results point to a bright future of applying RAD-Seq to population genomic studies for non-model species even under low-to-medium sequencing efforts. The genomic resources provide valuable information for cucurbit genome research.

分类号：

  • 相关文献

[1]Phenylalanine ammonia-lyase gene families in cucurbit species: Structure, evolution, and expression. Dong Chun-juan,Cao Ning,Zhang Zhi-gang,Shang Qing-mao. 2016

[2]Using Cucurbita Rootstocks to educe Fusarium Wilt Incidence and Increase Fruit Yield and Carotenoid Content in Oriental Melons. Zhou, Xianzhi,Wu, Yufen,Chen, Sheng,Chen, Yang,Zhang, Weiguang,Sun, Xintao,Zhao, Yijie.

[3]Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys. Zhou, Xuming,Liu, Zhijin,Wang, Boshi,Wang, Ziming,Liu, Guangjian,Ren, Baoping,Shi, Fanglei,Li, Ming,Zhou, Xuming,Peterfi, Zalan,Gladyshev, Vadim N.,Meng, Xuehong,Tian, Shilin,Cao, Yinchuan,Gao, Lianju,Cao, Zhisheng,Jiang, Zhi,Li, Ruiqiang,Chang, Jiang,Li, Junsheng,Li, Mingzhou,Tian, Shilin,Orozco-ter Wengel, Pablo,Bruford, Michael W.,Wen, Changlong,Yu, Shuancang,Garber, Paul A.,Garber, Paul A.,Pan, Huijuan,Ye, Xinping,Xiang, Zuofu,Edwards, Scott V.,Li, Dayong,Li, Baoguo.

[4]Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. Li, Ying-hui,Yan, Long,Qi, Xiao-tian,Zhang, Le,Chang, Ru-zhen,Guo, Yong,Wang, Xiao-bo,Guan, Rong-xia,Liu, Yu-lin,Jin, Long-guo,Liu, Zhang-xiong,Zhang, Li-juan,Wang, Ke-jing,Qiu, Li-juan,Zhao, Shan-cen,Li, Dong,Li, Jun,Guo, Xiao-sen,He, Wei-ming,Liang, Qin-si,Ye, Chen,Tao, Yong,Wang, Jun-yi,Zhang, Xiu-qing,Chen, Jie,Nielsen, Rasmus,Li, Rui-qiang,Wang, Jian,Wang, Jun,Ma, Jian-xin,Yan, Long,Zhang, Meng-chen,Tao, Yong,Nielsen, Rasmus,Wang, Jun,Wang, Jun-yi,Nielsen, Rasmus,Nielsen, Rasmus,Chen, Peng-yin,Li, Wen-bin,Reif, Jochen C.,Purugganan, Michael,Purugganan, Michael. 2013

[5]The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus. Wu, Shan,Sun, Honghe,Fei, Zhangjun,Shamimuzzaman, Md,Sui, Xuelian,Wilder, Alan,Levi, Amnon,Ling, Kai-Shu,Sun, Honghe,Xu, Yong,Salse, Jerome,Sui, Xuelian,Wu, Zujian,Sui, Xuelian,Wu, Zujian,Fei, Zhangjun. 2017

[6]Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle MosaicVirus-In fected Lagenaria siceraria Plants. Li, Junmin,Zheng, Hongying,Zhang, Chenhua,Han, Kelei,Wang, Shu,Peng, Jiejun,Lu, Yuwen,Zhao, Jinping,Xu, Pei,Wu, Xiaohua,Li, Guojing,Chen, Jianping,Yan, Fei,Li, Junmin,Zheng, Hongying,Han, Kelei,Peng, Jiejun,Lu, Yuwen,Zhao, Jinping,Chen, Jianping,Yan, Fei,Zhang, Chenhua,Chen, Jianping,Xu, Pei,Wu, Xiaohua,Li, Guojing. 2016

[7]Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica). Guo, Jian,Cao, Ke,Li, Yong,Wang, Qi,Zhu, Gengrui,Fang, Weichao,Chen, Changwen,Wang, Xinwei,Guan, Liping,Ding, Tiyu,Wang, Lirong,Yao, Jia-Long,Deng, Cecilia. 2018

[8]Characterization of 19 polymorphic microsatellite markers for Asian yellow pond turtle (Mauremys mutica). Zhao, Jian,Wen, Ping,Li, Wei,Zhang, Dandan,Zhu, Xinping,Zhao, Jian,Wen, Ping.

[9]Accumulated chilling hours during endodormancy impact blooming and fruit shape development in peach (Prunus persica L.). Li Yong,FANG Weichao,ZHU Gengrui,CAO Ke,CHEN Changwen,WANG Xinwei,WANG Lirong. 2016

[10]High-density genetic map construction and QTLs analysis of grain yield-related traits in Sesame (Sesamum indicum L.) based on RAD-Seq techonology. Wu, Kun,Liu, Hongyan,Yang, Minmin,Wu, Wenxiong,Zuo, Yang,Zhao, Yingzhong,Tao, Ye,Ma, Huihui. 2014

[11]Accumulated chilling hours during endodormancy impact blooming and fruit shape development in peach (Prunus persica L.). Li Yong,Fang Wei-chao,Zhu Geng-rui,Cao Ke,Chen Chang-wen,Wang Xin-wei,Wang Li-rong. 2016

[12]Genetic analysis for rice grain quality traits in the YVB stable variant line using RAD-seq. Hu, Yuanyi,Mao, Bigang,Shao, Ye,Sheng, Xiabing,Li, Yaokui,Xia, Yumei,Yuan, Longping,Zhao, Bingran,Xiang, Haitao,Ni, Xuemei,Zhang, Gengyun,Quan, Zhiwu,Pan, Yinlin.

[13]Mapping of quantitative trait loci corroborates independent genetic control of apple size and shape. Chang, Yuansheng,Sun, Rui,Sun, Huanhuan,Wang, Yi,Zhang, Xinzhong,Han, Zhenhai,Zhao, Yongbo,Chen, Dongmei,Han, Yuepeng.

[14]Mapping of Sihc1, which controls hull color, using a high-density genetic map based on restriction site-associated DNA sequencing in foxtail millet [Setaria italica (L.) P. Beauv.]. Wang, Jun,Yang, Huiqing,Wang, Zhilan,Du, Xiaofeng,Guo, Erhu,Yuan, Feng,Zhang, Linyi,Peng, Shuzhong,Du, Guohua,Zou, Hongfeng,Li, Yunfei,Peng, Jianxiang,Yong, Jianpeng,Cai, Wei,Xia, Qiuju,Yuan, Guobao,Ni, Xuemei,Du, Guohua,Zou, Hongfeng,Li, Yunfei,Peng, Jianxiang,Yong, Jianpeng,Cai, Wei,Xia, Qiuju,Yuan, Guobao,Ni, Xuemei,Han, Fang.

[15]The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis. Zhang, Hai-Bin,Li, Kui,Zhang, Qun-Jie,Zhang, Yun,Liu, Yuan,Zhu, Ting,Li, Wei,Huang, Hui,Tong, Yan,Nan, Hong,Shi, Cong,Shi, Chao,Jiang, Jian-Jun,Mao, Shu-Yan,Jiao, Jun-Ying,Zhang, Dan,Zhao, You-Jie,Zhang, Li-Ping,Liu, Yun-Long,Gao, Li-Zhi,Xia, En-Hua,Zhang, Hai-Bin,Li, Kui,Liu, Yuan,Li, Wei,Huang, Hui,Shi, Chao,Jiang, Jian-Jun,Zhang, Dan,Gao, Li-Zhi,Xia, En-Hua,Nan, Hong,Shi, Cong,Sheng, Jun,Zhao, Yuan,Zhang, Qun-Jie,Kim, Changhoon,Yu, Yue,Zhu, Ting,Liu, Ben-Ying,Shao, Sheng-Fu,Ni, De-Jiang,Eichler, Evan E.. 2017

[16]Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics. Zhang, Xian,Liu, Xueduan,Dong, Weiling,Yin, Huaqun,Zhang, Xian,Liu, Xueduan,Yin, Huaqun,He, Qiang,Zhang, Xiaoxia,Fan, Fenliang,Peng, Deliang,Huang, Wenkun. 2016

[17]Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. Ma, Shisong,Ding, Zehong,Li, Pinghua. 2017

[18]pirAB(vp)-Bearing Vibrio parahaemolyticus and Vibrio campbellii Pathogens Isolated from the Same AHPND-Affected Pond Possess Highly Similar Pathogenic Plasmids. Dong, Xuan,Wang, Hailiang,Zou, Peizhuo,Xie, Guosi,Wan, Xiaoyuan,Yang, Qian,Zhu, Yanping,Chen, Mengmeng,Guo, Chengcheng,Wang, Wenchao,Huang, Jie,Bi, Dexi,Zou, Peizhuo,Chen, Mengmeng,Liu, Zhen. 2017

[19]Identification and functional analysis of anthocyanin biosynthesis genes in Phalaenopsis hybrids. Wang, L. M.,Zhang, J.,Dong, X. Y.,Fu, Z. Z.,Jiang, H.,Zhang, H. C.. 2018

[20]Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes. Chen, Zhiwen,Nie, Hushuai,Pei, Haili,Li, Shuangshuang,Hua, Jinping,Wang, Yumei,Zhang, Lida. 2017

作者其他论文 更多>>

微信小程序