您好，欢迎访问浙江省农业科学院 机构知识库！
浙江省农业科学院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

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

作者： Xu, Pei 1 ; Xu, Shizhong 2 ; Wu, Xiaohua 1 ; Tao, Ye 3 ; Wang, Baogen 1 ; Wang, Sha 1 ; Qin, Dehui 4 ; Lu, Zhongfu 1 ; Li, G 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Vegetables, Hangzhou 310021, Zhejiang, Peoples R China

2.Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA

3.Majorbio Pharm Technol Co Ltd, Shanghai 201203, Peoples R China

4.Zhejiang Acad Agr Sci, Inst Hort, Hangzhou 310021, Zhejiang, Peoples R China

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.

  • 相关文献

[1]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

[2]Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes. Xu, Hai-Ming,Kong, Xiang-Dong,Chen, Fei,Huang, Ji-Xiang,Zhao, Jian-Yi,Lou, Xiang-Yang. 2015

作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：浙江省农业科学院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台