您好，欢迎访问江苏省农业科学院 机构知识库！
江苏省农业科学院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing

文献类型： 外文期刊

作者： Zhang, Tifu 1 ; Gu, Minfeng 2 ; Liu, Yuhe 3 ; Lv, Yuanda 1 ; Zhou, Ling 1 ; Lu, Haiyan 1 ; Liang, Shuaiqiang 1 ; Bao, Hua 1 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Prov Key Lab Agrobiol, Nanjing 210014, Jiangsu, Peoples R China

2.Xinyang Agr Expt Stn Yancheng City, Yancheng 224336, Jiangsu, Peoples R China

3.Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA

关键词： Quinoa;SNP;InDel;Genetic diversity;Population structure;Core germplasm

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2017 年 18 卷

页码：

收录情况： SCI

摘要： Background: Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and to develop novel Insertion/Deletion (InDel) markers for quinoa by whole-genome re-sequencing. Results: We re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7x to 23x the quinoa genome. Based on the 1453-megabase (Mb) assembly from the reference accession Riobamba, 8,441,022 filtered bi-allelic single nucleotide polymorphisms (SNPs) and 842,783 filtered InDels were identified, with an estimated SNP and InDel density of 5.81 and 0.58 per kilobase (kb). From the genomic InDel variations, 85 dimorphic InDel markers were newly developed and validated. Together with the 62 simple sequence repeat (SSR) markers reported, a total of 147 markers were used for genotyping the 129 quinoa accessions. Molecular grouping analysis showed classification into two major groups, the Andean highland (composed of the northern and southern highland subgroups) and Chilean coastal, based on combined STRUCTURE, phylogenetic tree and PCA (Principle Component Analysis) analyses. Further analysis of the genetic diversity exhibited a decreasing tendency from the Chilean coast group to the Andean highland group, and the gene flow between subgroups was more frequent than that between the two subgroups and the Chilean coastal group. The majority of the variations (approximately 70%) were found through an analysis of molecular variation (AMOVA) due to the diversity between the groups. This was congruent with the observation of a highly significant F-ST value (0.705) between the groups, demonstrating significant genetic differentiation between the Andean highland type of quinoa and the Chilean coastal type. Moreover, a core set of 16 quinoa germplasms that capture all 362 alleles was selected using a simulated annealing method. Conclusions: The large number of SNPs and InDels identified in this study demonstrated that the quinoa genome is enriched with genomic variations. Genetic population structure, genetic core germplasms and dimorphic InDel markers are useful resources for genetic analysis and quinoa breeding.

  • 相关文献

[1]Genome re-sequencing of two accessions and fine mapping the locus of lobed leaflet margins in mungbean. Jiao, Keyuan,Guo, Wuxiu,Jiao, Keyuan,Li, Xin,Yuan, Xingxing,Yuan, Xingxing,Cui, Xiaoyan,Chen, Xin.

[2]Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers. Cai, Hongwei,Guan, Xuanli,Cai, Hongwei,Guan, Xuanli,Cai, Hongwei,Yuyama, Nana,Cai, Hongwei,Stewart, Alan,Ding, Chenglong,Xu, Nengxiang,Kiyoshi, Takako. 2017

[3]Exploiting Illumina sequencing for the development of InDel markers in watermelon (Citrullus lanatus). Liu, G.,Xu, J. H.,Zhang, M.,Li, P. F.,Yao, X. F.,Hou, Q.,Zhu, L. L.,Ren, R. S.,Yang, X. P..

[4]利用分子标记对‘淮稻5号’进行品种真实性鉴定. 顾伟航,田佳琪,朱明超,文正怀,严卫古,王兴龙,张大兵,袁政. 2018

[5]甘薯IbANR基因的多态性分析. 武传建,戚骁,李仁赛,封功成,苏静静,葛海军,马代夫,王爱民. 2017

[6]8个水稻抗条纹叶枯病分子标记有效性的验证及评价. 张亚东,朱镇,陈涛,赵庆勇,周丽慧,于新,王才林. 2012

[7]玉米功台皂性Insertjon/Deletion(InDel)分子标记的挖掘及其在杂交种纯度鉴定中的应用. 张体付,葛敏,韦玉才,赵涵. 2012

[8]基于InDel标记分析305份中国甘薯登记品种遗传多样性. 唐芬,赵路宽,苏一钧,肖世卓,袁蕊,翁宗宽,戴习彬,周志林,陈艳丽,曹清河. 2024

[9]糯玉米杂交种纯度InDel分子标记鉴定与田间鉴定的相关性分析. 胡俏强,陆海燕,李炯,陈舜权,吴月琴,戴惠学. 2016

[10]玉米InDel标记20重PCR检测体系的建立. 冯博,许理文,王凤格,薛宁宁,刘文彬,易红梅,田红丽,吕远大,赵涵,金石桥,张力科,蔚荣海,赵久然. 2017

[11]三疣梭子蟹线粒体基因组单核苷酸多态性. 赵莲,李志辉,张培,薛蓓,赖晓芳,高焕,阎斌伦. 2018

[12]三疣梭子蟹线粒体基因组SNP在增殖放流家系识别中的应用. 赵莲,李志辉,张培,薛蓓,赖晓芳,张庆起,高焕,阎斌伦. 2018

[13]SNP分子标记技术在经济甲壳动物中的应用进展. 赵莲,薛蓓,高焕,阎斌伦. 2017

[14]斑点叉尾MSTN基因4个SNP位点及其与生长性状的相关性. 张世勇,王明华,钟立强,秦钦,潘建林,陈校辉,边文冀. 2017

[15]斑点叉尾GHRH基因3个SNPs位点及其单倍型组合与生长性状的关联分析. 张世勇,钟立强,秦钦,王明华,潘建林. 2016

[16]猪Toll样受体4基因(TLR4)外显子SNP检测及生物信息学分析. 刘筱,方晓敏,任守文,李碧侠,王学敏. 2011

[17]大豆四种游离氨基酸高含量优异种质鉴定及GWAS分析. 熊雅文,贾倩茹,周苗苗,张红梅,陈华涛. 2024

[18]猪产仔数的全基因组关联分析. 付言峰,赵为民,李辉,李碧侠,程金花,徐小波,任守文. 2022

[19]大豆籽粒皂苷含量的全基因组关联分析. 唐威,熊雅文,李岩哲,张红梅,张威,许文静,陈熙,陈华涛. 2023

[20]玉米叶片硝酸盐积累性状的全基因组关联分析. 邬奇,孙扬名,桑俊伟,周玲,赵涵. 2024

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：江苏省农业科学院

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