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.
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