Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing.
Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing.
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DOI：
10.1186/s12864-017-4093-8
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发表时间：
2017-09-05
期刊：
影响因子：
4.4
通讯作者：
Zhao H
中科院分区：
文献类型：
--
作者：
Zhang T;Gu M;Liu Y;Lv Y;Zhou L;Lu H;Liang S;Bao H;Zhao H
藜麦（藜麦野生）是一种营养均衡的作物，但由于缺乏有关其遗传和基因组学的信息，其育种改进受到限制。因此，有必要通过全基因组重测序来了解藜麦的基因组变异、群体结构和遗传多样性，并开发新的插入/删除（InDel）标记。我们对11份藜麦材料进行了重新测序，获得了藜麦基因组约7 - 23倍的覆盖深度。基于参考库Riobamba的1453兆碱基（Mb）序列，共鉴定出8,441,022个过滤后的双等位基因单核苷酸多态性（SNP）和842,783个过滤后的InDel，估计SNP和InDel密度分别为5.81和0.58 /千碱基（kb）。从InDel基因组变异中，新开发并验证了85个InDel二态标记。加上已报道的62个SSR标记，共147个标记对129份藜麦材料进行了基因分型。结合结构、系统发育树和主成分分析，将其划分为安第斯高原（由北部和南部高原亚群组成）和智利沿海两大类群。进一步的遗传多样性分析显示，从智利海岸类群到安第斯高地类群的遗传多样性呈下降趋势，亚群之间的基因流动比两个亚群与智利海岸类群之间的基因流动更频繁。大多数变异（约70%）是通过分子变异分析（AMOVA）发现的，这是由于群体之间的多样性。这与观察到的组间FST值非常显著（0.705）一致，表明安第斯高原型藜麦和智利沿海型藜麦之间存在显著的遗传分化。此外，采用模拟退火方法选择了捕获所有362个等位基因的16个藜麦种质核心集。本研究中发现的大量snp和InDels表明藜麦基因组富含基因组变异。遗传群体结构、遗传核心种质和二态InDel标记是藜麦遗传分析和育种的重要资源。本文的在线版本（10.1186/s12864-017-4093-8）包含补充材料，授权用户可使用。
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. We re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7× to 23× 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 FST 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. 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. The online version of this article (10.1186/s12864-017-4093-8) contains supplementary material, which is available to authorized users.
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影响因子：
46.9
作者：
Li, Ying-hui;Zhou, Guangyu;Qiu, Li-juan
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影响因子：
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