Zhang Tifu, Gu Minfeng, Liu Yuhe, Lv Yuanda, Zhou Ling, Lu Haiyan, Liang Shuaiqiang, Bao Huabin, Zhao Han
Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China.
Xinyang Agricultural Experiment Station of Yancheng City, Yancheng, Jiangsu, 224336, China.
BMC Genomics. 2017 Sep 5;18(1):685. doi: 10.1186/s12864-017-4093-8.
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 F 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.
藜麦（Chenopodium quinoa Willd.）是一种营养均衡的作物，但其育种改良受到遗传和基因组信息匮乏的限制。因此，有必要通过全基因组重测序获取藜麦基因组变异、群体结构和遗传多样性方面的知识，并开发新型插入/缺失（InDel）标记。
我们对11份藜麦种质进行了重测序，获得了约7倍至23倍藜麦基因组覆盖深度。基于参考种质里奥班巴（Riobamba）的1453兆碱基（Mb）组装，鉴定出8,441,022个经过筛选的双等位基因单核苷酸多态性（SNP）和842,783个经过筛选的InDel，估计SNP和InDel密度分别为每千碱基（kb）5.81和0.58个。从基因组InDel变异中，新开发并验证了85个双态InDel标记。连同已报道的62个简单序列重复（SSR）标记，共147个标记用于对129份藜麦种质进行基因分型。基于STRUCTURE、系统发育树和主成分分析（PCA）的综合分析，分子分组分析显示可分为两个主要组，安第斯高地组（由北部和南部高地亚组组成）和智利沿海组。对遗传多样性的进一步分析表明，从智利沿海组到安第斯高地组呈现出递减趋势，亚组之间的基因流比两个亚组与智利沿海组之间的基因流更频繁。通过分子变异分析（AMOVA）发现，大部分变异（约70%）是由于组间多样性造成的。这与两组之间高度显著的F值（0.705）的观察结果一致，表明安第斯高地型藜麦和智利沿海型藜麦之间存在显著的遗传分化。此外，使用模拟退火方法选择了一组包含所有362个等位基因的16份藜麦核心种质。
本研究中鉴定出的大量SNP和InDel表明藜麦基因组富含基因组变异。遗传群体结构、遗传核心种质和双态InDel标记是遗传分析和藜麦育种的有用资源。
