School of Agriculture, Ningxia University, Yinchuan, China.
Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China.
PLoS One. 2020 May 5;15(5):e0231753. doi: 10.1371/journal.pone.0231753. eCollection 2020.
Lou onion (Allium fistulosum L. var. viviparum) is an abundant source of flavonols which provides additional health benefits to diseases. Genome-wide specific length amplified fragment (SLAF) sequencing method is a rapidly developed deep sequencing technologies used for selection and identification of genetic loci or markers. This study aimed to elucidate the genetic diversity of 122 onion accessions in China using the SLAF-seq method. A set of 122 onion accessions including 107 A.fistulosum L. var. viviparum Makino, 3 A.fistulosum L. var. gigantum Makino, 3 A.mongolicum Regel and 9 A.cepa L. accessions (3 whites, 3 reds and 3 yellows) from different regions in China were enrolled. Genomic DNA was isolated from young leaves and prepared for the SLAF-seq, which generated a total of 1,387.55 M reads and 162,321 high quality SNPs (integrity >0.5 and MAF >0.05). These SNPs were used for the construction of neighbor-joining phylogenetic tree, in which 10 A.fistulosum L. var. viviparum Makino accessions from Yinchuan (Ningxia province) and Datong (Qinghai province) had close genetic relationship. The 3 A.cepa L. clusters (red, white and yellow) had close genetic relationship especially with the 97 A.fistulosum L. var. viviparum Makino accessions. Population structure analysis suggested entire population could be clustered into 3 groups, while principal component analysis (PCA) showed there were 4 genetic groups. We confirmed the SLAF-seq approach was effective in genetic diversity analysis in red onion accessions. The key findings would provide a reference to the Lou onion germplasm in China.
露葱（Allium fistulosum L. var. viviparum）是类黄酮的丰富来源，为疾病提供了额外的健康益处。全基因组特异长度扩增片段（SLAF）测序方法是一种快速发展的深度测序技术，用于选择和鉴定遗传基因座或标记。本研究旨在利用 SLAF-seq 方法阐明中国 122 个洋葱品种的遗传多样性。一组包括 107 个 A.fistulosum L. var. viviparum Makino、3 个 A.fistulosum L. var. gigantum Makino、3 个 A.mongolicum Regel 和 9 个 A.cepa L.品种（3 个白皮、3 个红皮和 3 个黄皮）的洋葱品种，来自中国不同地区，被纳入研究。从幼叶中提取基因组 DNA，用于 SLAF-seq 制备，共产生了 1387.55 M 个读取和 162321 个高质量 SNP（完整性>0.5 和 MAF>0.05）。这些 SNP 用于构建邻接聚类系统进化树，其中来自宁夏银川和青海大通的 10 个 A.fistulosum L. var. viviparum Makino 品种具有密切的遗传关系。3 个 A.cepa L. 品种（红皮、白皮和黄皮）的遗传关系非常密切，特别是与 97 个 A.fistulosum L. var. viviparum Makino 品种。群体结构分析表明，整个群体可分为 3 个组，而主成分分析（PCA）表明存在 4 个遗传组。我们证实 SLAF-seq 方法在红洋葱品种遗传多样性分析中是有效的。主要发现将为中国的露葱种质资源提供参考。
