Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing

Abstract

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.

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

“…The application of the highly-developed and popular SLAF-sequence simplified genome sequencing approach has been extensively documented for a variety of crops, including Chinese lou onions [ 52 ], sweet potatoes [ 53 ], broomcorn millets [ 54 ], and others. It is more cost-effective than re-sequencing and can also produce a large number of SNPs with a uniform distribution.…”

Recent Advances in Molecular Genetics of Onion

“…Fang et al [47] performed a genome-wide assessment study on 122 accessions from twenty-three agro-climatic zones of China. Nine economic traits of onion bulbs and pseudostems were evaluated with 162,321 high-quality SNP markers via the genome-wide specific length amplified fragment (SLAF) sequencing method.…”

Population Genomic Evidence for the Diversification of Bellamya aeruginosa in Different River Systems in China

“…We used the FIGTREE v1.4.4 [51] to visualize and format the phylogenetic tree. We tested population structure using the block relaxation approach assignment test in the program ADMIXTURE v1.3 [52] to estimate the ancestry of individuals, with testing cluster values of K = 1 to K = 10 [53]. To determine the most appropriate value of K, we conducted a 10-fold cross-validation and selected the estimate with the lowest error, and the output was visualized in the R package pophelper.…”