SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

doi:10.1371/journal.pone.0058700

CORC > 中国农业科学院 > 蔬菜花卉研究所

	SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing
	Sun, Xiaowen 1; Liu, Dongyuan 2; Zhang, Xiaofeng 1; Li, Wenbin 2,3; Liu, Hui 2; Hong, Weiguo 2; Jiang, Chuanbei 2; Guan, Ning 2; Ma, Chouxian 2; Zeng, Huaping 2
刊名	PLOS ONE
	2013
卷号	8 期号:3 页码:-
ISSN号	1932-6203
DOI	10.1371/journal.pone.0058700
通讯作者	Sun, Xiaowen
英文摘要	Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.
学科主题	Multidisciplinary Sciences ; MULTIDISCIPLINARY SCIENCES
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000317562100035
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101902]
专题	蔬菜花卉研究所
作者单位	1.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Harbin, Peoples R China 2.Biomarker Technol Corp, Beijing, Peoples R China 3.Northeast Agr Univ, Key Lab Soybean Biol, Chinese Minist Educ, Harbin, Peoples R China 4.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100193, Peoples R China
推荐引用方式 GB/T 7714	Sun, Xiaowen,Liu, Dongyuan,Zhang, Xiaofeng,et al. SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing[J]. PLOS ONE,2013,8(3):-.
APA	Sun, Xiaowen.,Liu, Dongyuan.,Zhang, Xiaofeng.,Li, Wenbin.,Liu, Hui.,...&Zheng, Hongkun.(2013).SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing.PLOS ONE,8(3),-.
MLA	Sun, Xiaowen,et al."SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing".PLOS ONE 8.3(2013):-.