An improved allele-specific PCR primer design method for SNP marker analysis and its application

doi:10.1186/1746-4811-8-34

	An improved allele-specific PCR primer design method for SNP marker analysis and its application
	Liu, Jing 1; Huang, Shunmou 1; Sun, Meiyu 1; Liu, Shengyi 1; Liu, Yumei 2; Wang, Wanxing 2; Zhang, Xiurong 1; Wang, Hanzhong 1; Hua, Wei 1
刊名	PLANT METHODS
	2012
卷号	8 页码:-
关键词	SNP AS-PCR Mismatch Polymorphism Destabilization
ISSN号	1746-4811
DOI	10.1186/1746-4811-8-34
通讯作者	Liu, Jing
英文摘要	Background: Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3'end (SNP site) have been used in AS-PCR. However, for one SNP site, nine possible mismatches can be generated among the three bases and how to select the right one to increase primer specificity is still a challenge.Results: In this study, different from the previous reports which used a limited quantity of primers randomly (several or dozen pairs), we systematically investigated the effects of mismatch base pairs, mismatch sites and SNP types on primer specificity with 2071 primer pairs, which were designed based on SNPs from Brassica oleracea 01-88 and 02-12. According to the statistical results, we (1) found that the primers designed with SNP (A/T), in which the mismatch (CA) in the 3rd nucleotide from the 3' end, had the highest allele-specificity (81.9%). This information could be used when designing primers from a large quantity of SNP sites; (2) performed the primer design principle which forms the one and only best primer for every SNP type. This is never reported in previous studies. Additionally, we further identified its availability in rapeseed (Brassica napus L.) and sesame (Sesamum indicum). High polymorphism percent (75%) of the designed primers indicated it is a general method and can be applied in other species.Conclusion: The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods. The high allele-specific efficiency of the SNP primer allows the feasibility for low-to moderate-throughput SNP analyses and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops.
学科主题	Biochemical Research Methods ; Plant Sciences ; PLANT SCIENCES
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000311424000001
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101090]
专题	蔬菜花卉研究所_十字花科研究室
作者单位	1.Chinese Acad Agr Sci, Key Lab Biol & Genet Improvement Oil Crops, Minist Agr, Oil Crops Res Inst, Wuhan 430062, Peoples R China 2.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100081, Peoples R China
推荐引用方式 GB/T 7714	Liu, Jing,Huang, Shunmou,Sun, Meiyu,et al. An improved allele-specific PCR primer design method for SNP marker analysis and its application[J]. PLANT METHODS,2012,8:-.
APA	Liu, Jing.,Huang, Shunmou.,Sun, Meiyu.,Liu, Shengyi.,Liu, Yumei.,...&Hua, Wei.(2012).An improved allele-specific PCR primer design method for SNP marker analysis and its application.PLANT METHODS,8,-.
MLA	Liu, Jing,et al."An improved allele-specific PCR primer design method for SNP marker analysis and its application".PLANT METHODS 8(2012):-.