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Journal of Integrative Agriculture  2017, Vol. 16 Issue (02): 464-470    DOI: 10.1016/S2095-3119(16)61405-3
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato
KOU Meng1, 2*, XU Jia-lei1*, LI Qiang1, 2, LIU Ya-ju1, WANG Xin1, 2, TANG Wei1, YAN Hui1, ZHANG Yun-gang1, MA Dai-fu1, 2

1 Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, P.R.China 2 School of Life Science, Jiangsu Normal University, Xuzhou 221116, P.R.China

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Abstract  The information of single nucleotide polymorphisms (SNPs) is quite unknown in sweetpotato.  In this study, two sweetpotato varieties (Xushu 18 and Xu 781) were sequenced by Illumina technology, as well as de novo transcriptome assembly, functional annotation, and in silico discovery of potential SNP molecular markers.  Tetra-primer Amplification Refractory Mutation System PCR (ARMS-PCR) is a simple and sufficient method for detecting different alleles in SNP locus.  Total 153 sets of ARMS-PCR primers were designed to validate the putative SNPs from sequences.  PCR products from 103 sets of primers were different between Xu 781 and Xushu 18 via agarose gel electrophoresis, and the detection rate was 67.32%.  We obtained the expected results from 32 sets of primers between the two genotypes.  Furthermore, we ascertained the optimal annealing temperature of 32 sets of primers.  These SNPs might be used in genotyping, QTL mapping, or marker-assisted trait selection further in sweetpotato.  To our knowledge, this work was the first study to develop SNP markers in sweetpotato by using tetra-primer ARMS-PCR technique.  This method was a simple, rapid, and useful technique to develop SNP markers, and will provide a potential and preliminary application in discriminating cultivars in sweetpotato.
Keywords:   sweetpotato      SNPs      RNA-seq      tetra-primer ARMS-PCR  
Received: 22 February 2016   Accepted:

The work was supported by the China Agriculture Research System (CARS-11), the National High-Tech R&D Program of China (2012AA101204), and the Jiangsu Independent Inno­vation Funds of Agriculture, China (CX (13) 2032)

Corresponding Authors:  LI Qiang, Tel: +86-516-82189203, Fax: +86-516-82189209, E-mail:    
About author:  KOU Meng, E-mail:

Cite this article: 

KOU Meng, XU Jia-lei, LI Qiang, LIU Ya-ju, WANG Xin, TANG Wei, YAN Hui, ZHANG Yun-gang, MA Dai-fu. 2017. Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato. Journal of Integrative Agriculture, 16(02): 464-470.

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