Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato
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...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
KeAi Communications Co., Ltd.
2017-02-01
|
| Series: | Journal of Integrative Agriculture |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311916614053 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1839643002383892480 |
|---|---|
| author | Meng KOU Jia-lei XU Qiang LI Ya-ju LIU Xin WANG Wei TANG Hui YAN Yun-gang ZHANG Dai-fu MA |
| author_facet | Meng KOU Jia-lei XU Qiang LI Ya-ju LIU Xin WANG Wei TANG Hui YAN Yun-gang ZHANG Dai-fu MA |
| author_sort | Meng KOU |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-2a35d1a6144e4f01b6b05ffc6ec4f261 |
| institution | Matheson Library |
| issn | 2095-3119 |
| language | English |
| publishDate | 2017-02-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-2a35d1a6144e4f01b6b05ffc6ec4f2612025-07-02T04:51:56ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192017-02-01162464470Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotatoMeng KOU0Jia-lei XU1Qiang LI2Ya-ju LIU3Xin WANG4Wei TANG5Hui YAN6Yun-gang ZHANG7Dai-fu MA8Xuzhou 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; School of Life Science, Jiangsu Normal University, Xuzhou 221116, P.R. ChinaXuzhou 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. ChinaXuzhou 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; School of Life Science, Jiangsu Normal University, Xuzhou 221116, P.R. China; Correspondence LI Qiang, Tel: +86-516-82189203, Fax: +86-516-82189209Xuzhou 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. ChinaXuzhou 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; School of Life Science, Jiangsu Normal University, Xuzhou 221116, P.R. ChinaXuzhou 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. ChinaXuzhou 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. ChinaXuzhou 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. ChinaXuzhou 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; School of Life Science, Jiangsu Normal University, Xuzhou 221116, P.R. ChinaThe 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.http://www.sciencedirect.com/science/article/pii/S2095311916614053sweetpotatoSNPsRNA-seqtetra-primer ARMS-PCR |
| spellingShingle | Meng KOU Jia-lei XU Qiang LI Ya-ju LIU Xin WANG Wei TANG Hui YAN Yun-gang ZHANG Dai-fu MA Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato Journal of Integrative Agriculture sweetpotato SNPs RNA-seq tetra-primer ARMS-PCR |
| title | Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato |
| title_full | Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato |
| title_fullStr | Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato |
| title_full_unstemmed | Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato |
| title_short | Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato |
| title_sort | development of snp markers using rna seq technology and tetra primer arms pcr in sweetpotato |
| topic | sweetpotato SNPs RNA-seq tetra-primer ARMS-PCR |
| url | http://www.sciencedirect.com/science/article/pii/S2095311916614053 |
| work_keys_str_mv | AT mengkou developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT jialeixu developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT qiangli developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT yajuliu developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT xinwang developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT weitang developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT huiyan developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT yungangzhang developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato AT daifuma developmentofsnpmarkersusingrnaseqtechnologyandtetraprimerarmspcrinsweetpotato |