Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato

doi:10.1016/S2095-3119(16)61405-3

Journal of Integrative Agriculture ›› 2017, Vol. 16 ›› Issue (02): 464-470.DOI: 10.1016/S2095-3119(16)61405-3

收稿日期:2016-02-22 出版日期:2017-02-20 发布日期:2017-01-31

Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato

KOU Meng^{1, 2*}, XU Jia-lei^1*, LI Qiang^{1, 2}, LIU Ya-ju¹, WANG Xin^{1, 2}, TANG Wei¹, YAN Hui¹, ZHANG Yun-gang¹, MA Dai-fu^{1, 2}

¹Xuzhou 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 ²School of Life Science, Jiangsu Normal University, Xuzhou 221116, P.R.China

Received:2016-02-22 Online:2017-02-20 Published:2017-01-31
Contact: LI Qiang, Tel: +86-516-82189203, Fax: +86-516-82189209, E-mail: instrong@163.com
About author:KOU Meng, E-mail: koumeng2113@163.com
Supported by:
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)

摘要/Abstract

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.

Key words: sweetpotato, SNPs, RNA-seq, tetra-primer ARMS-PCR

KOU Meng, XU Jia-lei, LI Qiang, LIU Ya-ju, WANG Xin, TANG Wei, YAN Hui, ZHANG Yun-gang, MA Dai-fu. [J]. Journal of Integrative Agriculture, 2017, 16(02): 464-470.

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

参考文献

Austin D F. 1987. The taxonomy, evolution and genetic diversity of sweetpotato and related absence of viruses in most symptomless fieldgrown sweetpotato in Uganda. Annals of Applied Biology, 130, 481–490.
Barbazuk W B, Emrich S J, Chen H D, Li L, Schnable P S. 2007. SNP discovery via 454 transcriptome sequencing. The Plant Journal, 51, 910–918.
Bovell-Benjamin A C. 2007. Sweet potato: A review of its past, present, and future role in human nutrition. Advances in Food and Nutrition Research, 52, 1–59.
Cervantes-Flores J C, Yencho G C, Kriegner A, Pecota K V, Faulk M A, Mwanga R O M, Sosinski B R. 2008. Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers. Molecular Breeding, 21, 511–532.
Cevallos-Casals B A, Cisneros-Zevallos L A. 2002. Bioactive and functional properties of purple sweetpotato (Ipomoea batatas L. Lam). Acta Horticultutae (ISHS), 583, 195–203.
Chopra R, Burow G, Farmer A, Mudge J, Simpson C E, Wilkins T A, Baring M R, Puppala N, Chamberlin K D, Burow M D. 2015. Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L. Molecular Genetics and Genomics, 290, 1169–1180.
Close T J, Bhat P R, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson J T, Wanamaker S, Bozdag S, Roose M L, Moscou M J, Chao S, Varshney R K, Szucs P, Sato K, Hayes P M, Matthews D E, Kleinhofs A, et al. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10, 582.
Collins A, Ke X. 2012. Primer1: primer design web service for tetra-primer ARMS-PCR. Open Bioinformatics Journal, 6, 55–58.
Hayashi K, Hashimoto N, Daigen M, Ashikawa I. 2004. Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theoretical and Applied Genetics, 108, 1212–1220.
Huang J C, Sun M. 2000. Genetic diversity and relationships of sweetpotato and its wild relatives in Ipomoea series Batatas (Convolvulaceae) as revealed by inter-simple sequence repeat (ISSR) and restriction analysis of chloroplast DNA. Theoretical and Applied Genetics, 100, 1050–1060.
Jones A. 1986. Sweet-potato heritability estimates and their use in breeding. HortScience, 21, 14–17.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Research, 36, 480–484.
Kwok P Y. 2001. Methods for genotyping single nucleotide polymorphisms. Annual Review of Genomics and Human Genetics, 2, 235–258.
Li Q, Li P, Liu Q C, Ma D F, Li X Y, Wang X, Cao Q H, Zhai H. 2008a. Genetic difference of sweetpotato cultivars in East Asia as revealed by AFLP marker. Molecular Plant Breeding, 6, 905–911. (in Chinese)
Li Q, Liu Q C, Zhai H, Ma D F, Wang X, Li X Q, Wang Y P. 2008b. Genetic diversity in main parents of sweetpotato in China as revealed by ISSR marker. Acta Agronomica Sinica, 34, 972–977. (in Chinese)
Mortazavi A, Williams B A, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNASeq. Nature Methods, 5, 621–628.
Morozova O, Hirst M, Marra M A. 2009. Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics, 10, 135–151.
Moulin M M, Rodrigues R, Gonçalves L S A, Sudre C P, Pereira M G. 2012. A comparison of RAPD and ISSR markers reveals genetic diversity among sweet potato landraces (Ipomoea batatas (L.) Lam.). Acta Scientiarum-Agronomy, 34, 139–147.
Ozias-Akins P, Jarret R L. 1994. Nuclear DNA content and ploidy levels in the genus Ipomoea. Journal of American Society for Horticultural Science, 119, 110–115.
Schafleitner R, Tincopa L R, Palomino O, Rossel G, Robles R F, Alagon R, Rivera C, Quispe C, Rojas L, Pacheco J A. 2010. A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics, 11, 604–613.
Tao X, Gu Y H, Wang H Y, Zheng W, Li X, Zhao C W, Zhang Y Z. 2012. Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato (Ipomoea batatas (L.) Lam.). PLOS ONE, 7, e36234.
Ukoskit K, Thompson P G. 1997. Autopolyploidy verus allopolyploidy and low-density randomly amplified polymorphic DNA linkage maps of sweetpotato. Journal of American Society for Horticultural Science, 122, 822–828.
Wang Z Y, Fang B P, Chen J Y, Zhang X J, Luo Z X, Huang L F, Chen X L, Li Y J. 2010. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics, 11, 726–739.
Wang Z Y, Li J, Luo Z X, Huang L F, Chen X L, Fang B P, Li Y J, Chen J Y, Zhang X J. 2011. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biology, 11, 1-9.
Wei L B, Miao H M, Li C, Duan Y H, Niu J J, Zhang T D, Zhao Q Y, Zhang H Y. 2014. Development of SNP and InDel markers via de novo transcriptome assembly in Sesamum indicum L. Molecular Breeding, 34, 2205–2217.
Wu X L, Ren C W, Joshi T, Vuong T, Xu D, Nguyen H T. 2010. SNP discovery by high-throughput sequencing in soybean. BMC Genomics, 11, 1-10.
Xie F L, Burklew C E, Yang Y F, Liu M, Xiao P, Zhang B H, Qiu D Y. 2012. De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta, 236, 101–113.
Xu J L, Li Q, Hou M, Liu Y J, Wang X, Tang W, Yan H, Zhang Y G, Ma D F. 2015a. A rapid and efficient method for detecting sweetpotato (Ipomoea batatas L.) SNP markers. Molecular Plant Breeding, 13, 891–897. (in Chinese)
Xu J L, Wang Y, Hou M, Li Q. 2015b. Progress on detection methods of SNP. Molecular Plant Breeding, 13, 475–482. (in Chinese)
Xu X, Liu X, Ge S, Jensen J D, Hu F Y, Li X, Dong Y, Gutenkunst R N, Fang L, Huang L, Li J X, He W M, Zhang G J, Zheng X M, Zhang F M, Li Y R, Yu C, Kristiansen K, Zhang X Q, Wang J, et al. 2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 30, 105–111.
Yamasaki M, Tenaillon M I, Bi I V, Schroeder S G, Sanchez-Villeda H, Doebley J F, Gaut B S, McMullen M D. 2005. A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. The Plant Cell, 17, 2859–2872.
Ye S, Dhillon S, Ke X, Collins A R, Day I N. 2001. An eficient procedure for genotyping single nueleotide polymorphisms. Nucleic Acids Research, 29, 88.
Zhao N. 2012. Construction of high-density molecular linkage maps of sweetpotato, Ipomoea batatas (L.) Lam. Ph D thesis, China Agricultural University, China. (in Chinese)
Zhao N, Zhai H, Yu X X, Liu Z S, He S Z, Li Q, Ma D F, Liu Q C. 2013. Development of SRAP markers linked to a gene for stem nematode resistance in sweetpotato, Ipomoea batatas (L.) Lam. Journal of Integrative Agriculture, 12, 414–419.
Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H. 2014. Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics, 15, 1–14.

Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato

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