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BioMed Research International
Volume 2016, Article ID 3524908, 10 pages
Research Article

SNP Mining in Functional Genes from Nonmodel Species by Next-Generation Sequencing: A Case of Flowering, Pre-Harvest Sprouting, and Dehydration Resistant Genes in Wheat

Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China

Received 30 December 2015; Accepted 18 February 2016

Academic Editor: Hongwei Wang

Copyright © 2016 Zhong-Xu Chen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


As plenty of nonmodel plants are without genomic sequences, the combination of molecular technologies and the next generation sequencing (NGS) platform has led to a new approach to study the genetic variations of these plants. Software GATK, SOAPsnp, samtools, and others are often used to deal with the NGS data. In this study, BLAST was applied to call SNPs from 16 mixed functional gene’s sequence data of polyploidy wheat. In total 1.2 million reads were obtained with the average of 7500 reads per genes. To get accurate information, 390,992 pair reads were successfully assembled before aligning to those functional genes. Standalone BLAST tools were used to map assembled sequence to functional genes, respectively. Polynomial fitting was applied to find the suitable minor allele frequency (MAF) threshold at 6% for assembled reads of each functional gene. SNPs accuracy form assembled reads, pretrimmed reads, and original reads were compared, which declared that SNPs mined from the assembled reads were more reliable than others. It was also demonstrated that mixed samples’ NGS sequences and then analysis by BLAST were an effective, low-cost, and accurate way to mine SNPs for nonmodel species. Assembled reads and polynomial fitting threshold were recommended for more accurate SNPs target.