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 t...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 techn!que to develop SNP markers, and will provide a potential and preliminary application in discriminating cultivars in sweetpotato.展开更多
为研究荷斯坦牛隐性遗传缺陷的SNP单倍型检测方法准确性,并探索在实际生产中应用单倍型检测结果的策略,本研究共选取500头中国荷斯坦母牛进行基因组芯片检测和单倍型分析,并利用分子直接检测方法进行验证。通过单倍型检测发现86头牛疑...为研究荷斯坦牛隐性遗传缺陷的SNP单倍型检测方法准确性,并探索在实际生产中应用单倍型检测结果的策略,本研究共选取500头中国荷斯坦母牛进行基因组芯片检测和单倍型分析,并利用分子直接检测方法进行验证。通过单倍型检测发现86头牛疑似携带8种不同的遗传缺陷,进而以ARMS-PCR(Amplification Refractory Mutation System PCR)分子检测结果作为参考标准,对这些单倍型携带者以及随机选取的64头非单倍型携带者进行了验证。结果表明,HH1和HH4位点的单倍型检测与ARMS-PCR结果完全吻合,而对于HH2、HH3、HH5、HH6、HCD和CVM缺陷,单倍型检测出现了一定数量的假阳性和假阴性结果,其中HH2和HCD的阳性预测值仅有62.5%和60.0%。研究结果证明单倍型检测对于奶牛遗传缺陷的鉴定尚存在技术局限性,在实际应用中应将单倍型检测与直接分子检测结合,建立高效、准确且低成本的奶牛遗传缺陷筛查策略。展开更多
基金supported by the China Agriculture Research System (CARS-11)the National High-Tech R&D Program of China (2012AA101204)the Jiangsu Independent Inno vation Funds of Agriculture,China (CX(13)2032)
文摘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 techn!que to develop SNP markers, and will provide a potential and preliminary application in discriminating cultivars in sweetpotato.
文摘为研究荷斯坦牛隐性遗传缺陷的SNP单倍型检测方法准确性,并探索在实际生产中应用单倍型检测结果的策略,本研究共选取500头中国荷斯坦母牛进行基因组芯片检测和单倍型分析,并利用分子直接检测方法进行验证。通过单倍型检测发现86头牛疑似携带8种不同的遗传缺陷,进而以ARMS-PCR(Amplification Refractory Mutation System PCR)分子检测结果作为参考标准,对这些单倍型携带者以及随机选取的64头非单倍型携带者进行了验证。结果表明,HH1和HH4位点的单倍型检测与ARMS-PCR结果完全吻合,而对于HH2、HH3、HH5、HH6、HCD和CVM缺陷,单倍型检测出现了一定数量的假阳性和假阴性结果,其中HH2和HCD的阳性预测值仅有62.5%和60.0%。研究结果证明单倍型检测对于奶牛遗传缺陷的鉴定尚存在技术局限性,在实际应用中应将单倍型检测与直接分子检测结合,建立高效、准确且低成本的奶牛遗传缺陷筛查策略。
