Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping

文献类型： 外文期刊

第一作者： Raghavan, Chitra

作者： Raghavan, Chitra;Naredo, Ma. Elizabeth B.;Wang, Hehe;Atienza, Genelou;Liu, Bin;Qiu, Fulin;McNally, Kenneth L.;Leung, Hei

作者机构：

关键词： agarose;rice

期刊名称：MOLECULAR BREEDING （ 影响因子：2.589； 五年影响因子：2.75 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： TILLING (Targeting Induced Local Lesions IN Genomes) exploits the fact that CEL I endonuclease cleaves heteroduplexes at positions of single nucleotide or small indel mismatches. To detect single nucleotide polymorphisms (SNPs) across a population, DNA pools are created and a target locus under query is PCR-amplified and subjected to heteroduplex formation, followed by CEL I cleavage. Currently, the common method used to detect cleaved products is by polyacrylamide gel electrophoresis using a high-throughput genotyping platform. Exact SNPs are then determined by sequencing. We sought to simplify the detection of CEL I-cleaved products on conventional agarose gels to make the technique more accessible to collaborating partners in developing countries where access to instrumentation could be limiting. Here, we used a panel of stress-related genes to evaluate SNP detection across 48 rice genotypes by contrasting them individually against IR64 and Nipponbare. SNP detection calls corresponded perfectly with those obtained from the Li-Cor genotypers. We were able to detect SNPs in pools of eight DNA templates, suggesting that the agarose gel system could be used to screen for SNPs with comparable throughput as that of the Li-Cor genotypers and showed that the throughput can be increased by analyzing larger amplicons (~3 kb). The agarose method offers a significant advantage by alleviating the need for labeled primers. We further demonstrated that the agarose method can be effectively used in gene mapping, an application particularly useful for parental lines with low levels of polymorphism. The lower cost and simplicity of the technique make it possible for broader applications of SNP-based markers for germplasm characterization and mapping studies.

分类号： Q94

  • 相关文献

[1]GELS MIMICKING ANTIBODIES IN THEIR SELECTIVE RECOGNITION OF PROTEINS. Hjerten, S,Liao, JL,Nakazato, K,Wang, Y,Zamaratskaia, G,Zhang, HX.

[2]Diffusion characteristics of agarose hydrogel used in diffusive gradients in thin films for measurements of cations and anions. Wang, Yan,Ding, Shiming,Gong, Mengdan,Xu, Shiwei,Xu, Weimin,Zhang, Chaosheng.

[3]Phytochrome B Negatively Affects Cold Tolerance by Regulating OsDREB1 Gene Expression through Phytochrome Interacting Factor-Like Protein OsPIL16 in Rice. He, Yanan,Li, Yaping,Cui, Lixin,Xie, Lixia,Zheng, Chongke,Zhou, Guanhua,Zhou, Jinjun,Xie, Xianzhi,Li, Yaping,Cui, Lixin. 2016

[4]A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Hu, Zejun,Sun, Fan,Xin, Xiaoyun,Qian, Xi,Yang, Jingshui,Luo, Xiaojin,Hu, Zejun,He, Haohua,Wang, Wenxiang,Zhang, Shiyong. 2012

[5]Genome-wide identification of microRNAs and their targets in wild type and phyB mutant provides a key link between microRNAs and the phyB-mediated light signaling pathway in rice. Sun, Wei,wu, Xiu,Xie, Xianzhi,Xu, Xiao Hui,Lu, Xingbo,Sun, Hongwei,Wang, Yong. 2015

[6]Overexpression of an S-like ribonuclease gene, OsRNS4, confers enhanced tolerance to high salinity and hyposensitivity to phytochrome-mediated light signals in rice. Zheng, Jun,Wang, Yingying,He, Yanan,Zhou, Jinjun,Li, Yaping,Liu, Qianqian,Xie, Xianzhi,Zheng, Jun,Wang, Yingying,He, Yanan,Zhou, Jinjun,Xie, Xianzhi. 2014

[7]Distribution Characteristics of Soil Cadmium in Different Textured Paddy Soil Profiles and Its Relevance with Cadmium Uptake by Crops. Wang Zheng-yin,Qin Yu-sheng,Zhan Shao-jun,Yu Hua,Tu Shi-hua. 2013

[8]Overexpression of OsPIL15, a phytochromeinteracting factor- like protein gene, represses etiolated seedling growth in rice. Zhou, Jinjun,Liu, Qianqian,Wang, Yingying,Zhang, Shiyong,Cheng, Huimin,Yan, Lihua,Li, Li,Xie, Xianzhi,Zhou, Jinjun,Wang, Yingying,Zhang, Shiyong,Xie, Xianzhi,Liu, Qianqian,Xie, Xianzhi,Zhang, Fang,Chen, Fan. 2014

[9]DISTRIBUTION CHARACTERISTICS, BIOACCUMULATION, AND SOURCES OF MERCURY IN RICE AT NANSI LAKE AREA, SHANDONG PROVINCE, CHNIA. Liu, H.,Zhang, J.,Dai, J. L.,Wang, L. H.,Zhang, J.,Li, G. X.. 2015

[10]Nitrogen Status Diagnosis of Rice by Using a Digital Camera. Fan Ming-sheng,Zhang Fu-suo,Chen Xin-ping,Jia Liang-liang,Sun Yan-ming,Lue Shi-hua. 2009

[11]Influence of unflooded mulching cultivation on nitrogen uptake and utilization of fertilizer nitrogen by rice. Liu, Xuejun,Zhang, Fusuo,Mao, Daru,Zeng, Xingzhong,Lu, Shihua,Wang, Mingtian. 2008

[12]Overexpression of a phytochrome-regulated tandem zinc finger protein gene, OsTZF1, confers hypersensitivity to ABA and hyposensitivity to red light and far-red light in rice seedlings. Zhou, Jinjun,Fan, Zhongxue,Xie, Xianzhi,Zhang, Cheng,Zhou, Jinjun,Fan, Zhongxue,Xie, Xianzhi,Zhang, Cheng,Ma, Huiquan,Zhang, Fang,Chen, Fan. 2012

[13]Enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor Tu receptor EFR. Lu, Fen,Wang, Huiqin,Wang, Shanzhi,Jiang, Wendi,Yang, Jun,Sun, Wenxian,Lu, Fen,Wang, Huiqin,Wang, Shanzhi,Jiang, Wendi,Yang, Jun,Sun, Wenxian,Shan, Changlin,Li, Bin,Shan, Changlin,Li, Bin,Yang, Jun,Zhang, Shiyong. 2015

[14]A missense mutation in the transmembrane domain of CESA9 affects cell wall biosynthesis and plant growth in rice. Wang, Daofeng,Lan, Jinhao,Wang, Daofeng,Zhao, Jinfeng,Li, Xueyong,Yuan, Shoujiang,Yin, Liang,Guo, Baotai. 2012

[15]Mutations in the MIT3 gene encoding a caroteniod isomerase lead to increased tiller number in rice. Liu, Lihua,Peng, Peng,Qiu, Haiyang,Zhao, Jinfeng,Fang, Jingjing,Patil, Suyash Bhimgonda,Li, Xueyong,Xie, Tingting,Zhang, Wenhui,Wang, Yiqin,Fang, Shuang,Chu, Jinfang,Yuan, Shoujiang. 2018

[16]Detection of epistatic interactions of three QTLs for heading date in rice using single segment substitution lines. Ding, Han-Feng,Liu, Xu,Li, Run-Fang,Wang, Wen-Ying,Zhang, Y.,Zhang, Xiao-Dong,Yao, Fang-Yin,Li, Guang-Xian,Jiang, Ming-Song,Ding, Han-Feng.

[17]Delimitation of the PSH1(t) gene for rice purple leaf sheath to a 23.5 kb DNA fragment. Wang, Wen-Ying,Ding, Han-Feng,Li, Run-Fang,Liu, Xu,Zhang, Yu,Yao, Fang-Yin,Li, Guang-Xian,Jiang, Ming-Song.

[18]Determination of 5-hydroxymethyl-2-deoxycytidine in Rice by High-performance Liquid Chromatography-Tandem Mass Spectrometry with Isotope Dilution. Wang, Xiaoli,Wang, Shanshan,Chen, Xiangfeng,Chen, Yue,Yuan, Jinpeng,Zhao, Rusong,Guo, Tao. 2017

[19]Functional Marker Development and Effect Analysis of Grain Size Gene GW2 in Extreme Grain Size Germplasm in Rice. Zhang Ya-dong,Zheng Jia,Liang Yan-li,Zhao Chun-fang,Chen Tao,Zhao Qing-yong,Zhu Zhen,Zhou Li-hui,Yao Shu,Zhao Ling,Yu Xing,Wang Cai-lin. 2015

[20]Synonymous codon usage and gene function are strongly related in Oryza sativa. Liu, QP,Dou, SJ,Ji, ZJ,Xue, QZ. 2005

作者其他论文 更多>>

微信小程序