[1]王为,叶泗洪,潘宗瑾,等.棉花分子标记冗余性检测与评价的方法[J].江苏农业学报,2015,(02):247-252.[doi:10.3969/j.issn.1000-4440.2015.02.004]
　WANG Wei,YE Si-hong,PAN Zong-jin,et al.An approach to detecting and evaluating molecular marker redundancy in cotton[J].,2015,(02):247-252.[doi:10.3969/j.issn.1000-4440.2015.02.004]
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棉花分子标记冗余性检测与评价的方法()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2015年02期
页码:
247-252
栏目:
遗传育种·生理生化
出版日期:
2015-04-30

文章信息/Info

Title:
An approach to detecting and evaluating molecular marker redundancy in cotton
作者:
王为12; 叶泗洪3; 潘宗瑾1; 王海洋1; 高进1; 蔡立旺1; 陈建平1; 王永慧1; 潘群斌1; 王长彪4
（1.江苏沿海地区农业科学研究所/农业部沿海盐碱地科学观测实验站，江苏盐城224002；2.中国农业科学院棉花研究所/棉花生物学国家重点实验室，河南安阳455000；3.安徽省农业科学院棉花研究所，安徽安庆246003；4.山西省农业科学院生物技术中心，山西太原030031）
Author(s):
WANG Wei12; YE Si-hong3; PAN Zong-jin1; WANG Hai-yang1; GAO Jin1; CAI Li-wang1; CHEN Jian-ping1; WANG Yong-hui1; PAN Qun-bin1; WANG Chang-biao4〖JP〗
(1.Institute of Agricultural Sciences in the Coastal District of Jiangsu Province/Observation and Experimental Station of Saline Land in Coastal Area, Ministry of Agriculture, Yancheng 224002, China;2.Cotton Research Institute, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, China;3.Cotton Research Institute, Anhui Academy of Agricultural Sciences，Anqing 246003, China；4.Bio-technology Research Center，Shanxi Academy of Agricultural Sciences, Taiyuan 030031, China)
关键词:
棉花; 分子标记; SSR; 冗余性软件; 检测; 预测
Keywords:
cotton; molecular marker; SSR; redundancy software; detection; prediction
分类号:
S562.032
DOI:
10.3969/j.issn.1000-4440.2015.02.004
文献标志码:
A
摘要:
网上数据库公布的棉花分子标记引物序列存在冗余性，至今也鲜见合适的软件同时分析一对引物的冗余性。为减少不同研究者的重复开发，节约时间和成本，提高对网上序列信息的利用率，借助自主开发的能同时分析一对引物和已释放的引物间是否存在冗余性的软件SSRD1.0，利用90对前人已开发的并用该软件预测过相互间存在冗余性的SSR引物，以TM-1、海7124基因组为模板分别进行扩增、电泳、测序。结果表明软件预测和基因型水平检测有88.8%的吻合度；在Identity阈值设为50%、70%时，测序结果表明序列水平和软件预测分别有75.0%、53.8%的吻合度。分别从软件预测、基因型、序列3个水平进行检测、验证，结果表明这一冗余软件和冗余性预测方法是较为有效、可行的。
Abstract:
Currently there exists redundancy among the sequences of cotton molecular markers which amplifie the same regions on the genome. However, softwares which can be used to simultaneously analyze the redundancy of a pair of primers are not available. To improve the utilization of sequence information, a software named SSRD1.0 was developed to analyze the redundancy between a pair of primers. In addition, 90 pairs of SSR primers in which redundancy was detected by the software were selected to perform amplification, electrophoresis and sequencing using the cotton genotypes of TM-1 and 7124. The consistency were 75.0% and 53.8% between the software prediction and sequence level with a threshold of 50% identity and 70% identity, respectively. Verification from the levels of software prediction, electrophoresis and sequencing revealed that the software and the redundancy prediction method were effective and feasible.

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备注/Memo

备注/Memo:
收稿日期：2014-08-02 基金项目：棉花生物学国家重点实验室开放课题(CB2014A02)；中国博士后科学基金项目(2012M520473)；国家自然科学基金项目(31460359)；江苏省自然科学基金项目(BK20130429、BK20131204 )；江苏省“六大人才高峰”项目(NY-34)；公益性事业单位科研资助项目(KY2013056) 作者简介：王为（1980-），男，江苏泗阳人，博士，副研究员，从事棉花分子育种与种质创新研究工作。（E-mail） ww462@126.com。叶泗洪与王为具有同等贡献.。 通讯作者：王长彪，（E-mail）wcbkls@126.com
更新日期/Last Update: 2015-04-30