Analysis of SSRs Information in Capsicum spp. from EST Database

Agricultural Sciences in China Pub Date : 2011-10-01 Epub Date: 2011-10-21 DOI:10.1016/S1671-2927(11)60148-X

HUANG Huan-huan, ZHANG Zhong-hua, ZHANG Zheng-hai, MAO Sheng-li, WANG Li-hao, ZHANG Bao-xi

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引用次数: 9

Abstract

SSR markers are useful in pepper linkage mapping and gene location. 446 SSR markers have been reported, but they are insufficient. It is costly to develop SSR markers from DNA library, whereas it seems much easy to find in EST sequences in the GenBank of pepper through internet. In this study, attempts have been made to develop SSR markers in the EST sequences by using bioinformatics. EST sequences were trimmed by ‘est-trimmer.pr software, while 116915EST sequences were obtained without poly ‘A’ or poly ‘T’, ranged between 100 and 700 bp. Using ‘e-PCR’ and ‘del.pl’ softwares, SSR sequences were identified. 2 508 micro satellite loci (larger than 20 repeats) were established and 755 SSR primers were designed using SSR finder software and Primer 3 software. There were 498 (0.43%) mono-, 1 026 (0.89%) di-, 518 (0.45%) tn-, 245 (0.21%) tetra-, 114 (0.10%) penta-, and 107 (0.09%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/25.12 kb. According to the distribution of SSRs in pepper, the mean length of pepper SSRs was 22.68 bp and the adenine rich repeats such as A/T, AG, AT, AAG, AAAT, and AAAC were predominant in each type of SSRs (mono-, di-, tri-, tetra-, penta-, and hexa-), whereas the C/G, CG, CCG repeats were less abundant. 210 primers were tested in 8 pepper cultivars and the PCR result revealed the existence of polymorphism among 127 (60.48%) SSR primers within 8 pepper cultivars. It is confirmed that pepper EST database could be efficiently exploited for availability of SSR markers.

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EST数据库辣椒品种SSRs信息分析

摘要ssr标记在辣椒连锁定位和基因定位中具有重要意义。已报道的SSR标记有446个，但数量不足。从DNA文库中开发SSR标记成本高，而通过网络在辣椒基因库中的EST序列中寻找SSR标记似乎容易得多。本研究尝试利用生物信息学的方法在EST序列中开发SSR标记。EST序列用“EST -trimmer”进行裁剪。而不含poly ' A '或poly ' T '的116915EST序列，范围在100 ~ 700 bp之间。利用' e-PCR '和' del.pl '软件对SSR序列进行鉴定。利用SSR finder软件和Primer 3软件，共建立了2 508个重复数大于20的微卫星位点，设计了755条SSR引物。单核苷酸SSRs有498个(0.43%)，二核苷酸有1 026个(0.89%)，tn-有518个(0.45%)，四核苷酸有245个(0.21%)，五核苷酸有114个(0.10%)，六核苷酸有107个(0.09%)。SSRs的估计频率约为1/25.12 kb。根据辣椒ssr序列的分布，辣椒ssr序列的平均长度为22.68 bp，单、二、三、四、五、六种ssr序列以A/T、AG、AT、AAG、AAAT和AAAC等富含腺嘌呤的重复序列居多，C/G、CG、CCG重复序列较少。对8个辣椒品种的210条引物进行PCR检测，结果显示，8个辣椒品种的127条SSR引物(60.48%)存在多态性。结果表明，辣椒EST数据库可有效利用SSR标记。

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Agricultural Sciences in China AGRICULTURE, MULTIDISCIPLINARY-

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3.2 months