Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype
Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype
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DOI：
10.1007/s00122-008-0837-9
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发表时间：
2008-10-01
影响因子：
5.4
通讯作者：
Osborn, Thomas C.
中科院分区：
文献类型：
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作者：
Iniguez-Luy, Federico L.;Voort, Amy V.;Osborn, Thomas C.
传统的开发简单重复序列（SSR）或微卫星标记的探针杂交可能是耗时的，需要使用专门的实验室设备。在这项研究中，通过使用主要来自甘蓝的3，500个基因组克隆的序列信息来识别二，三，四和五核苷酸重复，从而避免了探针杂交。共开发了587对SSR侧翼引物。其中，420个SSR标记在B的两个亲本系中扩增出DNA。rapa（26%）和B的两个亲本系中的523。甘蓝（32%）为多态性。一个多样化的阵列的模体类型进行了鉴定，其特征在于，并与传统的SSR检测方法进行比较。发现的最丰富的基序是二核苷酸（38%）和三核苷酸（33%），其次是五核苷酸（16%）和四核苷酸（13%）基序。基序类型、基序长度和重复序列不代表多态性。B的频率。在基因组鸟枪法序列中，估计每4Kb有1个SSR。在一般情况下，平均基序长度和重复数短于以前获得的探针杂交，它们包含了一个更平衡的代表性的SSR基序类型的基因组中，通过识别那些不杂交以及DNA探针。芸苔属植物基因组DNA序列信息是开发大量芸苔属SSR分子标记的重要资源。
The traditional development of simple sequence repeat (SSR) or microsatellite markers by probe hybridization can be time-consuming and requires the use of specialized laboratory equipment. In this study, probe hybridization was circumvented by using sequence information on 3,500 genomic clones mainly from Brassica oleracea to identify di, tri, tetra and penta-nucleotide repeats. A total of 587 primer pairs flanking SSR were developed using this approach. From these, 420 SSR markers amplified DNA in two parental lines of B. rapa (26% were polymorphic) and 523 in two parental lines of B. oleracea (32% were polymorphic). A diverse array of motif types was identified, characterized and compared with traditional SSR detection methods. The most abundant motifs found were di- (38%) and trinucleotides (33%) followed by penta- (16%) and tetranucleotide (13%) motifs. The type of motif class, motif length and repeat were not indicative of polymorphisms. The frequency of B. oleracea SSRs in genomic shotgun sequence was estimated to be 1 every 4 Kb. In general, the average motif length and repeat numbers were shorter than those obtained previously by probe hybridization, and they contained a more balanced representation of SSR motif types in the genome by identifying those that do not hybridize well to DNA probes. Brassica genomic DNA sequence information is a promising resource for developing a large number of SSR molecular markers in Brassica species.