Characterization of tomato SSR markers developed using BAC-end and cDNA sequences from genome databases
Characterization of tomato SSR markers developed using BAC-end and cDNA sequences from genome databases
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DOI：
10.1007/s11032-009-9265-z
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发表时间：
2009-05-01
影响因子：
3.1
通讯作者：
Fukuoka, Hiroyuki
中科院分区：
文献类型：
--
作者：
Ohyama, Akio;Asamizu, Erika;Fukuoka, Hiroyuki
我们开发了近700个非冗余的2-或3-碱基的简单序列重复（SSR）标记，从番茄从开放基因组数据库中获得的序列数据。在各种类型的核心基序中，AT在来自cDNA末端的SSR（相似于53%）和细菌人工染色体（BAC）末端的SSR（相似于72%）中最丰富。在至少一对供试的6个品种（系）中，多态性等位基因的检出率（杂合度值; Hv）与所有显示多态性的标记的核心基序重复数之间均呈正相关（r = 0.566**）。BAC端SSR标记的平均Hv（0.5左右）高于cDNA端SSR标记的平均Hv（0.3左右）。BAC末端SSR的这些特征对于利用近缘品种和品系进行遗传研究是有用的。然而，BAC-末端衍生的SSR倾向于聚集在着丝粒区域（类似于80%）。本文讨论了番茄高密度连锁图的构建方案。
We developed nearly 700 non-redundant 2- or 3-base simple sequence repeat (SSR) markers from tomato using sequence data obtained from open genome databases. Among various types of core motifs, AT was most abundant in SSRs derived from cDNAs (similar to 53%) and bacterial artificial chromosome (BAC) ends (similar to 72%). There was a positive correlation between the rate of detection of polymorphic alleles (heterozygosity value; Hv) and the repeat number of the core motif in all markers showing polymorphisms among at least one pair of six cultivars or lines tested (r = 0.566**). The average Hv of BAC-end-derived SSR markers (similar to 0.5) was higher than that of cDNA-derived markers (similar to 0.3). These characteristics of BAC-end-derived SSRs are useful for genetic studies using closely related cultivars and lines. However, BAC-end-derived SSRs tended to cluster in centromeric regions (similar to 80%). A scheme for the construction of a high-density linkage map of tomato is discussed.