EST-derived microsatellites from Actinidia species and their potential for mapping
EST-derived microsatellites from Actinidia species and their potential for mapping
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DOI：
10.1007/s00122-003-1517-4
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发表时间：
2004-04-01
影响因子：
5.4
通讯作者：
De Silva, HN
中科院分区：
文献类型：
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作者：
Fraser, LG;Harvey, CF;De Silva, HN
为了提高构建猕猴桃属（奇异果）遗传图谱的速度并降低成本，以便用于育种和功能基因组学项目，我们从表达序列标签（EST）中选取微卫星进行采样，以评估其出现频率和多态性水平。我们选择了完美的二核苷酸重复序列作为微卫星，发现它们在所代表基因的5'端和3'端都大量存在。这些微卫星长度各异，大多数是具有(CT)(n)/(GA)(n)模式的重复序列。选取了150个每个都具有10个以上二核苷酸重复单元的微卫星作为可能的标记，当对这些标记进行扩增时，发现93.5%在作图群体中具有多态性且发生分离，其中22.6%扩增出不止一个位点。确定了四种标记类别。完全信息标记占总数的27%，36.2%为雌性信息标记，25.8%为雄性信息标记，10%为部分信息标记。作图群体是二倍体中华猕猴桃种内的杂交群体，亲本是根据果实和植株特性的差异以及地理上的分离来选择的。使用“Joinmap”软件并以3的LOD值进行连锁检测。考虑到样本量较小、连锁群数量（31个）超过了n = 29的染色体数目以及一些标记未被分配到任何组，基于EST的标记在所得连锁群上的分布似乎是随机的。一些扩增出不止一个位点的微卫星标记被定位到不同的连锁群。根据我们在中华猕猴桃中的研究，源自EST的微卫星能够非常迅速且以合理成本提供大量可能的标记。这些标记具有高度多态性，在作图群体中发生分离，并通过提供一些功能信息增加了基因组图谱的价值。
To increase the speed and reduce the cost of constructing a genetic map of Actinidia species (kiwifruit), for use in both breeding and functional genomics programmes, we sampled microsatellites from expressed sequence tags (ESTs) to evaluate their frequency of occurrence and level of polymorphism. Perfect dinucleotide repeats were the microsatellites selected, and these were found to be numerous in both the 5' and 3' ends of the genes represented. The microsatellites were of various lengths, the majority being repeats with the pattern (CT)(n)/(GA)(n). One hundred and fifty microsatellites, each with more than 10 dinucleotide repeat units, were chosen as possible markers, and when these were amplified, 93.5% were found to be polymorphic and segregating in a mapping population, with 22.6% amplifying more than one locus. Four marker categories were identified. Fully informative markers made up 27% of the total, 36.2% were female informative, 25.8% were male informative and 10% partly informative. The mapping population was an intraspecific cross in the diploid species Actinidia chinensis, with parents chosen for their diversity in fruit and plant characteristics, and for their geographical separation. Linkage was tested using the software 'Joinmap' and a LOD value of 3. The distribution of the EST-based markers over the linkage groups obtained appeared to be random, taking into consideration the small sample size, that the number of linkage groups (31) exceeded the chromosome number of n=29, and that a number of markers were not assigned to any group. Some microsatellite markers which amplified more than one locus mapped to separate linkage groups. According to our study in A. chinensis, EST-derived microsatellites give large numbers of possible markers very quickly and at reasonable cost. The markers are highly polymorphic, segregate in the mapping population, and increase the value of the genomic map by providing some functional information.