Bakhtiarizadeh M R, Arefnejad B, Ebrahimie E, Ebrahimi M
Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Tehran, Iran.
Genet Mol Res. 2012 May 21;11(2):1558-74. doi: 10.4238/2012.May.21.12.
Many years of domestication and breeding have given rise to the wide range of chicken breeds that exist today; however, an increasing number of local chicken breeds are under threat of extinction. A comprehensive characterization of chicken markers (especially type I markers) is needed to monitor and conserve genetic diversity in this species. The explosion of genomics and functional genomics information in recent years has opened new possibilities for the generation of molecular markers. We analyzed a large number of expressed sequence tags (ESTs) to test the possibility of using EST-derived microsatellite markers for investigating the Gallus gallus genome. Chromosomal locations for the majority of these SSRs were predicted. Of the 31,576 unigenes assembled from the 544,150 redundant EST sequences, 1757 SSR markers were discovered on 1544 ESTs, using the SSRLocator software, with an average density of 28.7 kb per SSR. The dimer motifs were the most frequent (46.38%), followed by trimeric (38.58%), tetrameric (10.19%), pentameric (4.5%), and hexameric (<1%) markers. Different from the case for cattle and sheep, AT/TA was the most abundant dimeric repeat, accounting for 41.71% of all dimeric repeats in the chicken ESTs. The EST-SSR distribution was not uniform among the chromosomes; the majority of the EST-SSRs were located on chromosomes GGA2 and GGA10. We found that most of the EST-SSRs are involved in positive regulation of cellular and metabolic processes. This is the first time that EST sequences have been mined to find chicken microsatellites. On average, 3.8% of the G. gallus UniGene sequences could be exploited for development of EST-SSRs, indicating a good source for molecular markers as well as for functional genome analysis.
多年的驯化和选育造就了如今种类繁多的鸡品种；然而，越来越多的地方鸡品种正面临灭绝的威胁。需要对鸡的标记（尤其是I型标记）进行全面表征，以监测和保护该物种的遗传多样性。近年来基因组学和功能基因组学信息的爆炸式增长为分子标记的产生开辟了新的可能性。我们分析了大量表达序列标签（EST），以测试使用EST衍生的微卫星标记研究原鸡基因组的可能性。预测了这些微卫星序列中大多数的染色体位置。利用SSRLocator软件，从544,150条冗余EST序列组装的31,576个单基因中，在1544个EST上发现了1757个SSR标记，平均每个SSR的密度为28.7 kb。二聚体基序最为常见（46.38%），其次是三聚体（38.58%）、四聚体（10.19%）、五聚体（4.5%）和六聚体（<1%）标记。与牛和羊的情况不同，AT/TA是鸡EST中最丰富的二聚体重复序列，占所有二聚体重复序列的41.71%。EST-SSR在染色体间的分布并不均匀；大多数EST-SSR位于GGA2和GGA10染色体上。我们发现大多数EST-SSR参与细胞和代谢过程的正调控。这是首次挖掘EST序列来寻找鸡微卫星。平均而言，3.8%的原鸡单基因序列可用于开发EST-SSR，这表明其是分子标记以及功能基因组分析的良好来源。
