Zhang Jin, Ma Wenge, Song Xiaomin, Lin Qiaohong, Gui Jian-Fang, Mei Jie
Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
Molecules. 2014 Oct 13;19(10):16402-15. doi: 10.3390/molecules191016402.
Yellow catfish (Pelteobagrus fulvidraco) is one of the most important freshwater fish due to its delicious flesh and high nutritional value. However, lack of sufficient simple sequence repeat (SSR) markers has hampered the progress of genetic selection breeding and molecular research for yellow catfish. To this end, we aimed to develop and characterize polymorphic expressed sequence tag (EST)-SSRs from the 454 pyrosequencing transcriptome of yellow catfish. Totally, 82,794 potential EST-SSR markers were identified and distributed in the coding and non-coding regions. Di-nucleotide (53,933) is the most abundant motif type, and AC/GT, AAT/ATT, AAAT/ATTT are respective the most frequent di-, tri-, tetra-nucleotide repeats. We designed primer pairs for all of the identified EST-SSRs and randomly selected 300 of these pairs for further validation. Finally, 263 primer pairs were successfully amplified and 57 primer pairs were found to be consistently polymorphic when four populations of 48 individuals were tested. The number of alleles for the 57 loci ranged from 2 to 17, with an average of 8.23. The observed heterozygosity (HO), expected heterozygosity (HE), polymorphism information content (PIC) and fixation index (fis) values ranged from 0.04 to 1.00, 0.12 to 0.92, 0.12 to 0.91 and -0.83 to 0.93, respectively. These EST-SSR markers generated in this study could greatly facilitate future studies of genetic diversity and molecular breeding in yellow catfish.
黄颡鱼（Pelteobagrus fulvidraco）因其肉质鲜美、营养价值高，是最重要的淡水鱼之一。然而，缺乏足够的简单序列重复（SSR）标记阻碍了黄颡鱼遗传选育和分子研究的进展。为此，我们旨在从黄颡鱼的454焦磷酸测序转录组中开发和鉴定多态性表达序列标签（EST）-SSR。总共鉴定出82,794个潜在的EST-SSR标记，并分布在编码区和非编码区。二核苷酸（53,933）是最丰富的基序类型，AC/GT、AAT/ATT、AAAT/ATTT分别是最常见的二、三、四核苷酸重复。我们为所有鉴定出的EST-SSR设计了引物对，并随机选择其中300对进行进一步验证。最后，当对4个群体共48个个体进行测试时，成功扩增出263对引物，发现57对引物具有一致的多态性。57个位点的等位基因数从2到17不等，平均为8.23。观察到的杂合度（HO）、期望杂合度（HE）、多态性信息含量（PIC）和固定指数（fis）值分别为0.04至1.00、0.12至0.92、0.12至0.91和-0.83至0.93。本研究中产生的这些EST-SSR标记可极大地促进未来黄颡鱼遗传多样性和分子育种的研究。
