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http://dx.doi.org/10.5713/ajas.15.0172

SNP Discovery from Transcriptome of Cashmere Goat Skin  

Wang, Lele (College of Animal Science, Inner Mongolia Agricultural University)
Zhang, Yanjun (College of Animal Science, Inner Mongolia Agricultural University)
Zhao, Meng (College of Animal Science, Inner Mongolia Agricultural University)
Wang, Ruijun (College of Animal Science, Inner Mongolia Agricultural University)
Su, Rui (College of Animal Science, Inner Mongolia Agricultural University)
Li, Jinquan (College of Animal Science, Inner Mongolia Agricultural University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.28, no.9, 2015 , pp. 1235-1243 More about this Journal
Abstract
The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.
Keywords
Single Nucleotide Polymorphism; Transcriptome; Goats; Capra hircus; RNA Sequencing;
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