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Abstract
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Article Information:
Identification of SNPs in Goats (Capra hircus) using RNA-Seq Analysis
Upasna Sharma, Priyanka Banerjee, Jyoti Joshi and Ramesh Kumar vijh
Corresponding Author: Ramesh Kumar Vijh
Submitted: June 19, 2012
Accepted: July 10, 2012
Published: August 20, 2012 |
Abstract:
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Single Nucleotide Polymorphisms (SNPs) have become the marker of choice for genome-wide
association studies. In order to provide the best genome coverage for the analysis of performance and production
traits, a large number of relatively evenly distributed SNPs are needed. Gene-associated SNPs may fulfill these
requirements of large numbers and genome wide distribution. In addition, gene-associated SNPs could themselves
be causative SNPs for traits. The main objective of our work was to identify large numbers of gene-associated SNPs
using high-throughput next generation sequencing. Transcriptome sequencing was conducted on 2 tissues viz. liver
and kidney for 5 breeds of goat (Kanniadu, Osmanabadi, Black Bengal, Changthangi and Sirohi) using Illumina next
generation sequencing technology. Approximately 46.4 million reads for Black Bengal, 61.9 from Kanniadu, 58.2
from Changthangi, 47.3 from Osmanabadi, 73.2 from Sirohi were obtained by sequencing gene transcripts derived
from kidney while 37, 27.2, 19.4, 56.9 and 80.7 million reads were obtained by gene transcripts derived from liver.
The analysis of total number of SNPs in liver and kidney revealed that out of a total of 68597 SNPs in liver, the total
number of transversions was 21300 and the number of transitions was 47297. A total of 1574 SNPs of liver were
complex. Similarly for kidney the total number of 72047 SNPs were categorised into 22774 transversions and 49273
transitions. The total number of complex SNPs in kidney was 1597. The number of transitions is more than double
the number of transversions in both the tissues. Further analysis of transversion revealed a preponderance of
cytosine and guanine change compared to other nucleotides. 12863 and 11319 transversions out of 21300 and 22774
transversions respectively for liver and kidney revealed this bias. When multiple individuals with different genetic
backgrounds were used, RNA-Seq was very effective for the identification of SNPs. The SNPs identified in this
report provides a much needed resource for genetic studies in goat and shall contribute to the development of a highdensity
SNP array. Validation and testing of these SNPs using SNP arrays will form the material basis for genome
association studies and whole genome-based selection in goats.
Key words: Capra hircus , transcriptome, RNA-Seq, Single nucleotide polymorphism, , ,
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Cite this Reference:
Upasna Sharma, Priyanka Banerjee, Jyoti Joshi and Ramesh Kumar vijh, . Identification of SNPs in Goats (Capra hircus) using RNA-Seq Analysis. International Journal of Animal and Veterinary Advances, (4): 272-283.
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ISSN (Online): 2041-2908
ISSN (Print): 2041-2894 |
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