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Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology
Chandra Shekhar Pareek1, Rafał Smoczyński1, Haja N Kadarmideen2
1Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland.
Plos One
|September 9, 2016
Summary
This study developed a breed-specific model to detect single nucleotide polymorphisms (SNPs) in bovine pituitary glands. The findings aid in genomic selection strategies for cattle growth and reproduction traits.
Area of Science:
- Genomics
- Animal Breeding
- Transcriptomics
Background:
- Single nucleotide polymorphisms (SNPs) in candidate genes (CGs) and quantitative trait loci (QTLs) regions are crucial for understanding genomic variations influencing economic traits in cattle.
- Strand-specific RNA-sequencing (RNA-seq) of the bovine pituitary gland transcriptome offers a method for detecting these SNPs.
Purpose of the Study:
- To establish a breed-specific model for detecting SNPs in the pituitary glands of young bulls from Polish Holstein-Friesian (HF), Polish Red, and Hereford breeds.
- To identify genomic variations contributing to economically important traits through SNP analysis.
Main Methods:
- Preparation and sequencing of 18 bovine pituitary gland polyA transcriptome libraries using Illumina NextSeq 500.
- Read alignment using Burrows-Wheeler Aligner (BWA) and construction of breed-specific SNP databases.
- Application of stringent filtering parameters and validation of SNP discoveries using KASP™ SNP genotyping assay.
Main Results:
- Over 113 million raw paired-end reads were obtained, with high mapping percentages for Polish HF (93.04%), Polish Red (94.39%), and Hereford (83.46%) breeds.
- A comprehensive breed-specific SNP database containing 13,775,885 SNPs was constructed, averaging 765,326 SNPs per bull.
- Analysis identified KCNIP4, CCSER1, DPP6, MAP3K5, and GHR as candidate genes with the highest SNP hit loci across all breeds and ages, while CAST showed high SNPs in Polish HF and Hereford breeds.
Conclusions:
- The study successfully developed a breed-specific SNP detection model for bovine pituitary transcriptomes.
- The generated SNP database and identified candidate genes are valuable resources for developing genomic selection strategies for bovine growth and reproduction traits.
- This research contributes to the identification and construction of tissue-specific and breed-specific SNP databases for cattle improvement.
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