Genomic data have the potential to contribute valuable information for animal selection and are being increasingly used in the genetic evaluation of animals and design of genetic improvement programs. Single Nucleotide Polymorphisms (SNPs) are the most abundant source of genetic variation. Thanks to the availability of very high-throughput genotyping technologies, SNPs have become the genetic markers of choice for high resolution genetics and genome-wide association studies. The aim of this study was the development and the technological transfer of a high-throughput, easy-to-use and inexpensive DNA chip technology for the SNP bovine genotyping. Therefore, the first step of this study was to define a 50 SNP panel to genotype bovine polymorphisms located in candidate genes involved in cow milk protein and fat biosynthesis in order to identify those associated with milk performance traits (daily milk yield, fat yield, fat content, protein yield and protein content) and genes responsible for genetic disease susceptibility in Italian Friesian breed. Starting with data obtained from NCBI (www.ncbi.nlm.nih.gov/entrez/query.fgci) we identified different genes potentially affecting milk quality and production such as CSN1S1, CNS2, CNS3 (?s1-casein, ?-casein and ?-casein, respectively), SCD (Stearoil Co-A desaturase), DGAT1 (acylCoA:diacylglicerol acyltransferase 1), PROP1 bovin (PROP paired-like homeobox 1), LEP (leptin), PRL (prolactin), FASN (fatty acid synthase), CXCR1 (interleukin 8 receptor, alpha), ABCG2 (ATP-binding cassette, sub-family G (WHITE), member 2), POU1F1 (POU class 1 homeobox 1), STAT5 (signal transducer and activator of transcription 5A) and LTF (lactoferrin). For each gene, using the NCBI dbSNP collection (http://www.ncbi.nlm.nih.gov/sites/entrez) and The Bovine SNP Retriever (http://www.itb.cnr.it/ptp/bovine_snp_retriever/), a user-friendly tool for bovine SNP retrieval, annotations indicating the gene position on the chromosome, the type of mutation (missense or silent), the SNP location within the gene (intron, exon, 5'- or 3'-flanking regions), the association with a specific QTL trait, the SNP validation state, allelic frequencies data and the correlated breed were collected. The SNP panel was created choosing validated SNPs located in exons, causative for any phenotypic variance and, where possible, with allelic frequencies data. The identified SNP will be validated with one hundred not-related Italian Friesian, in order to obtain a final panel of 50 SNPs.
Development of a SNP panel for bovine genotyping
Paola Cremonesi;Stefania Chessa
2009
Abstract
Genomic data have the potential to contribute valuable information for animal selection and are being increasingly used in the genetic evaluation of animals and design of genetic improvement programs. Single Nucleotide Polymorphisms (SNPs) are the most abundant source of genetic variation. Thanks to the availability of very high-throughput genotyping technologies, SNPs have become the genetic markers of choice for high resolution genetics and genome-wide association studies. The aim of this study was the development and the technological transfer of a high-throughput, easy-to-use and inexpensive DNA chip technology for the SNP bovine genotyping. Therefore, the first step of this study was to define a 50 SNP panel to genotype bovine polymorphisms located in candidate genes involved in cow milk protein and fat biosynthesis in order to identify those associated with milk performance traits (daily milk yield, fat yield, fat content, protein yield and protein content) and genes responsible for genetic disease susceptibility in Italian Friesian breed. Starting with data obtained from NCBI (www.ncbi.nlm.nih.gov/entrez/query.fgci) we identified different genes potentially affecting milk quality and production such as CSN1S1, CNS2, CNS3 (?s1-casein, ?-casein and ?-casein, respectively), SCD (Stearoil Co-A desaturase), DGAT1 (acylCoA:diacylglicerol acyltransferase 1), PROP1 bovin (PROP paired-like homeobox 1), LEP (leptin), PRL (prolactin), FASN (fatty acid synthase), CXCR1 (interleukin 8 receptor, alpha), ABCG2 (ATP-binding cassette, sub-family G (WHITE), member 2), POU1F1 (POU class 1 homeobox 1), STAT5 (signal transducer and activator of transcription 5A) and LTF (lactoferrin). For each gene, using the NCBI dbSNP collection (http://www.ncbi.nlm.nih.gov/sites/entrez) and The Bovine SNP Retriever (http://www.itb.cnr.it/ptp/bovine_snp_retriever/), a user-friendly tool for bovine SNP retrieval, annotations indicating the gene position on the chromosome, the type of mutation (missense or silent), the SNP location within the gene (intron, exon, 5'- or 3'-flanking regions), the association with a specific QTL trait, the SNP validation state, allelic frequencies data and the correlated breed were collected. The SNP panel was created choosing validated SNPs located in exons, causative for any phenotypic variance and, where possible, with allelic frequencies data. The identified SNP will be validated with one hundred not-related Italian Friesian, in order to obtain a final panel of 50 SNPs.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
