Possibilities of collecting, analyzing and managing a SNP data.

KRUPA, Emil, SCHRÖFFELOVÁ, Daniela, ŽÁKOVÁ, Eliška, NĚMCOVÁ, Lucie, KRUPOVÁ, Zuzana and VRTKOVÁ, Irena. Possibilities of collecting, analyzing and managing a SNP data.. Náš chov, 2019, vol. 79(11), p. 31-34. ISSN 0027-8068.
CathegoryPublication in specialized journals
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The aim of the presented study was to design an optimal system of animal selection, sample collection, sample analysis and to find out the possibilities of using a system for managing a large range of SNP data for the purposes of animal genotyping and subsequent genomic evaluation. The Real SNPs from the already existing system of animal genotyping within the National Program for Pig Breeding – CzePig and simulated SNP were used as data source. Real data represent SNPs obtained from 24 animals by using lllumina PorcineSNP60 v2 BeadChips with declared 64,232 SNPs. The suitability of standard biological sources of DNA was assessed: non-coagulated blood, ear tissue, bristly bulbs, and snout swab. Subsequently, the suitability of selected DNA isolation methods was compared: precipitation method, CHELEX method, silicate column method, magnetosilicon particle method. Animals included in DNA analysis were selected based on their breed and number of offspring evaluated in performance control… Real data were processed using PLINK and R-project commands. The simulated SNPs were generated by using the PLINK program for a total of 20k animals each with 64,232 SNPs (or 10,000 SNPs) in two basic data formats. The bristly bulbs appears to be the most optimal source of samples in terms of ease of collection, non-invasiveness, laboriousness, requirements for preservation and the risk of degradation. Nasal swabs were evaluated as completely unsuitable source for DNA analysis. The DNA isolation method by the magnetosilicon particle method seems to be the most optimal in relation to various DNA sources. The total size of the real data file was 233 MB (64K chip in 24 animals). The simulated data file size was up to 4 GB. The SNPPitit was used for SNP data management. The data storage rate was around 90 million SNPs per second.