Volume reduction and automation of DNAprep libraries for low pass sequencing
Résumé
To characterize a population's haplotypic variability, low pass sequencing represents an interesting alternative to genotyping DNA-microarrays. Although this new technology is also costly, it offers greater precision of genetic information. We have therefore reduced reagent and DNA volumes by automating our Illumina DNA Prep library preparation protocol with the Mosquito HV (SPT LabTech, UK). For this purpose, we intend to evaluate this strategy for the porcine species. We used a family F2 protocol based on crossbreeds between Large White (LW) and Meishan (MS) individuals. It comprises around 1000 pigs, including 12 F0 (6 LW and 6 MS), 30 F1 (6 males and 24 females) and 1000 F2. In addition to the evaluation of bioinformatic phasing methods for the imputation and reconstruction of haplotypes. The exploitation of these data will enable the precise characterization of recombination sites. This will provide an understanding of the reasons why a large region of the X chromosome recombines or not. The SeqOccIn porcine pilot project gave us the opportunity to (i) automate the DNA prep protocol to significantly reduce volumes with very good results and (ii) generate good quality low pass sequencing data for genotype imputation (validated by Mendelian compatibility)
Domaines
Sciences de l'environnement| Origine | Fichiers produits par l'(les) auteur(s) |
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