The effect of DNA quality on the sequencing success of cattle

Abstract

The extraction of amplifiable DNA is a crucial step for genetic analysis of farm animals. The aim of present study was to determine the quality and the quantity of DNA extracted from blood, milk, hair and tissue in cattle. It has been shown that milk and hair samples can be used as a reliable source for obtaining good quality and quantity of DNA ready for the next generation sequencing (NGS). Commercially available kit, with several modifications, was included in the evaluation. Raw milk or milk somatic cell pellet storage under -80 °C or -20 °C has shown to be a reliable procedure for preservation when large number of milk samples were collected at once. The quality (purity) and the quantity of extracted DNA were measured using a nanophotometer. The adequacy of the DNA extract was assessed by estimating average read depth of all captured bases of whole NGS mitogenome sequences. Although DNA extracted from different types of samples was suitable for NGS analysis, hair samples showed the largest variation of DNA quantity, low purity and DNA integrity. Non-invasive sampling methods such as milk and hair collection can be used for dairy cattle while sampling from free-range requires handling, capturing and caution. Milk and hair can be used for obtaining optimal DNA concentrations for NGS analysis.

Keywords

• cattle
• DNA extraction
• NGS
• quality and quantity of DNA