Technical note: A comparison of DNA collection methods in cattle and yaks1

Abstract

A variety of biological materials are suitable for the analysis of bovine DNA. The objective of this study was to evaluate the ease of collection, storage, and cost as well as quality and quantity of DNA samples obtained from Bos taurus (European cattle) and Bos grunniens (yak) using 2 different sample types: whole blood sampling and nasal swabs. Hair follicle DNA samples from yaks were also analyzed. Deoxyribonucleic acid samples were collected from 1 herd of Black Angus yearling bulls (n = 166) and 1 herd of yaks (n = 24). A NanoDrop Bioanalyzer ND1000 was used to quantify DNA. To assess DNA purity, absorbance ratios were determined at wavelengths of 260 nm relative to 280 nm and 260 nm relative to 230 nm. Single nucleotide polymorphism genotyping was performed using a competitive allele-specific PCR (KASP) genotyping system and the call rates to 3 specific SNP were compared. Using a commercially available nonautomated ethanol DNA extraction technique, nasal swabs yielded a greater quantity of DNA than blood (P < 0.0001) and a greater quality DNA sample than blood (P < 0.0001). Blood and nasal swab performance in SNP genotyping assays were similar (P = 0.5). The greater expense of nasal swabs was offset by their ease of use: less time, skill, and equipment was needed to obtain a sample and the storage of samples was more convenient (room temperature). In yaks, accessing the coccygeal vein, which is relatively straightforward in cattle, was difficult. Nasal swabbing and hair follicle sampling in yaks was performed relatively easily. Yak hair follicles were a poor source of DNA. In conclusion, DNA collection using nasal swabs was more convenient and provided a greater quantity of DNA and better quality sample than blood collection in both Angus and yak. Notably, yak hair was a poor source of DNA, and yak blood was difficult to obtain.

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions

“…; Neary et al. ). These kits were also the ones giving low DNA yield from the ileal digesta samples.…”

“…; Neary et al. ). However, this was not affecting further DNA usage, as a 1:10 dilution was suitable for successful amplification of the 16S rRNA gene for all DNA extracts using either T‐RFLP or Illumina amplicon sequencing.…”

Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair

“…Tail-hair samples have the least requirements, where no special training or assistants are needed, no collection tools, and minimal camel handling time (leading to fast sample collection), and easy transportation and storage of specimens in envelopes at room temperature (personal observation). These minimal requirements for tail-hair collection makes them more suitable than whole-blood and buccal swabs for establishing a DNA biobank, as recognized for other domesticated animals such as cattle and yaks [36].…”

Novel extraction of high quality genomic DNA from frozen bovine blood samples by using detergent method

“…Few studies have mentioned EDTA vacationers to be the best to store the whole blood samples for long storage in frozen condition (Permenter et al, 2015). The study by Neary et al (2014) reported a lesser amount of yield in the blood sample (11.7±0.7) ng/µl as compared to that of the saliva swabs (574±28.9) ng/µl in European cattle breed (Neary et al, 2014). Some of the authors mentioned using the different kinds of detergents from various manufacturers (Airel, Active wheel, Tide, Henko stain Champion, Rin, and Ezee) to get the better yield of the genomic DNA from goat blood samples (Kumar et al, 2006).…”

“…DNA isolation methods should be ideally is efficient, reliable, quick and reproducible. Whole blood is a vital resource for the isolation of genomic DNA from bovine and yak (Neary et al, 2014). In molecular biology studies, which includes the breed recognition, food nutritional functions and food traceability, genetic difference along with animals, marker-assisted studies of breeding, in genetic hybridization studies requires high-quality genomic DNA for southern blotting test (Murphy et al, 2002).…”