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

Abstract

Camels are livestock with unique adaptations to hot-arid regions. To effectively study camel traits, a biobank of camel DNA specimens with associated biological information is needed. We examined whole-blood, saliva (buccal swabs), and tail-hair follicle samples to determine which is the best source for establishing a DNA biobank. We inspected five amounts of each of whole-blood, buccal swabs, and tail-hair follicles in nine camels, both qualitatively via gel electrophoresis and quantitatively using a NanoDrop spectrophotometer. We also tested the effects of long term-storage on the quality and quantity of DNA, and measured the rate of degradation, by analyzing three buccal swab samples and 30 tail-hair follicles over a period of nine months. Good quality DNA, in the form of visible large size DNA bands, was extracted from all three sources, for all five amounts. The five volumes of whole-blood samples (20-100μl) provided ~0.4-3.6 μg, the five quantities of buccal swabs (1-5) produced ~0.1-12 μg, while the five amounts of tail-hair follicles (10-50) resulted in ~0.7-25 μg. No differences in the rate of degradation of buccal swab and tail-hair follicle DNA were detected, but there was clearly greater deterioration in the quality of DNA extracted from buccal swabs when compared to tail-hair follicles. We recommend using tail-hair samples for camel DNA biobanking, because it resulted in both an adequate quality and quantity of DNA, along with its ease of collection, transportation, and storage. Compared to its success in studies of other domesticated animals, we anticipate that using ~50 tail-hair follicles will provide sufficient DNA for sequencing or SNP genotyping.

Fig 1. The three sources, and the five quantities, of the camel DNA samples used in the study.

DNA extractions were performed on the five different quantities, of each one of the three DNA sources.

Fig 2. Quantity and purity of camel DNA extracted from whole-blood, saliva, and tail-hair follicles.

(a-c) DNA quantity (μg) on the x-axis and 260/280 nm ratio on the y-axis from whole-blood, buccal swabs, and tail-hair follicles, respectively. Each circle corresponds to a measurement (DNA quantity and 260/280 nm ratio) from the first elution (E1 = 100μl) and the size of the circle represents the different amounts of starting material (blood = 20, 40, 60, 80, 100μl, saliva = 1, 2, 3, 4, 5 swabs, hair = 10, 20, 30, 40, 50 follicles). Dashed horizontal lines are the mean 260/280 nm ratio.

Fig 3. Electrophoretic analysis of the degradation of DNA extracted from buccal swabs and tail-hair follicles over a 9-month period.

(a) 1.5% agarose gels of DNA extracted from three camel buccal swabs every three months, for a period of 9 months. (b) 1.5% agarose gels of DNA extracted from thirty camel tail-hair follicles every three months, for a period of 9 months. C1-C3: Majaheem, C4-C6: Sofor, C7-9: Waddah. Each buccal swab and tail-hair follicle quantity of each of the nine camels (C1-9) was extracted three times (replicas). The DNA in the gels is that of the first elution (E1). The two ladders used in the gels are 100 bp (left side) and lambda-HindIII molecular markers (right side). The ladders in the bottom gels are in reversed positions. Note: the six months gels contain marks but the presence and absence of large size DNA bands and smears are visible for comparison.

Fig 4. Quantity and purity of camel DNA extracted from saliva (buccal swabs) and tail-hair follicles over a nine-month period.

DNA quantity (μg) on the x-axis and 260/280nm ratio on the y-axis over a nine-month period (0, 3, 6, and 9 month) extraction times, from (a) buccal swabs and (b) tail-hair follicles. Each circle corresponds to a single measurement (DNA quantity and 260/280nm ratio) from the first elution (100μl). The dashed horizontal line is the mean 260/280nm ratio and the dashed vertical line is the mean of the DNA quantities (μg).

Fig 5. Scatterplot of time vs. extracted DNA amount (μg).

Samples are separated by DNA source (saliva vs. tail-hair). The amount of DNA is that obtained from the first and second elutions combined (total). Best-fit lines are also shown for each DNA source.