Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus)

Abstract

Cit a tio n fo r fin al p u blis h e d ve r sio n: M a gliolo, Mi c h ell e, P r o s t, S t ef a n, O r oz c o Te r We n g el, P a blo, Kro pff, An n a S., Kotz e, Antoi n e t t e , G r o bl e m , J. P a ul a n d D alt o n, D e si r e e Le e 2 0 2 1 . U nloc ki n g t h e p o t e n ti al of a v alid a t e d si n gl e n u cl e o ti d e p oly m o r p hi s m a r r a y fo r g e n o mi c m o ni t o ri n g of t r a d e in c h e e t a h s (Acino nyx ju b a t u s). M ol e c ul a r Biolo gy R e p o r t s 4 8 , p p .

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

“…We generated genome‐wide data for all subspecies, which can function as a baseline for the development of reduced SNP sets, for example, for genotyping using SNP arrays or real‐time PCR, enabling more cost‐effective and large‐scale genetic monitoring. We recently developed a SNP array for A. j. jubatus to monitor its legal and illegal trade (Magliolo et al, 2021). However, this approach was only based on individuals from one subspecies.…”

A systematic review of DNA‐based methods in authentication of game and less common meat species

“…Deer antlers, elephant ivory, shark fins, rhino horns, sea turtles, and cheetahs (Cardeñosa et al., 2017; Ewart et al., 2018; Jiang et al., 2018; Kitpipit et al., 2016; Magliolo et al., 2021; Pertiwi et al., 2020) are some animals and animal products illegally exploited in the literature reviewed. Samples for molecular analysis in wildlife preservation testing differ slightly from the authentication of game meat products.…”

Simulated genetic efficacy of metapopulation management and conservation value of captive reintroductions in a rapidly declining felid

“…A validated 240 SNP array for cheetah was used to genotype all samples (Magliolo et al ., 2021). DNA extracts and TaqMan OpenArray MasterMix were added in equal volumes to 96‐well plates and transferred to 384‐well plates, where both steps were followed by centrifugation at 4,100 rpm for 1 minute.…”

“…Amongst relatedness indices, this estimate shows low sensitivity to sampling error (introduced by estimating population allele frequencies) and shows a low sampling variance (Blouin, 2003). This relatedness coefficient ( r w ) ranges from 0 to 1, where 0 indicates that candidate pairs are unrelated, whilst 0.5 indicates highly related pairs (e.g., parent‐offspring or full‐sibling), however, such estimates can range from 0.37 to 0.61 (Visscher et al ., 2006), thus cheetah of known relation we used to ground‐truth r w variability (Magliolo et al ., 2021).…”