Methylation‐based markers for the estimation of age in African cheetah, Acinonyx jubatus

• Published in: Molecular ecology resources Vol. 24; no. 4; pp. e13940 - n/a
• Main Authors: Le Clercq, Louis‐Stéphane, Kotzé, Antoinette, Grobler, J. Paul, Dalton, Desiré L.
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.05.2024; Wiley/Blackwell
• Subjects: Acinonyx - genetics; Acinonyx jubatus; African; Age; Age determination; age estimation; Aging; Animal genetics; Animals; Animals, Wild - genetics; Arrays; Base Sequence; Biodiversity and Ecology; biological clocks; biomarker; Biomarkers; cheetah; Chronology; Conservation; Correlation analysis; DNA methylation; Environmental Sciences; Epigenetics; Genes; Genetics; Humans; Life Sciences; mass array; Methylation; Morbidity; Nucleotide sequence; Senescence; Wildlife; Wildlife conservation; Year class; biological clocks; mass array; age estimation; genes; methylation; cheetah; Acinonyx jubatus; biomarker; age; African
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.13940

Age is a key demographic in conservation where age classes show differences in important population metrics such as morbidity and mortality. Several traits, including reproductive potential, also show senescence with ageing. Thus, the ability to estimate age of individuals in a population is critical in understanding the current structure as well as their future fitness. Many methods exist to determine age in wildlife, with most using morphological features that show inherent variability with age. These methods require significant expertise and become less accurate in adult age classes, often the most critical groups to model. Molecular methods have been applied to measuring key population attributes, and more recently epigenetic attributes such as methylation have been explored as biomarkers for age. There are, however, several factors such as permits, sample sovereignty, and costs that may preclude the use of extant methods in a conservation context. This study explored the utility of measuring age‐related changes in methylation in candidate genes using mass array technology. Novel methods are described for using gene orthologues to identify and assay regions for differential methylation. To illustrate the potential application, African cheetah was used as a case study. Correlation analyses identified six methylation sites with an age relationship, used to develop a model with sufficient predictive power for most conservation contexts. This model was more accurate than previous attempts using PCR and performed similarly to candidate gene studies in other mammal species. Mass array presents an accurate and cost‐effective method for age estimation in wildlife of conservation concern. Ouderdom is ‘n sluitsteen kenmerk in dier bewaring waar ouderdoms klasse verskille toon in belangrike populasie maatstawwe soos morbiditeit en mortaliteit. Verskeie eienskappe, soos voortplantings potensiaal, toon ook aansienlike verandering met veroudering. Dus is die vermoë om ouderdom te bepaal vir individue binne ‘n populasie krities tot die ontleding van huidige struktuur en toekomstige welstand. Verskeie metodes bestaan reeds vir ouderdom bepaling waarvan meeste gebruik maak van morfologiese kenmerke wat voorspelbare verandering toon met ouderdom. Hierdie metode vereis egter merkwaardige kennis en word minder akkuraat in volwassene klasse wat die mees krities is om te bepaal. Molekulêre metodes word reeds aangewend om kern populasie eienskappe te bepaal en meer onlangs is epigenetiese eienskappe soos metilering ondersoek as ‘n biologiese merker vir ouderdom. Daar is egter verskeie faktore soos permitte, monster eienaarskap, en kostes wat die toepassing van huidige metilering metodes in ‘n bewaring konteks mag inperk. Die huidige studie ondersoek die gebruiklikheid van ouderdom verwante verandering in metilering, soos gemeet deur massa‐skikking tegnologie, in kandidaat gene. Nuwe metodiek word beskryf vir die gebruik van ortologiese gene om teikens te identifiseer en skerm vir differensiële metilering. Om die spesifieke toepassing te illustreer is die Afrika jagluiperd as gevallestudie gebruik. Korrelasie analise het ses gemetileerde teikens ïdentifiseer met ‘n ouderdoms verwante profiel wat ingesluit is in die ontwikkeling van ‘n model vir ouderdom bepaling met genoegsame akkuraatheid vir meeste bewaring kontekste. Die model was meer akkuraat as voormalige proewe met PKR en het soortgelyk gevaar as ander kandidaat geen studies in verskeie soogdiere. Massa‐skikking bied dus ‘n akkurate en bekostigbare metode om ouderdom te bepaal in wilde diere van belang vir bewaring.