Functional Genomics of Free-ranging Wildlife
Free-ranging wild species adapts to the varying environment via their phenotypic diversity as determined by genomic diversity. Understanding the genetic basis of phenotypic variation is of tremendous importance for uncovering the mechanisms of animals’ adaptation and diversity. In particular, coat colour and pattern are prominent morphological features in mammals and play an essential role in adaptation and survival.
Tigers have intrigued human society for thousands of years, so as the elusive white tiger, a rare variant characterized by dark stripes on a white fur background. White tigers are occasionally observed in wilderness on the Indian subcontinent, with the oldest record dating back to the 1500s. In 1951, a male white tiger named Mohan was captured in Rewa, now part of Madhya Pradesh in India, from which numerous white tigers were bred for captivity around the world. Previous studies have proved that the white coat is inherited as a recessive monogenetic trait, but the precise genetic mechanism remains unknown until now.
We collaborate with Chimelong Wildlife Safari, Guangzhou, China, and use the tiger as a model to decode natural genetic polymorphisms in wildlife, with state-of-art high-throughput genome sequencing platform. We employed a pedigree-based genome-wide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADSeq), followed by whole-genome sequencing (WGS), to map the Mendelian trait. Our results revealed the causative mutation of white tiger to be a single amino acid change (A477V) in transporter protein SLC45A2, the polymorphisms of which are associated with skin and hair pigmentation in several species, including the human. Protein structural homology modeling further suggested a functional effect of the A477V substitution on SLC45A2 and the melanin synthesis process. Since the SLC45A2 A477V substitution only affects the white tiger’s pigmentation and does not cause severe physiological defects, we argue that the white tiger morph is a naturally occurring and viable feature of the genetic diversity in tigers (Xu et al. 2013. Current Biology).
We are currently working on subsequent functional studies of the mutation and another genomic project on identifying other tiger coat color variations, e.g. “golden tiger” and “snow tiger”.
- Genomic studies of the domestic cat (Felis catus)
- Conservation genomics of endangered wildlife species
- Field ecology and landscape conservation of the tiger