Genome-wide investigation of microsatellite polymorphism in coding region of the giant panda (Ailuropoda melanoleuca) genome: a resource for study of phenotype diversity and abnormal traits

Repeat number variations of coding simple sequence repeats (coding SSRs) generate phenotype diversity for environmental adaptation and rapid adaptive evolution. Despite the positive potential of coding SSR mutations, the repeat variations have also been shown to cause hereditary disorders and severe diseases. However, there have been few reports on the analysis of SSR polymorphism in genome-wide coding regions. We identified 1016 coding SSRs, of which 283 SSRs (27.9%) were polymorphic with 2 to 8 alleles, using 33 re-sequenced giant panda genomes. The 283 polymorphic coding SSRs were mapped on 260 genes, which were assigned into 547 GO terms. Functional analysis of 260 genes showed that four significantly enriched pathways: thyroid hormone signaling pathway, pancreatic secretion, gastric acid secretion, and thyroid hormone synthesis, were relevant to digestion and metabolism. The comparison analysis of gene functions exhibited positive regulation of transcription, DNA-templated term (GO:0045893), the poly(A) RNA-binding term (GO:0008270), and zinc ion–binding term (GO:0044822) which were only significantly enriched in genes containing polymorphic coding SSRs. This indicates coding SSR polymorphism may be involved in binding and regulation functions that can affect the expression of their downstream genes and contribute to diverse phenotypes. Our results provide a solid foundation for further study regarding the effect of coding SSR polymorphism on the adaptation, adaptive evolution, and abnormal traits of the giant panda.