Genetic variation and balancing selection at MHC class II exon 2 in cultured stocks and wild populations of orange-spotted grouper (Epinephelus coioides)

Abstract

ABSTRACT. Major histocompatibility complex (MHC) molecules play vital roles in triggering adaptive immune responses and are considered the most variable molecules in vertebrates. Recently, many studies have focused on the polymorphism and evolution mode of MHC in both model and non-model organisms. Here, we analyzed the MHC class II exon 2-encoding β chain in comparison with the mitochondrial Cytb gene and our previously published microsatellite data set in three cultured stocks and four wild populations of the orange-spotted grouper (Epinephelus coioides) in order to investigate its genetic variation and mechanism of evolution. We detected one to four alleles in one individual, suggesting that at least two loci exist in the orange-spotted grouper, as well as a particularly high level of allelic diversity at the MHC loci. Furthermore, the cultured stocks exhibited reduced allelic diversity compared to the wild counterparts. We found evidence of balancing selection at MHC class II exon 2, and codon sites under positive selection were largely correspondent to the proteinbinding region. In addition, MHC class II exon 2 revealed significant differences between population differentiation patterns from the neutral mitochondrial Cytb and microsatellites, which may indicate local adaptation at MHC loci in orange-spotted grouper originating from the South China Sea and Southeast Asia.

Transcriptome Analysis of the Trachinotus ovatus: Identification of Reproduction, Growth and Immune-Related Genes and Microsatellite Markers

“…Aquaculture practices have been found to reduce genetic variability in hatchery-reared stocks, which may result in loss of disease resistance [53] – [54] . In recent years, frequent outbreaks of infectious diseases in fish farming have become a great threat to the Trachinotus ovatus industry [5] – [6] .…”

Divergence and polymorphism analysis of IGF1Ra and IGF1Rb from orange-spotted grouper, Epinephelus coioides (Hamilton)

“…Survey and utilization of the germplasm resource of this species is at the preliminary stage. Although this species is widely distributed in the open sea, resource investigations are limited within small regions, mainly in Southeast Asia (Antoro et al, 2006;Wang et al, 2009;Meng et al, 2012). In recent years, next generation sequencing (NGS) has revolutionized nucleotide sequencing (Helyar et al, 2011).…”