Genetic Diversity Analysis of Wild and Artificially Bred Blue Populations in Symphysodon aequifasciatus

Abstract

【Objective】The study was conducted to investigate the genetic diversity of Symphysodon aequifasciatus, analyze the kinship and the genetic differences of a wild population and two artificially bred blue populations, identify candidate genomic regions and loci associated with body color, and provide references for the formulation of classification system of discus fish.【Method】Whole-genome resequencing was conducted on 9 individuals from the wild population (WF), 8 individuals from the solid blue population (BF) and 10 individuals from the albino blue population (ABF), respectively. Single nucleotide polymorphism (SNP) loci were obtained to calculate population genetic diversity indices, analyze population genetic structure, and perform selective sweep analysis between populations. The candidate SNPs were validated by considering SNP annotation and mutation rates combined with PCR and Sanger sequencing.【Result】A total of 1 360 293 SNPs are identified among the 3 Symphysodon aequifasciatus populations. Genetic diversity, as measured by PIC, Pi, Ho, and He, indicates a decreasing trend from the wild population to the solid blue and albino blue populations, with low heterozygosity in the selected populations. Phylogenetic tree, population structure analysis, and principal component analysis of polymorphic loci all indicate that the three populations are independent of each other and cluster within themselves. Linkage disequilibrium decay analysis indicates that the albino blue population is under significant selection pressure, followed by the solid blue population. The result of population selective sweep based on the population differentiation index (FST) and nucleotide polymorphism (Pi) reveals strong selection signals in large regions of chromosomes 3, 12, 13, 18, and 20 in the solid blue population and chromosomes 1, 16, 18, and 19 in the albino blue population. Thirteen and nine candidate SNPs are identified in the solid blue and albino blue populations, respectively.【Conclusion】The genetic diversity of the 3 Symphysodon aequifasciatus populations is relatively low, and the genetic relationships are consistent with the process of artificial breeding. USP43, FGFR2, DENND4, and MLL1 genes may be closely related to the body color formation of Symphysodon aequifasciatus.

Keywords

• symphysodon aequifasciatus
• population genetics
• genetic diversity
• single nucleotide polymorphism (snp)
• selective sweep analysis