Analysis On Genetic Diversity And Body Color Selection Signal Of Wild And Artificially Breeding Blue Discus Fish Population Based On Whole Genome Sequencing

Symphysodon spp.,commonly known as the discus fish,is a popular ornamental fish in the Cichlidae family.After years of hybridization and selective breeding,numerous artificial fish with bright colors and intricate patterns have been successfully cultivated.To produce new strains with specific morphological feathers,multiple generations of artificial breeding involving hybridization,backcrossing,and inbreeding have been carried out on discus fish.However,due to the lack of standardized records on the genetic origins of most strains,classification based solely on their diverse morphological characteristics is challenging.Therefore,it is crucial to understand the phylogenetic relationships among existing strains and use molecular genetics for scientific classification to maintain the genetic stability of popular strains and develop rational breeding programs.Our team obtained a high-quality genome sequences assembled into chromosomes of discus fish,then conducted a whole-genome resequencing to analyze the genetic diversity and selection signals related to the formation of blue body color in both wild and artificially breeding discus fish.To begin with,we conducted whole-genome resequencing on 9 wild discus fish,8 solid blue discus fish,and 10 albino blue discus fish,using a second-generation highthroughput sequencing technology.The obtained sequencing data amounted 253.029 Gb,out of which 242.538 Gb was considered clean data,with Q20 greater than 96.84%and Q30 greater than 92.21%.The GC content ranged between 42.21% to 44.64%,indicating normal sequencing quality.We observed an average alignment rate of 99.04%to the reference genome,and an average sequencing depth of 8.24 X.From our analysis,we detected a total of 3,601,828 Single Nucleotide Polymorphism(SNP)loci,out of which we selected and filtered 1,360,293 high-quality SNPs for further analysis.Afterwards,we explored the population genetic diversity of discus fish and analyzed the genetic relationships and differences among the wild type and two artificially bred blue populations.We utilized four SNP-based genetic diversity indicators,including polymorphic information content(PIC),nucleotide diversity(Pi),expected heterozygosity(He),and observed heterozygosity(Ho).The PIC values for all three populations were moderate to low,while Pi,He,and Ho demonstrated a decreasing trend in genetic diversity from the wild type to the solid blue and albino blue populations.The two artificially bred populations displayed low heterozygosity,which is consistent with their breeding history.The outcomes of individual phylogenetic trees,population structure analysis,and principal component analysis validated one another,demonstrating that the genetic profiles of the three populations were consistent with their breeding history,with distinct independent clusters and clear internal aggregation.The linkage disequilibrium decay analysis revealed that the albino blue population was under significant selection pressure,followed by the solid blue population.Finally,we calculated the population differentiation index(Fst)and nucleotide polymorphism(Pi)for the wild type,solid blue,and albino blue populations based on SNP data.We used a sliding window approach to analyze signals of population selection and performed Fst&Pi selective elimination analysis to identify selection signals for the solid blue population compared to the wild type(referred to as BF vs WF)and for the albino blue population compared to the solid blue population(referred to as AF vs BF),and evaluated genomic regions related to color formation.The results showed strong selection signals in large regions of chromosomes 3,12,13,18,and 20 for the solid blue population and chromosomes 1,16,18,and 19 for the albino blue population.By combining SNP functional annotation and frequency across populations,we narrowed down the range of selected SNPs.Subsequently,we verified the authenticity of the SNPs using a combination of polymerase chain reaction(PCR)and Sanger sequencing.We identified 13 candidate SNPs in the solid blue population,located at positions LG03＿47060063 、 LG03＿47060487 、 LG12＿2861101 、LG12＿2877165 、 LG13＿21490048 、 LG13＿21491162 、 LG13＿21534604 、LG13＿21534625 、 LG13＿24930478 、 LG13＿24977861 、 LG13＿24988445 、LG13＿24988658、LG20＿7991831.We identified 9 candidate SNPs in the albino blue population,located at positions LG01＿15349057、LG01＿15349102、LG01＿27388385、LG02＿44971028、LG12＿418716、LG16＿24260773、LG16＿24292657、LG19＿19949950、LG23＿6733984.