Research Of Whole Genomic Selection For Large Yellow Croaker(Larimichthys Crocea) Against Cryptocaryon Irritans Infection

Large yellow croaker is one of the most important marine aquaculture species in China,the industry of which is mainly located in the southeast coastal waters of China.Its annual production ranks first among all marine aquaculture species,providing huge economic income for the society.However,intensification of aquaculture production,such as deterioration of water and habit destruction,is creating a suitable environment for the outbreaks of many pathogenic microorganisms.Among all kinds of diseases occurring in the aquaculture of large yellow croaker,the white spot disease caused by Cryptocaryon irritans is the most serious.Up to now,there is still no effective disease prevention and control measures to alleviate economic loss caused by white spot disease.In view of this,this study aims to use genomic selection（GS）to cultivate new strains of large yellow croaker that are resistant to C.irritans.The main results of this paper are as follows:（1）Artificial C.irritans infection of large yellow croaker showed that the survival rate of challenge was linear correlated with the infection dose.Dead individuals at different experimental stages have different death characteristics;The survival state after the end of the challenge test was demonstrated as the best indicator to measure the resistance of large yellow croaker against C.irritans.（2）Based on the GWAS analysis of the resistance of large yellow croaker to C.irritans in two independent populations（YC₂017 and YC₂018）in Ningde,Fujian,the following conclusions can be drawn.The heritability of resistant phenotype was estimated relatively high as approximately 0.44;15 QTL were detected to be related to the resistant phenotype,and these QTL accounted for about 30%of the total genetic variance,which indicated that the resistant trait of large yellow croaker against C.irritans had a complex genetic architecture,which could be expressed as the trait controlled by a few QTL with small effect-size and a large amount of genetic loci with micro-effect;A lot of the candidate genes were clumped into some biological pathways that are potentially related to C.irritans resistance,such as hormone transport,apoptosis process,acute inflammation,NF-kappa B signaling pathway.In addition,two key candidate genes,casp8 and traf6,were detected,which play an important role in mediating apoptosis and inflammation,respectively.（3）Basing on different real and simulated data sets,the research results of the impact of different parameters on the GS model showed that the use of low-density SNP marker panel evenly or randomly distributed on each chromosome could achieve equivalent prediction accuracy as the use of all markers;Under the premise that the trait was controlled by a small number of QTL,the use of low-density marker panel composed of markers with small P value or a large effect-size had higher prediction accuracy than using all markers;The prediction accuracy of GS model increased with the increasing number of reference populations,and increase rate gradually slowed down;Under the premise that the trait was controlled by a small number of QTL,Bayesian shrinkage estimation methods have higher prediction accuracy than other mathematical methods.（4）The above established GS model with optimization was applied to the practice of selective breeding of large yellow croaker against C.irritans,and then two resistant strains（GS3 and GS3R）were cultivated.In the artificial C.irritans challenge,the two strains both showed significantly strong resistant performance against C.irritans,which indicating that GS not only had theoretical feasibility,but also had strong applicability and repeatability.（5）Basing on the population genetics of resistant strain GS3R and its parental generation,the conclusion that GS3R was certainly generated through directional artificial selection and had genetic differentiation compared with the parental generation population,can be obtained;Basing on the results of genome selection pressure scanning and GWAS result integration,a total of 14 genomic regions potentially related to C.irritans resistance were detected.In conclusion,this paper using five consecutive research steps,constructing a appropriate way to measure the resistance of large yellow croaker against C.irritans,revealing genetic architecture of resistant phenotype by GWAS,construction and optimization of GS model,application of GS to selective breeding of large yellow croaker against C.irritans,population genetics and selection pressure analysis of resistant strain,logically proved that it is feasible to apply GS technology to the selective breeding of large yellow croaker for resistance to C.irritans.The present study provides a good example for selective breeding of disease resistance for other aquatic animals and promotes the innovation of selective breeding technology.