Construction of high-density genetic map and disease resistance QTL mapping for tilapia

【Objective】 This study constructed a genetic linkage map for disease resistance in tilapia,identified QTL loci and candidate genes related to disease resistance traits,which could provide theoretical guidance for molecular marker assisted accelerated breeding of new disease resistant tilapia varieties. 【Method】 A total of 150 individuals from the F₁ generation of the entire sibling family,obtained by crossbreeding resistant and susceptible individuals selected during the early breeding process of the new tilapia variety Zhuanglou 1,were used as the mapping population. Based on wholegenome resequencing technology,GATK software was used to mine single nucleotide polymorphism（SNP） markers throughout the genome. Lep-MAP3 was used to construct a high-density genetic linkage map of high-quality SNP markers selected. The composite interval mapping method of MapQTL 6.0 was used to locate QTL related to disease resistant traits. Then,the physical positions corresponding to the positioning intervals were used to refer the genome of tilapia to find the corresponding intervals,and combined with gene functional annotation,candidate genes for disease resistance were screened. 【Result】 The results showed that resequencing generated 34861.49 raw reads（3487.35 Gb）,and after quality control,34565.24 clean reads（3456.97 Gb） were obtained,with an average of 218.90 clean reads（21.90 Gb） per F₁ offspring. The average Q30 and GC content of the F₁ offspring were 93.25% and 40.86%. A total of 247228 high-quality SNP markers were classified into 3029 Bin markers. The total length of the high-density genetic linkage map was 1521.56 cM,divided into 22 linkage groups,with an average distance between markers of 0.50 cM. Based on phenotypic data of disease resistance traits,a QTL related to resistance to Streptococcus agalactiae was located on the genetic map LG9 linkage group,with a confidence interval of 0.67-6.67 cM. Functional annotation was performed on the genes within the interval,and 5 immune related genes were screened,including the segregation defect gene 3（PARD3）,microtubule associated protein 4（MAP4）,adhesive spot protein gene（SVIL）,Kruppel like factor gene（KLF6）,and bone morphogenetic protein 6 gene（BMP6）. 【Conclusion】 Based on resequencing technology,a genetic linkage map of disease resistance traits in tilapia is drawn,and 1 disease resistance related QTL and 5 disease resistance candidate genes are located,providing technical support for the subsequent implementation of molecular marker assisted breeding of disease resistance traits and research on disease resistance functional genes in tilapia.