罗非鱼高密度遗传图谱构建及抗病QTL定位

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

  • 摘要: 【目的】 通过构建罗非鱼抗病遗传连锁图谱,挖掘出与抗病性状相关的QTL位点和候选基因,为开展分子标记辅助加快罗非鱼抗病新品种选育提供理论指导。【方法】 以前期开展罗非鱼壮罗1号新品种选育过程中选获的抗病个体与易感病个体杂交得到的全同胞家系F1代150个个体为作图群体,基于全基因组重测序技术,利用GATK软件进行全基因组单核苷酸多态性(SNP)标记的挖掘,对过滤筛选到的高质量SNP标记利用Lep-MAP3构建高密度遗传连锁图谱,采用MapQTL 6.0的复合区间作图法对抗病性状相关QTL进行定位,然后利用定位区间所对应的物理位置,参考罗非鱼的基因组找到对应区间,并结合基因功能注释筛选抗病候选基因。【结果】 全基因组重测序共获得34861.49 Raw reads(3487.35 Gb),经质控后共得到34565.24 Clean reads(3456.97 Gb),平均每个F1代为218.90 Clean reads(21.90 Gb),F1代的平均Q30和GC含量分别为93.25%和40.86%。将247228个高质量SNP标记划分为3029个Bin标记。构建的罗非鱼遗传连锁图谱全长为1521.56 cM,共划分为22个连锁群,标记间平均距离为0.50 cM。结合抗病性状的表型数据,在遗传图谱LG9连锁群上定位得到1个与无乳链球菌病抗性相关QTL,其置信区间为0.67~6.67 cM,对区间内的基因进行功能注释,筛选出5个免疫相关基因,分别为分离缺陷基因3(PARD3)、微管相关蛋白4基因(MAP4)、黏着斑蛋白基因(SVIL)、Kruppel样因子基因(KLF6)及骨形态发生蛋白6基因(BMP6)。【结论】 基于重测序技术绘制罗非鱼抗病性状遗传连锁图谱,定位到抗病相关QTL 1个和抗病候选基因5个,为后续实施罗非鱼抗病性状分子标记辅助育种及抗病功能基因研究提供标记资源。

     

    Abstract: 【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.

     

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