Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait.
Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait.
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DOI：
10.1186/1471-2164-10-368
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发表时间：
2009-08-07
期刊：
影响因子：
4.4
通讯作者：
Kjøglum S
中科院分区：
文献类型：
--
作者：
Moen T;Baranski M;Sonesson AK;Kjøglum S
传染性胰腺坏死（Infectious pancreatic necrosis，IPN）是世界范围内大西洋鲑（Atlantic salmon，萨尔莫salar）养殖中最普遍和最具经济破坏性的疾病之一。该疾病在鱼苗和二龄鲑后期都造成大量死亡。通过使用受控的挑战试验进行增加IPN抗性的家族选择，其中记录同胞组的存活率。然而，由于挑战测试的动物不能作为育种候选人，家庭内的选择不进行，只有一半的遗传变异的IPN抗性被利用。因此，与影响IPN抗性的数量性状基因座（QTL）连锁的DNA标记将是一个强大的选择工具。本研究的目的是确定和精细定位大西洋鲑鱼IPN抗性QTL，用于标记辅助选择，以提高该性状的遗传改良率。使用10个大的全同胞家庭的挑战测试大西洋鲑鱼后小鲑鱼和微卫星标记分布在整个基因组进行基因组扫描。一个主效QTL的IPN抗性检测，解释29%和83%的表型和遗传变异，分别。这个QTL映射到相同的位置，最近在苏格兰大西洋鲑鱼种群中检测到的QTL。QTL被发现是分离的20个作图父母中的10个，和随后的精细作图与额外的标记缩小了QTL峰值连锁群21上的4 cM区域。用经检验的鱼苗表明，QTL对鱼苗和二龄鲑后的影响相同，鱼苗中QTL位置的置信区间与二龄鲑后的置信区间重叠。共检测了178个亲本的QTL分离，鉴定出72个QTL杂合亲本。QTL杂合亲本的基因型用于确定潜在DNA多态性等位基因与单标记或多标记单倍型等位基因之间的连锁相位。一个四标记单倍型被认为是最好的QTL等位基因的预测，并成功地用于推断基因型的基础多态性在72%的父母的下一代内的育种核。一个高度显着的人口水平的相关性之间的推断等位基因在潜在的多态性和后代群体的存活率在鱼苗挑战试验中，父母与三个推断基因型（QQ，Qq，qq）的平均后代死亡率分别为0.13，0.32和0.49。高抗等位基因（Q）在群体中的频率估计为0.30。除了这个主效QTL外，还检测到一个与IPN抗性相关的显著QTL，位于连锁群4上。在这项研究中确认的QTL代表了一个主基因的情况下，解释了一个假定的复杂性状的遗传变异的大部分。QTL基因型推断的2005年一代的主要育种公司的大多数父母，提供了一个坚实的框架，连锁为基础的MAS在整个人口在随后的几代。由于在群体水平上发现了有效的单倍型-性状关联，因此也存在基于连锁不平衡（LD）的MAS的潜力。然而，为了在多代中使用MAS而不重新评估标记和潜在多态性之间的连锁阶段，QTL需要以更高的准确性定位。这将需要比目前可用的更高的标记密度。
Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar) farming worldwide. The disease causes large mortalities at both the fry- and post-smolt stages. Family selection for increased IPN resistance is performed through the use of controlled challenge tests, where survival rates of sib-groups are recorded. However, since challenge-tested animals cannot be used as breeding candidates, within-family selection is not performed and only half of the genetic variation for IPN resistance is being exploited. DNA markers linked to quantitative trait loci (QTL) affecting IPN resistance would therefore be a powerful selection tool. The aim of this study was to identify and fine-map QTL for IPN-resistance in Atlantic salmon, for use in marker-assisted selection to increase the rate of genetic improvement for this trait. A genome scan was carried out using 10 large full-sib families of challenge-tested Atlantic salmon post-smolts and microsatellite markers distributed across the genome. One major QTL for IPN-resistance was detected, explaining 29% and 83% of the phenotypic and genetic variances, respectively. This QTL mapped to the same location as a QTL recently detected in a Scottish Atlantic salmon population. The QTL was found to be segregating in 10 out of 20 mapping parents, and subsequent fine-mapping with additional markers narrowed the QTL peak to a 4 cM region on linkage group 21. Challenge-tested fry were used to show that the QTL had the same effect on fry as on post-smolt, with the confidence interval for QTL position in fry overlapping the confidence interval found in post-smolts. A total of 178 parents were tested for segregation of the QTL, identifying 72 QTL-heterozygous parents. Genotypes at QTL-heterozygous parents were used to determine linkage phases between alleles at the underlying DNA polymorphism and alleles at single markers or multi-marker haplotypes. One four-marker haplotype was found to be the best predictor of QTL alleles, and was successfully used to deduce genotypes of the underlying polymorphism in 72% of the parents of the next generation within a breeding nucleus. A highly significant population-level correlation was found between deduced alleles at the underlying polymorphism and survival of offspring groups in the fry challenge test, parents with the three deduced genotypes (QQ, Qq, qq) having mean offspring mortality rates of 0.13, 0.32, and 0.49, respectively. The frequency of the high-resistance allele (Q) in the population was estimated to be 0.30. Apart from this major QTL, one other experiment-wise significant QTL for IPN-resistance was detected, located on linkage group 4. The QTL confirmed in this study represents a case of a major gene explaining the bulk of genetic variation for a presumed complex trait. QTL genotypes were deduced within most parents of the 2005 generation of a major breeding company, providing a solid framework for linkage-based MAS within the whole population in subsequent generations. Since haplotype-trait associations valid at the population level were found, there is also a potential for MAS based on linkage disequilibrium (LD). However, in order to use MAS across many generations without reassessment of linkage phases between markers and the underlying polymorphism, the QTL needs to be positioned with even greater accuracy. This will require higher marker densities than are currently available.
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作者：
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