Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon.
Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon.
复制标题
DOI：
10.1186/1471-2164-13-244
复制
发表时间：
2012-06-15
期刊：
影响因子：
4.4
通讯作者：
Taggart JB
中科院分区：
文献类型：
--
作者：
Houston RD;Davey JW;Bishop SC;Lowe NR;Mota-Velasco JC;Hamilton A;Guy DR;Tinch AE;Thomson ML;Blaxter ML;Gharbi K;Bron JE;Taggart JB
限制性位点相关DNA测序（RAD-Seq）是一种基因组复杂性降低技术，其促进大规模标记发现和通过测序进行基因分型。RAD-Seq最近的应用包括连锁和QTL定位，特别关注非模式物种。在目前的研究中，我们将RAD-Seq应用于来自商业育种计划的两个大西洋鲑鱼家族。根据感染性胰腺坏死（IPN）攻击实验中的存活率/死亡率，将这些家系的后代分为抗性或易感基因型，并在主要IPN抗性QTL处推定纯合抗性或易感基因型。从每个家庭中，两个杂合父母和每个IPN表型和基因型的7个后代的基因组DNA用SbfI酶消化，并在多重池中测序。从两个家族中的大约70，000个RAD基因座获得序列，并鉴定了6，712个分离SNP的过滤组。在两个家庭的全基因组RAD标记分离模式的分析表明，SNP的发现对所有29个大西洋鲑鱼染色体对，并强调缺乏男性重组。使用系谱样本，使我们能够区分分离SNPs从推定的旁系同源序列变异产生的相对较新的鲑鱼物种的基因组重复。在分离的SNP中，50个与QTL连锁。将这些QTL连锁的SNP的子集转换为高通量测定，并在IPNV攻击的鲑鱼鱼苗的大商业群体中进行基因分型。几个SNP显示出高度显着的连锁和关联与IPN的抗性，和群体连锁不平衡为基础的SNP测试的电阻被确定。我们使用RAD-Seq成功地识别和鉴定了纯种水产养殖大西洋鲑鱼中的高密度遗传标记。这些结果强调了RAD-Seq作为在大型复杂基因组中快速有效生成QTL靶向和全基因组标记数据的工具的有效性，以及其在养殖动物选择程序中的可能效用。
Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs.
登录
查看更多内容
影响因子：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
3.1
作者：
Danzmann, RG;Cairney, M;Woram, RA
通讯作者：
Woram, RA
影响因子：
3.3
作者：
Gjoen, HM;Bentsen, HB
通讯作者：
Bentsen, HB
影响因子：
1.6
作者：
HARTLEY, SE;HORNE, MT
通讯作者：
HORNE, MT