Department of Biology, 20014, University of Turku, Finland.
BMC Genomics. 2010 Mar 8;11:156. doi: 10.1186/1471-2164-11-156.
For decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (approximately 75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms.
Here we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (Salmo salar) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment.
The INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.
几十年来，连锁图谱一直是阐明具有医学、农业和进化重要性的表型性状遗传结构的最强大和最广泛使用的方法之一。然而，孟德尔和数量表型性状的成功定位在很大程度上取决于快速且最好是高通量的基因分型平台的可用性。近年来，已经开发了几种基于阵列的单核苷酸多态性（SNP）基因分型平台用于遗传模式生物，但这些方法中的大多数对于筛选大量个体来说都过于昂贵。因此，仍然需要廉价、简单和灵活的基因分型解决方案，以便在广泛的生物体中进行 QTL 图谱应用，能够快速筛选数百至数千个个体中的中等数量的（大约 75-300）基因座。
在这里，我们描述了插入缺失（INDEL）多态性的发现和应用，这种多态性可用于经济高效的中等通量基因分型，能够在单个自动测序电泳柱中分析超过 75 个基因座，使用标准实验室设备。INDEL 基因分型的启动成本低，包含很少的标准样本处理步骤，并且适用于具有可用表达序列标签（EST）集合的广泛物种。作为原理验证，我们在大西洋鲑（Salmo salar）中生成了部分 INDEL 连锁图谱，并快速确定了许多影响早期生活史性状的数量性状基因座（QTL），这些性状预计在自然环境中具有重要的适应意义。
INDEL 基因分型能够快速粗定位包含 QTL 的染色体区域，从而为在多个杂交和大系谱中进行遗传结构特征提供了有效的手段。这不仅能够发现更多数量的具有相对较小表型效应的 QTL，而且还为评估在异交种群中分离 QTL 的频率提供了一种经济有效的方法，这对于进一步了解表型性状下的遗传变异如何在野外中得到维持很重要。
