Department of Anatomy and Structural Biology, Centre for Reproduction and Genomics, University of Otago, Dunedin, New Zealand.
Mol Ecol Resour. 2011 May;11(3):503-13. doi: 10.1111/j.1755-0998.2010.02962.x. Epub 2010 Dec 28.
Understanding genetic variation responsible for phenotypic differences in natural populations is significantly hampered by a lack of genomic data for many species. Levels of variation can, however, be estimated using microsatellite markers, which may be useful for relating individual fitness to genetic diversity. Prior studies have demonstrated correlations between heterozygosity and individual fitness in some species. These correlations are sometimes driven by a subset of markers, and it is unclear whether this is because those markers best reflect genome-wide heterozygosity, or whether they are linked to fitness-related genes. Differentiating between these scenarios is hindered when the genomic location of markers is unknown. Here, we develop a predicted genomic map of pinniped microsatellite loci based on conservation of primary sequence and genomic location between dog, cat and giant panda. We mapped 210 of 260 (81%) microsatellites from pinnipeds to locations in dog, cat and giant panda genomes. Based on the demonstrable synteny between the genomes of closely related taxa within the Carnivora, we use these data to identify those microsatellites with the greatest chance of cross-species amplification success and demonstrate successful amplification of 21 of 26 loci for cat, dog and two seal species. We also demonstrate the potential to identify candidate genes that may underpin the functional relationship with individual fitness. Overall, we show that this approach provides a rapid and robust method to elucidate genome organisation for nonmodel organisms and have established a resource that facilitates further genetic research on pinnipeds that also has wider applicability to other carnivores.
了解自然种群中表型差异所涉及的遗传变异，受到许多物种缺乏基因组数据的严重阻碍。然而，可以使用微卫星标记来估计变异水平，这对于将个体适应性与遗传多样性联系起来可能是有用的。先前的研究已经在一些物种中证明了杂合度与个体适应性之间的相关性。这些相关性有时是由一组标记驱动的，目前尚不清楚这是因为这些标记最能反映全基因组的杂合度，还是因为它们与适应性相关的基因有关。当标记的基因组位置未知时，区分这些情况会受到阻碍。在这里，我们根据犬科、猫科和大熊猫的一级序列和基因组位置的保守性，开发了一个预测的鳍足类微卫星基因座的基因组图谱。我们将 260 个鳍足类微卫星中的 210 个（81%）映射到犬科、猫科和大熊猫基因组中的位置。基于在食肉目亲缘关系密切的分类群中基因组的明显同线性，我们利用这些数据来识别那些最有可能跨物种扩增成功的微卫星，并成功地对猫科、犬科和两种海豹物种的 21 个位点进行了扩增。我们还展示了识别可能是个体适应性功能关系基础的候选基因的潜力。总的来说，我们表明，这种方法为非模式生物阐明基因组结构提供了一种快速而稳健的方法，并建立了一个资源，为鳍足类动物的进一步遗传研究提供了便利，同时也为其他食肉动物提供了更广泛的适用性。
