Genetic analysis of morphological traits in cavefish, Astyanax mexicanus.

描述（由申请人提供）：在过去的十年中，基因组资源已经被开发并成功地用于帮助定义传统模型系统中性状的遗传基础。然而，这些资源尚未广泛应用于自然种群的性状研究。许多新兴的模式系统，包括洞穴鱼Astyanax mexicanus，是研究许多尚不清楚的发育过程的特别有利的生物。具体来说，在过去的1万年中，对洞穴微环境的适应导致了各种退化特征的积累，例如完全失去眼睛和色素沉着。这种属的一个种内成员在河面上居住的持久性使得这些鱼可以杂交产生杂交后代。Tabin实验室利用数百个微卫星标记开发了一个基于重组的连锁图谱，以促进数量性状位点（QTL）的研究。由于洞穴鱼在系统发育上与被充分研究过的鱼类丹尼奥·雷里奥（Danio rerio）有密切的亲缘关系，它们在基因组上具有显著的同质性。这些鱼的地质和自然历史在大量的古典和当代文献中都有很好的记载。此外，居住在墨西哥中部Sierra de El Abra地区多个洞穴中的几个洞穴鱼种群，允许对从地质上孤立的洞穴种群进化而来的Astyanax不同种群的平行进化和表型特征趋同进行分析。最后，洞穴鱼是一种强壮的生物，很容易在Tabin实验室中维持和繁殖。为了更好地了解Astyanax退化形态的遗传基础，提出了一个三重策略。首先，由Tabin实验室先前构建并发表的由数百个微卫星标记组成的全基因组连锁图谱将被分析，以确定它们在Astyanax最近的近亲斑马鱼Danio rerio基因组中的合成位置。这项工作将旨在锚定洞穴鱼的链接地图到斑马鱼的物理地图。其次，利用QTL分析，我将确定与四个性状发展相关的候选基因的位置：视觉系统退化，黑色素产生细胞的丧失，肋骨数和形态的变异，以及面部骨骼发育不良。第三，与上述QTL密切相关的基因将进行功能分析，以了解和表征它们在这些特征丧失中的潜在作用。在洞穴形态的Astyanax中存在的一些退行性特征可能在人类退行性疾病中具有相同或平行的基础。因此，在本研究中提出的qtl中获得的结果也可能对更好地表征导致类似人类临床疾病的遗传事件具有启示意义

DESCRIPTION (provided by applicant): Genomic resources have been developed and used successfully over the past decade to help define the genetic basis for traits in traditional model systems. These resources, however, have not been applied widely to the study of traits in natural populations. Many emerging model systems, including the cavefish Astyanax mexicanus, are especially favorable organisms for the study of numerous poorly-understood developmental processes. Specifically, adaptation to the cave microenviroment in the past 10,000 years has resulted in the accumulation of a variety of degenerate traits, e.g., complete loss of eyes and pigmentation. The persistence of a surface river-dwelling, intraspecific member of this genus has allowed these fish to be interbred to create hybrids. The Tabin lab has developed a recombination-based linkage map using hundreds of microsatellite markers to facilitate quantitative trait locus (QTL) studies. Since cavefish are close phylogenetic relatives of the well-studied fish, Danio rerio, they share a remarkable level of genomic synteny. The geological and natural history of these fish are well-rooted in a sizeable classical and contemporary literature. In addition, several populations of cavefish residing in multiple caves within the Sierra de El Abra region of central Mexico, allow for analyses of parallel evolution and the convergence of phenotypic traits in different populations of Astyanax having evolved from geologically-isolated cave populations. Finally, cavefish are robust organisms that are easily maintained and bred in the Tabin laboratory. To better understand the genetic basis for degenerate morphologies in Astyanax, a three-fold strategy is proposed. First, a genome-wide linkage map, previously constructed and published by the Tabin laboratory, comprised of hundreds of microsatellite markers will be analyzed for their syntenic positions in the closest relative of Astyanax with a sequenced genome, the zebrafish Danio rerio. This work will be aimed at anchoring the cavefish linkage map to the zebrafish physical map. Second, utilizing QTL analyses, I will identify the location of candidate genes associated with the development of four traits: visual system degeneration, loss of melanin-producing cells, variability in rib number and morphology, and facial bone dysgenesis. Third, genes closely linked to the QTL described above will be subjected to functional assays to understand and characterize their potential role(s) in the loss of these characteristics. Several of the degenerative traits present in the cave-form of Astyanax may have equivalent or parallel bases in human degenerative disorders. Thus, results obtained in the QTLs proposed in this study may also have implications for better characterizing genetic events leading to analogous human clinical diseases