Smith Seth R, Amish Stephen J, Bernatchez Louis, Le Luyer Jeremy, C Wilson Chris, Boeberitz Olivia, Luikart Gordon, Scribner Kim T
Conservation Genomics Group; Wildlife Biology Program, University of Montana, Missoula, MT,
Flathead Lake Biological Station, Division of Biological Sciences, University of Montana Polson, MT.
G3 (Bethesda). 2020 Jun 1;10(6):1929-1947. doi: 10.1534/g3.120.401184.
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout () are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char () are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species.
了解适应性种内表型变异的基因组基础是保护遗传学和进化生物学的核心目标。湖鳟（Salvelinus namaycush）是研究适应性变异遗传基础的优良物种，因为它们在其分布范围内表现出显著程度的生态表型变异；然而，必要的基因组资源却很匮乏。在此，我们利用最近开发的分析方法和测序技术来：（1）构建湖鳟的高密度连锁图谱和着丝粒图谱；（2）鉴定区分湖鳟生态表型和种群的性状变异的潜在基因座；（3）确定湖鳟性别决定基因座的位置；（4）鉴定湖鳟与不同分化程度的其他鲑科鱼类之间的染色体同源性。所得的连锁图谱包含15740个单核苷酸多态性（SNP），定位到42个连锁群，可能代表42条湖鳟染色体。雌性和雄性连锁群长度分别为43.07至134.64厘摩和1.97至92.87厘摩。我们通过确定42个着丝粒中41个的坐标改进了该图谱，得到了一个包含8条中着丝粒染色体和34条近端着丝粒或端着丝粒染色体的图谱。我们利用该图谱定位性别决定基因座和多个与种内表型分化相关的数量性状基因座（QTL），包括与生长和身体状况、皮肤色素沉着模式相关的性状，以及两个量化体型的复合地貌测量变量。两个有蠕虫状斑纹和斑点存在的QTL被高度确定地定位到连锁群Sna3的一条臂上，与生长相关的性状定位到连锁群Sna1和Sna12上的两个QTL，并且在六个不同的连锁群上检测到了假定的体型QTL。性别决定基因座被高度确定地定位到Sna4上。同线性分析表明，湖鳟和同属的北极红点鲑（Salvelinus alpinus）可能通过三到四次染色体裂变、可能一次染色体融合以及6次或更多次大的倒位而分化。将着丝粒图谱信息与假定的倒位坐标相结合表明，区分湖鳟与其他鲑科鱼类的大多数检测到的倒位是臂间倒位，且位于近端着丝粒和端着丝粒连锁群上。我们的结果表明，该属内的物种形成和适应性分化可能与主要发生在近端着丝粒和端着丝粒染色体上的多次臂间倒位有关。这里呈现的连锁图谱将是推进湖鳟保护导向的基因组研究以及探索鲑科物种内部和之间染色体进化的关键资源。
