Data from: Genomic variation underlying complex life history traits revealed by genome sequencing in Chinook salmon

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life history variation and phenotypic traits for this species. Whole genome resequencing of populations with distinct life history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.

自然生物中广泛存在的表型多样性（phenotypic diversity）可抵御开发利用压力，并提升受干扰生态系统中物种的存续能力。解析驱动生态与进化适应（ecological and evolutionary adaptation）的基因组变异（genomic variation），可成为深化对自然表型变异认知的有力手段。本研究构建了奇努克鲑（Chinook salmon，*Oncorhynchus tshawytscha*；2.36 Gb）的染色体水平参考基因组组装序列，为该物种的生活史变异与表型性状关联定位提供了支撑。对具有独特生活史性状的种群开展全基因组重测序（whole genome resequencing），结果显示系统发育谱系（phylogenetic lineages）内部及谱系间的基因组广泛存在歧化选择，表明该物种中存在与本地适应及生活史变异相关的广泛表型多样性。基于数百万个全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）的关联分析显示，28号染色体上一个具有显著效应的基因组区域，与提前抵达产卵场的早熟表型及适时抵达产卵场的成熟表型相关，且该关联在三个不同的系统发育谱系中均保持一致。本研究结果证实，基因组资源（genomic resources）可阐明开发利用物种已知表型的遗传基础，并助力解析自然种群中难以直接观测的表型变异。