Chromosome 28 genotypes and phenotypes for all samples used in the analyses, full panel of 298 genotypes, and R script for R-squared values

Recent studies have begun to elucidate the genetic basis for phenotypic
traits in salmonid species, but many questions remain before these
candidate genes can be directly incorporated into conservation management.
In Chinook Salmon (Oncorhynchus tshawytscha), a region of major effect for
migration timing has been discovered that harbors two adjacent candidate
genes (greb1L, rock1), but there has been limited work to examine the
association between these genes and migratory phenotypes at the
individual, compared to the population, level. To provide a more thorough
test of individual phenotypic association within lineages of Chinook
Salmon, 33 candidate markers were developed across a 220 Kb region on
chromosome 28 previously associated with migration timing. Candidate and
neutral markers were genotyped in individuals from representative
collections that exhibit phenotypic variation in timing of arrival to
spawning grounds from each of three lineages of Chinook Salmon.
Association tests confirmed the majority of markers on chromosome 28 were
significantly associated with arrival timing and the strongest association
was consistently observed for markers within the rock1 gene and the
intergenic region between greb1L and rock1. Candidate markers alone
explained a wide range of phenotypic variation for Lower Columbia and
Interior ocean-type lineages (29% and 78%, respectively), but less for the
Interior stream-type lineage (5%). Individuals that were heterozygous at
markers within or upstream of rock1 had phenotypes that suggested a
pattern of dominant inheritance for early arrival across populations.
Finally, previously published fitness estimates from the Interior
stream-type lineage enabled tests of association with arrival timing and
two candidate markers, which revealed that fish with homozygous mature
genotypes had slightly higher fitness than fish with premature genotypes,
while heterozygous fish were intermediate. Overall, these results provide
additional information for individual-level genetic variation associated
with arrival timing that may assist with conservation management of this
species.

近年来的研究已逐步阐明鲑科鱼类表型性状的遗传基础，但在将这些候选基因直接应用于物种保护管理前，仍有诸多问题有待解决。针对奇努克鲑鱼（Chinook Salmon，Oncorhynchus tshawytscha），研究人员已发现一个对洄游时间具有显著调控效应的基因组区域，该区域包含两个相邻的候选基因greb1L与rock1，但相较于种群水平，针对这两个基因与个体洄游表型之间关联的研究仍较为匮乏。为更全面地检验奇努克鲑鱼不同支系内个体表型与基因型的关联情况，研究人员针对28号染色体上一段此前被证实与洄游时间相关的220 Kb区域，开发了33个候选分子标记。研究人员从三个奇努克鲑鱼支系的代表性采样群体中选取个体，对候选标记与中性标记进行了基因分型，这些采样群体的个体在抵达产卵场的时间上存在明显表型差异。关联分析结果证实，28号染色体上的多数标记均与抵达时间存在显著关联，且rock1基因内部以及greb1L与rock1之间的基因间区的标记始终表现出最强的关联信号。仅使用候选标记即可解释下哥伦比亚河支系与内陆海洋型支系的大量表型变异（分别为29%与78%），但对内陆溪流型支系的表型变异解释度较低（仅5%）。在rock1基因内部或其上游区域的标记呈杂合状态的个体，其表型呈现出跨种群的早期抵达显性遗传模式。此外，借助已发表的内陆溪流型支系适合度评估数据，研究人员开展了抵达时间与两个候选标记的关联检验，结果显示携带纯合成熟基因型的个体，其适合度略高于携带早熟基因型的个体，而杂合个体的适合度则介于二者之间。总体而言，本研究结果为与抵达时间相关的个体水平遗传变异提供了更多信息，有望为该物种的保护管理提供辅助支撑。