DOI: 10.5061/dryad.08kprr5c3
title: Heritability and genomic basis of age-at-maturity in Chinook Salmon

description: Life history variation acts as a buffer against stochastic environmental
 variation. When these variations represent distinct phenotypic optima for
 males and females there may be sexually antagonistic selection, and with
 high heritability, the opportunity for intralocus sexual conflict. The age
 at return migration for Chinook Salmon (Oncorhynchus tshawytscha), or
 age-at-maturity, is one such trait, since male age-at-maturity appears to
 experience a divergent selective landscape from females. We investigated
 the heritability of age-at-maturity, genomic basis of both sex and
 age-at-maturity, and potential for intralocus sexual conflict regarding
 age-at-maturity in stocks of Chinook Salmon from the Columbia River Basin
 representing the three major lineages present there. We found that
 heritability of age-at-maturity was positive for both sexes as well as in
 opposite sex comparisons but was generally stronger for males. We
 identified regions of the genome associated with sex across all three
 lineages, as well as large regions of a single chromosome, but which
 chromosome (17 or 18) varied across lineages as well as within the
 interior stream-type lineage. Regions of these same chromosomes were
 associated with age-at-maturity in natural-origin stocks of the interior
 lineages, but was associated with different chromosomes in natural-origin
 male and female interior stream-type fish. Analyses of genotyped markers,
 as well as multi-marker haplotypes, confirmed the association of
 chromosome 17 with age-at-maturity. Association of age-at-maturity with
 the sex-chromosome could mediate intralocus sexual conflict in these fish,
 but stocks which show polymorphism for the sex-chromosome could exhibit
 disjunction between complementary compensating modifiers on the X and Y
 chromosomes.
description: GT-seq on Illumina NextSeq 4000
description: # Heritability and genomic basis of age-at-maturity in Chinook Salmon
 [https://doi.org/10.5061/dryad.08kprr5c3](https://doi.org/10.5061/dryad.08kprr5c3) ## Description of the data and file structure DNA was extracted using nondenatured Chelex protocols from the manufacturer (Sigma-Aldrich). Fish were genotyped using a genotyping-in-thousands panel (GT-seq; Campbell et al. 2015) consisting of dozens (hatchery-origin grandparents) to hundreds (natural-origin and 2018/2022 hatchery-origin broodstock) of SNP markers. NOR fish were initially genotyped and reported in Willis et al. (2021), while hatchery-origin broodstock from 2018 and 2022 were genotyped in those years and reported in PBT baselines utilized in Hess et al. (2024). The NOR and 2018 hatchery-origin broodstock fish, utilized in genomic analyses below, were genotyped a second time on an Illumina HiSeq 4000 using a panel of 359 markers plus sex marker to confirm that the correct sample was chosen for sequencing and that sex was identified accurately. One associated file contains the raw genotype data for all fish, while the second contains meta-data for those individuals, including PCA loadings for ordination across lineage and within lineage, total and ocean age, run-timing (chr28) genotype code, lineage, stock, hatchery or natural origin, sex, fork length (natural origin only) and coverage from the whole genome sequencing effort. ### Files and variables #### File: S.File-Ots\_AAM\_poolseq\_bams\_phenotypes\_covariates.txt **Description:** Meta-data for the genotyped individuals. Missing data are coded as NA. See data description for variable explanation. ##### Variables * bam: name of the alignment file * sample_group: analysis group; concatenation of origin, source, sex * indiv: individual name * origin: natural or hatchery origin * source: stock * sex: male or female * age: ocean age (o) or total age (t) in years * ocean_age: ocean age (duration) for natural origin fish in years * total_age: total (PBT) age (duration) for hatchery origin fish in years * sex_int: 0 for male and 1 for female * pca_lineage_axis1: first principle component for principle component analysis across lineages * pca_lineage_axis2: second principle component for principle component analysis across lineages * pca_lineage_axis3: third principle component for principle component analysis across lineages * lineage: for the Columbia basin: coastal, interior ocean-type, or interior stream-type * pca_internal_axis1: first principle component for principle component analysis within lineages * pca_internal_axis2: second principle component for principle component analysis within lineages * pca_internal_axis3: third principle component for principle component analysis within lineages * pca_internal_axis4: fourth principle component for principle component analysis within lineages * pca_internal_axis5: fifth principle component for principle component analysis within lineages * pca_internal_axis6: sixth principle component for principle component analysis within lineages * pca_internal_axis7: seventh principle component for principle component analysis within lineages * pca_internal_axis8: eighth principle component for principle component analysis within lineages * pca_internal_axis9: ninth principle component for principle component analysis within lineages * pca_internal_axis10: tenth principle component for principle component analysis within lineages * coverage: average number of reads per nucleotide site * chr28_RTvalue: migration (run)-timing value predicted from the haplotype at chromosome 28 markers 15-18 (from Willis et al. 2022) * fork: fork length in millimeters * origin_binary: hatchery (1) or natural (0) origin #### File: S.File-Ots\_AAM\_poolseqGTSeqGenos2\_5-13-24.txt **Description:** Raw genotype data for individuals whose genomes were sequenced at low-coverage, by GT-seq. ##### Variables * Individual_Name: individual name * Ots_SEXY3_1: sex locus genotype * Ots_102414_395: genotypes of SNP marker * Ots_105105_613: genotypes of SNP marker * Ots_106747_239: genotypes of SNP marker * Ots_110064_383: genotypes of SNP marker * Ots_113242_216: genotypes of SNP marker * Ots_113457_40R: genotypes of SNP marker * Ots_123048_521: genotypes of SNP marker * Ots_128757_61R: genotypes of SNP marker * Ots_94857_232R: genotypes of SNP marker * Ots_94903_99R: genotypes of SNP marker * Ots_96222_525: genotypes of SNP marker * Ots_96500_180: genotypes of SNP marker * Ots_96899_357R: genotypes of SNP marker * Ots_97077_179R: genotypes of SNP marker * Ots_AldB1_122: genotypes of SNP marker * Ots_ARNT: genotypes of SNP marker * Ots_arp_436: genotypes of SNP marker * Ots_AsnRS_60: genotypes of SNP marker * Ots_aspat_196: genotypes of SNP marker * Ots_Cath_D141: genotypes of SNP marker * Ots_CCR7: genotypes of SNP marker * Ots_CD59_2: genotypes of SNP marker * Ots_CD63: genotypes of SNP marker * Ots_cox1_241: genotypes of SNP marker * Ots_CRB211: genotypes of SNP marker * Ots_E2_275: genotypes of SNP marker * Ots_EndoRB1_486: genotypes of SNP marker * Ots_EP_529: genotypes of SNP marker * Ots_ETIF1A: genotypes of SNP marker * Ots_FARSLA_220: genotypes of SNP marker * Ots_FGF6B_1: genotypes of SNP marker * Ots_GDH_81x: genotypes of SNP marker * Ots_GH2: genotypes of SNP marker * Ots_GnRH_271: genotypes of SNP marker * Ots_GPDH_338: genotypes of SNP marker * Ots_GPH_318: genotypes of SNP marker * Ots_GST_207: genotypes of SNP marker * Ots_GST_375: genotypes of SNP marker * Ots_GTH2B_550: genotypes of SNP marker * Ots_hsc71_3__488: genotypes of SNP marker * Ots_hsp27b_150: genotypes of SNP marker * Ots_HSP90B_100: genotypes of SNP marker * Ots_IGF_I_1_76: genotypes of SNP marker * Ots_IL11: genotypes of SNP marker * Ots_Ikaros_250: genotypes of SNP marker * Ots_IL8R_C8: genotypes of SNP marker * Ots_mapK_3__309: genotypes of SNP marker * Ots_mapKpr_151: genotypes of SNP marker * Ots_MHC2: genotypes of SNP marker * Ots_mybp_85: genotypes of SNP marker * Ots_Myc_366: genotypes of SNP marker * Ots_myo1a_384: genotypes of SNP marker * Ots_myoD_364: genotypes of SNP marker * Ots_nkef_192: genotypes of SNP marker * Ots_NOD1: genotypes of SNP marker * Ots_nramp_321: genotypes of SNP marker * Ots_Ots311_101x: genotypes of SNP marker * Ots_P450: genotypes of SNP marker * Ots_P53: genotypes of SNP marker * Ots_PGK_54: genotypes of SNP marker * Ots_Prl2: genotypes of SNP marker * Ots_RAG3: genotypes of SNP marker * Ots_RAS1: genotypes of SNP marker * Ots_RFC2_558: genotypes of SNP marker * Ots_S7_1: genotypes of SNP marker * Ots_SClkF2R2_135: genotypes of SNP marker * Ots_SL: genotypes of SNP marker * Ots_SWS1op_182: genotypes of SNP marker * Ots_TAPBP: genotypes of SNP marker * Ots_TGFB: genotypes of SNP marker * Ots_TLR3: genotypes of SNP marker * Ots_TNF: genotypes of SNP marker * Ots_u07_07_161: genotypes of SNP marker * Ots_u07_17_135: genotypes of SNP marker * Ots_u07_18_378: genotypes of SNP marker * Ots_u07_20_332: genotypes of SNP marker * Ots_u07_25_325: genotypes of SNP marker * Ots_u07_49_290: genotypes of SNP marker * Ots_u07_53_133: genotypes of SNP marker * Ots_u07_57_120: genotypes of SNP marker * Ots_u07_64_221: genotypes of SNP marker * Ots_u202_161: genotypes of SNP marker * Ots_u211_85: genotypes of SNP marker * Ots_u4_92: genotypes of SNP marker * Ots_u6_75: genotypes of SNP marker * Ots_unk526: genotypes of SNP marker * Ots_ZR_575: genotypes of SNP marker * Ots_LWSop_638: genotypes of SNP marker * Ots_100884_287: genotypes of SNP marker * Ots_110201_363: genotypes of SNP marker * Ots_115987_325: genotypes of SNP marker * Ots_CirpA: genotypes of SNP marker * Ots_ntl_255: genotypes of SNP marker * Ots_ppie_245: genotypes of SNP marker * Ots_101554_407: genotypes of SNP marker * Ots_105132_200: genotypes of SNP marker * Ots_110495_380: genotypes of SNP marker * Ots_117432_409: genotypes of SNP marker * Ots_HMGB1_73: genotypes of SNP marker * Ots_OTDESMIN19_SNP1: genotypes of SNP marker * Ots_101704_143: genotypes of SNP marker * Ots_105385_421: genotypes of SNP marker * Ots_110551_64: genotypes of SNP marker * Ots_118205_61: genotypes of SNP marker * Ots_Thio: genotypes of SNP marker * Ots_105407_117: genotypes of SNP marker * Ots_110689_218: genotypes of SNP marker * Ots_118938_325: genotypes of SNP marker * Ots_Est740: genotypes of SNP marker * Ots_OTSTF1_SNP1: genotypes of SNP marker * Ots_redd1_187: genotypes of SNP marker * Ots_u1002_75: genotypes of SNP marker * Ots_102801_308: genotypes of SNP marker * Ots_112301_43: genotypes of SNP marker * Ots_123921_111: genotypes of SNP marker * Ots_NFYB_147: genotypes of SNP marker * Ots_u1008_108: genotypes of SNP marker * Ots_108820_336: genotypes of SNP marker * Ots_112419_131: genotypes of SNP marker * Ots_124774_477: genotypes of SNP marker * Ots_parp3_286: genotypes of SNP marker * Ots_txnip_321: genotypes of SNP marker * Ots_103122_180: genotypes of SNP marker * Ots_109525_816: genotypes of SNP marker * Ots_112820_284: genotypes of SNP marker * Ots_brp16_64: genotypes of SNP marker * Ots_IsoT: genotypes of SNP marker * Ots_pigh_105: genotypes of SNP marker * Ots_104415_88: genotypes of SNP marker * Ots_112876_371: genotypes of SNP marker * Ots_129458_451: genotypes of SNP marker * Ots_pop5_96: genotypes of SNP marker * Ots_GCSH: genotypes of SNP marker * Ots_tpx2_125: genotypes of SNP marker * Ots_vatf_251: genotypes of SNP marker * Ots_OTALDBINT1_SNP1: genotypes of SNP marker * Ots_101119_381: genotypes of SNP marker * Ots_102213_210: genotypes of SNP marker * Ots_102457_132: genotypes of SNP marker * Ots_102867_609: genotypes of SNP marker * Ots_106499_70: genotypes of SNP marker * Ots_107074_284: genotypes of SNP marker * Ots_107285_93: genotypes of SNP marker * Ots_107806_821: genotypes of SNP marker * Ots_108007_208: genotypes of SNP marker * Ots_108390_329: genotypes of SNP marker * Ots_108735_302: genotypes of SNP marker * Ots_109693_392: genotypes of SNP marker * Ots_111681_657: genotypes of SNP marker * Ots_112208_722: genotypes of SNP marker * Ots_117242_136: genotypes of SNP marker * Ots_117: genotypes of SNP marker