Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

. 2022 ; 13 () : 941340. [epub] 20220718

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid35923696

Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2-10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50-100 kb which are usual distances between markers of the medium-density chip.

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Altshuler D. L., Durbin R. M., Abecasis G. R., Bentley D. R., Chakravarti A., Clark A. G., et al. (2010). A Map of Human Genome Variation from Population-Scale Sequencing. Nature 467, 1061–1073. 10.1038/nature09534 PubMed DOI PMC

Anderson J. L., Rodríguez Marí A., Braasch I., Amores A., Hohenlohe P., Batzel P., et al. (2012). Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics. PLoS One 7, e40701. 10.1371/journal.pone.0040701 PubMed DOI PMC

Arias J. A., Keehan M., Fisher P., Coppieters W., Spelman R. (2009). A High Density Linkage Map of the Bovine Genome. BMC Genet. 10, 18. 10.1186/1471-2156-10-18 PubMed DOI PMC

Auton A., Brooks L. D., Durbin R. M., Garrison E. P., Kang H. M., Korbel J. O., et al. (2015). A Global Reference for Human Genetic Variation. Nature 526, 68–74. 10.1038/nature15393 PubMed DOI PMC

Baird N. A., Etter P. D., Atwood T. S., Currey M. C., Shiver A. L., Lewis Z. A., et al. (2008). Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS One 3, e3376. 10.1371/journal.pone.0003376 PubMed DOI PMC

Barría A., Christensen K. A., Yoshida G., Jedlicki A., Leong J. S., Rondeau E. B., et al. (2019). Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus Kisutch) Breeding Population Using a High-Density SNP Array. Front. Genet. 10, 498. 10.3389/fgene.2019.00498 PubMed DOI PMC

Barson N. J., Aykanat T., Hindar K., Baranski M., Bolstad G. H., Fiske P., et al. (2015). Sex-dependent Dominance at a Single Locus Maintains Variation in Age at Maturity in Salmon. Nature 528, 405–408. 10.1038/nature16062 PubMed DOI

Berthelot C., Brunet F., Chalopin D., Juanchich A., Bernard M., Noël B., et al. (2014). The Rainbow Trout Genome Provides Novel Insights into Evolution after Whole-Genome Duplication in Vertebrates. Nat. Commun. 5, 3657. 10.1038/ncomms4657 PubMed DOI PMC

Blay C., Haffray P., Bugeon J., D’Ambrosio J., Dechamp N., Collewet G., et al. (2021a). Genetic Parameters and Genome-wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus Mykiss . Front. Genet. 12, 639223. 10.3389/fgene.2021.639223 PubMed DOI PMC

Blay C., Haffray P., D’Ambrosio J., Prado E., Dechamp N., Nazabal V., et al. (2021b). Genetic Architecture and Genomic Selection of Fatty Acid Composition Predicted by Raman Spectroscopy in Rainbow Trout. BMC Genomics 22, 788. 10.1186/s12864-021-08062-7 PubMed DOI PMC

Bolger A. M., Lohse M., Usadel B. (2014). Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 PubMed DOI PMC

Boudry P., Allal F., Aslam M. L., Bargelloni L., Bean T. P., Brard-Fudulea S., et al. (2021). Current Status and Potential of Genomic Selection to Improve Selective Breeding in the Main Aquaculture Species of International Council for the Exploration of the Sea (ICES) Member Countries. Aquac. Rep. 20, 100700. 10.1016/j.aqrep.2021.100700 DOI

Broad Institute (2019). Picard Toolkit: Broad Institute, GitHub Repository. Available at: https://broadinstitute.github.io/picard/ (Accessed December 11, 2017).

Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., et al. (2009). BLAST+: Architecture and Applications. BMC Bioinform. 10, 421. 10.1186/1471-2105-10-421 PubMed DOI PMC

D’Ambrosio J., Phocas F., Haffray P., Bestin A., Brard-Fudulea S., Poncet C., et al. (2019). Genome-wide Estimates of Genetic Diversity, Inbreeding and Effective Size of Experimental and Commercial Rainbow Trout Lines Undergoing Selective Breeding. Genet. Sel. Evol. 51, 26. 10.1186/s12711-019-0468-4 PubMed DOI PMC

D’Ambrosio J., Morvezen R., Brard-Fudulea S., Bestin A., Acin Perez A., Guéméné D., et al. (2020). Genetic Architecture and Genomic Selection of Female Reproduction Traits in Rainbow Trout. BMC Genomics 21, 558. 10.1186/s12864-020-06955-7 PubMed DOI PMC

Daetwyler H. D., Capitan A., Pausch H., Stothard P., Van Binsbergen R., Brøndum R. F., et al. (2014). Whole-genome Sequencing of 234 Bulls Facilitates Mapping of Monogenic and Complex Traits in Cattle. Nat. Genet. 46, 858–865. 10.1038/ng.3034 PubMed DOI

Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., DePristo M. A., et al. (2011). The Variant Call Format and VCFtools. Bioinformatics 27, 2156–2158. 10.1093/bioinformatics/btr330 PubMed DOI PMC

Danecek P., Bonfield J. K., Liddle J., Marshall J., Ohan V., Pollard M. O., et al. (2021). Twelve Years of SAMtools and BCFtools. Gigascience 10, 1–4. 10.1093/gigascience/giab008 PubMed DOI PMC

Davey J. W., Hohenlohe P. A., Etter P. D., Boone J. Q., Catchen J. M., Blaxter M. L. (2011). Genome-wide Genetic Marker Discovery and Genotyping Using Next-Generation Sequencing. Nat. Rev. Genet. 12, 499–510. 10.1038/nrg3012 PubMed DOI

de Roos A. P. W., Hayes B. J., Spelman R. J., Goddard M. E. (2008). Linkage Disequilibrium and Persistence of Phase in Holstein-Friesian, Jersey and Angus Cattle. Genetics 179, 1503–1512. 10.1534/genetics.107.084301 PubMed DOI PMC

Fairley S., Lowy-Gallego E., Perry E., Flicek P. (2020). The International Genome Sample Resource (IGSR) Collection of Open Human Genomic Variation Resources. Nucleic Acids Res. 48, D941–D947. 10.1093/nar/gkz836 PubMed DOI PMC

Franěk R., Baloch A. R., Kašpar V., Saito T., Fujimoto T., Arai K., et al. (2020). Isogenic Lines in Fish-A Critical Review. Rev. Aquacult 12, 1412–1434. 10.1111/raq.12389 DOI

Fraslin C., Brard‐Fudulea S., D'Ambrosio J., Bestin A., Charles M., Haffray P., et al. (2019). Rainbow Trout Resistance to Bacterial Cold Water Disease: Two New Quantitative Trait Loci Identified after a Natural Disease Outbreak on a French Farm. Anim. Genet. 50, 293–297. 10.1111/age.12777 PubMed DOI

Fraslin C., Phocas F., Bestin A., Charles M., Bernard M., Krieg F., et al. (2020). Genetic Determinism of Spontaneous Masculinisation in XX Female Rainbow Trout: New Insights Using Medium Throughput Genotyping and Whole-Genome Sequencing. Sci. Rep. 10, 17693. 10.1038/s41598-020-74757-8 PubMed DOI PMC

Gao G., Nome T., Pearse D. E., Moen T., Naish K. A., Thorgaard G. H., et al. (2018). A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated through Whole Genome Resequencing. Front. Genet. 9, 147. 10.3389/fgene.2018.00147 PubMed DOI PMC

Gao G., Magadan S., Waldbieser G. C., Youngblood R. C., Wheeler P. A., Scheffler B. E., et al. (2021). A Long Reads-Based De-novo Assembly of the Genome of the Arlee Homozygous Line Reveals Chromosomal Rearrangements in Rainbow Trout. G3 Genes Genomes Genetics 11, jkab052. 10.1093/g3journal/jkab052 PubMed DOI PMC

Garrison E., Marth G. (2012). Haplotype-based Variant Detection from Short-Read Sequencing, arXiv [q-bio.GN]. Available at: https://arxiv.org/abs/1207.3907 (Accessed November 13, 2018).

Gautier M., Laloë D., Moazami-Goudarzi K. (2010). Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds. PLoS One 5, e13038. 10.1371/journal.pone.0013038 PubMed DOI PMC

Goddard M. E., Kemper K. E., MacLeod I. M., Chamberlain A. J., Hayes B. J. (2016). Genetics of Complex Traits: Prediction of Phenotype, Identification of Causal Polymorphisms and Genetic Architecture. Proc. R. Soc. B 283, 20160569. 10.1098/rspb.2016.0569 PubMed DOI PMC

Gonzalez-Pena D., Gao G., Baranski M., Moen T., Cleveland B. M., Kenney P. B., et al. (2016). Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus Mykiss). Front. Genet. 7, 203. 10.3389/fgene.2016.00203 PubMed DOI PMC

Gorjanc G., Dumasy J.-F., Gonen S., Gaynor R. C., Antolin R., Hickey J. M. (2017). Potential of Low-Coverage Genotyping-By-Sequencing and Imputation for Cost-Effective Genomic Selection in Biparental Segregating Populations. Crop Sci. 57, 1404–1420. 10.2135/cropsci2016.08.0675 DOI

Gui J.-F., Zhou L., Li X.-Y. (2022). Rethinking Fish Biology and Biotechnologies in the Challenge Era for Burgeoning Genome Resources and Strengthening Food Security. Water Biol. Secur. 1, 100002. 10.1016/j.watbs.2021.11.001 DOI

Guyomard R., Boussaha M., Krieg F., Hervet C., Quillet E. (2012). A Synthetic Rainbow Trout Linkage Map Provides New Insights into the Salmonid Whole Genome Duplication and the Conservation of Synteny Among Teleosts. BMC Genet. 13, 15. 10.1186/1471-2156-13-15 PubMed DOI PMC

Haenel Q., Laurentino T. G., Roesti M., Berner D. (2018). Meta-analysis of Chromosome-Scale Crossover Rate Variation in Eukaryotes and its Significance to Evolutionary Genomics. Mol. Ecol. 27, 2477–2497. 10.1111/mec.14699 PubMed DOI

Hayes B. J., Daetwyler H. D. (2019). 1000 Bull Genomes Project to Map Simple and Complex Genetic Traits in Cattle: Applications and Outcomes. Annu. Rev. Anim. Biosci. 7, 89–102. 10.1146/annurev-animal-020518-115024 PubMed DOI

Hayes B. J., Visscher P. M., McPartlan H. C., Goddard M. E. (2003). Novel Multilocus Measure of Linkage Disequilibrium to Estimate Past Effective Population Size. Genome Res. 13, 635–643. 10.1101/gr.387103 PubMed DOI PMC

Hozé C., Fouilloux M.-N., Venot E., Guillaume F., Dassonneville R., Fritz S., et al. (2013). High-density Marker Imputation Accuracy in Sixteen French Cattle Breeds. Genet. Sel. Evol. 45, 33. 10.1186/1297-9686-45-33 PubMed DOI PMC

Johnston S. E., Bérénos C., Slate J., Pemberton J. M. (2016). Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis Aries). Genetics 203, 583–598. 10.1534/genetics.115.185553 PubMed DOI PMC

Karami A. M., Ødegård J., Marana M. H., Zuo S., Jaafar R., Mathiessen H., et al. (2020). A Major QTL for Resistance to Vibrio Anguillarum in Rainbow Trout. Front. Genet. 11, 607558. 10.3389/fgene.2020.607558 PubMed DOI PMC

Kardos M., Luikart G., Allendorf F. W. (2015). Measuring Individual Inbreeding in the Age of Genomics: Marker-Based Measures Are Better Than Pedigrees. Heredity 115, 63–72. 10.1038/hdy.2015.17 PubMed DOI PMC

Khanyile K. S., Dzomba E. F., Muchadeyi F. C. (2015). Population Genetic Structure, Linkage Disequilibrium and Effective Population Size of Conserved and Extensively Raised Village Chicken Populations of Southern Africa. Front. Genet. 6, 13. 10.3389/fgene.2015.00013 PubMed DOI PMC

Kijas J., Elliot N., Kube P., Evans B., Botwright N., King H., et al. (2017). Diversity and Linkage Disequilibrium in Farmed Tasmanian Atlantic Salmon. Anim. Genet. 48, 237–241. 10.1111/age.12513 PubMed DOI

Kranis A., Gheyas A. A., Boschiero C., Turner F., Yu L., Smith S., et al. (2013). Development of a High Density 600K SNP Genotyping Array for Chicken. BMC Genomics 14, 59. 10.1186/1471-2164-14-59 PubMed DOI PMC

Larson W. A., Palti Y., Gao G., Warheit K. I., Seeb J. E. (2018). Rapid Discovery of SNPs that Differentiate Hatchery Steelhead Trout from ESA-Listed Natural-Origin Steelhead Trout Using a 57K SNP Array. Can. J. Fish. Aquat. Sci. 75, 1160–1168. 10.1139/cjfas-2017-0116 DOI

Li H. (2013). Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM. arXiv [q-bio.GN]. Available at: https://arxiv.org/abs/1303.3997 (Accessed December 11, 2017).

Lien S., Koop B. F., Sandve S. R., Miller J. R., Kent M. P., Nome T., et al. (2016). The Atlantic Salmon Genome Provides Insights into Rediploidization. Nature 533, 200–205. 10.1038/nature17164 PubMed DOI PMC

Liu S., Gao G., Layer R. M., Thorgaard G. H., Wiens G. D., Leeds T. D., et al. (2021). Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing. Front. Genet. 12, 639355. 10.3389/fgene.2021.639355 PubMed DOI PMC

Marchini J., Howie B. (2010). Genotype Imputation for Genome-wide Association Studies. Nat. Rev. Genet. 11, 499–511. 10.1038/nrg2796 PubMed DOI

Mastrangelo S., Di Gerlando R., Di Gerlando R., Tolone M., Tortorici L., Sardina M. T., et al. (2014). Genome Wide Linkage Disequilibrium and Genetic Structure in Sicilian Dairy Sheep Breeds. BMC Genet. 15, 108. 10.1186/s12863-014-0108-5 PubMed DOI PMC

McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., et al. (2010). The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data. Genome Res. 20, 1297–1303. 10.1101/gr.107524.110 PubMed DOI PMC

Meuwissen T., Goddard M. (2010). Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing. Genetics 185, 623–631. 10.1534/genetics.110.116590 PubMed DOI PMC

Meuwissen T. H. E., Hayes B. J., Goddard M. E. (2001). Prediction of Total Genetic Value Using Genome-wide Dense Marker Maps. Genetics 157, 1819–1829. 10.1093/genetics/157.4.1819 PubMed DOI PMC

Moen T., Torgersen J., Santi N., Davidson W. S., Baranski M., Ødegård J., et al. (2015). Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon. Genetics 200, 1313–1326. 10.1534/genetics.115.175406 PubMed DOI PMC

Palti Y., Gao G., Miller M. R., Vallejo R. L., Wheeler P. A., Quillet E., et al. (2014). A Resource of Single-Nucleotide Polymorphisms for Rainbow Trout Generated by Restriction-Site Associated DNA Sequencing of Doubled Haploids. Mol. Ecol. Resour. 14, 588–596. 10.1111/1755-0998.12204 PubMed DOI

Palti Y., Gao G., Liu S., Kent M. P., Lien S., Miller M. R., et al. (2015). The Development and Characterization of a 57K Single Nucleotide Polymorphism Array for Rainbow Trout. Mol. Ecol. Resour. 15, 662–672. 10.1111/1755-0998.12337 PubMed DOI

Pasaniuc B., Rohland N., McLaren P. J., Garimella K., Zaitlen N., Li H., et al. (2012). Extremely Low-Coverage Sequencing and Imputation Increases Power for Genome-wide Association Studies. Nat. Genet. 44, 631–635. 10.1038/ng.2283 PubMed DOI PMC

Paul K., D'Ambrosio J., Phocas F. (2021). Temporal and Region‐specific Variations in Genome wide Inbreeding Effects on Female Size and Reproduction Traits of Rainbow Trout. Evol. Appl. 15, 645–662. 10.1111/eva.13308 PubMed DOI PMC

Pearse D. E., Barson N. J., Nome T., Gao G., Campbell M. A., Abadía-Cardoso A., et al. (2019). Sex-dependent Dominance Maintains Migration Supergene in Rainbow Trout. Nat. Ecol. Evol. 3, 1731–1742. 10.1038/s41559-019-1044-6 PubMed DOI

Petit M., Astruc J.-M., Sarry J., Drouilhet L., Fabre S., Moreno C. R., et al. (2017). Variation in Recombination Rate and its Genetic Determinism in Sheep Populations. Genetics 207, 767–784. 10.1534/genetics.117.300123 PubMed DOI PMC

Phillips R., Ráb P. (2001). Chromosome Evolution in the Salmonidae (Pisces): An Update. Biol. Rev. 76, 1–25. 10.1017/S1464793100005613 PubMed DOI

Phocas F. (2022). “Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools,” in Chapter 4 in: Complex Trait Prediction. Editors Ahmadi N., Bartholomé J. (New York, NY: Springer Protocols; ), 113–138. 10.1007/978-1-0716-2205-6_4 PubMed DOI

Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M. A. R., Bender D., et al. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am. J. Hum. Genet. 81, 559–575. 10.1086/519795 PubMed DOI PMC

Quillet E., Dorson M., Leguillou S., Benmansour A., Boudinot P. (2007). Wide Range of Susceptibility to Rhabdoviruses in Homozygous Clones of Rainbow Trout. Fish Shellfish Immunol. 22, 510–519. 10.1016/j.fsi.2006.07.002 PubMed DOI

R Core Team (2019). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Available at: https://www.R-project.org/ (Accessed January 27, 2022).

Reis Neto R. V., Yoshida G. M., Lhorente J. P., Yáñez J. M. (2019). Genome-wide Association Analysis for Body Weight Identifies Candidate Genes Related to Development and Metabolism in Rainbow Trout (Oncorhynchus Mykiss). Mol. Genet. Genomics 294, 563–571. 10.1007/s00438-018-1518-2 PubMed DOI

Ristow S. S., Grabowski L. D., Ostberg C., Robison B., Thorgaard G. H. (1998). Development of Long-Term Cell Lines from Homozygous Clones of Rainbow Trout. J. Aquatic Animal Health 10, 75–82. 10.1577/1548-8667(1998)010<0075:doltcl>2.0.co;2 DOI

Rodríguez F. H., Flores-Mara R., Yoshida G. M., Barría A., Jedlicki A. M., Lhorente J. P., et al. (2019). Genome-wide Association Analysis for Resistance to Infectious Pancreatic Necrosis Virus Identifies Candidate Genes Involved in Viral Replication and Immune Response in Rainbow Trout (Oncorhynchus Mykiss). G3 Genes Genomes Genet. 9, 2897–2904. 10.1534/g3.119.400463 PubMed DOI PMC

Rodríguez-Ramilo S. T., Fernández J., Toro M. A., Hernández D., Villanueva B. (2015). Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population. PLoS One 10, e0124157. 10.1371/journal.pone.0124157 PubMed DOI PMC

Sánchez C. C., Smith T. P., Wiedmann R. T., Vallejo R. L., Salem M., Yao J., et al. (2009). Single Nucleotide Polymorphism Discovery in Rainbow Trout by Deep Sequencing of a Reduced Representation Library. BMC Genomics 10, 559. 10.1186/1471-2164-10-559 PubMed DOI PMC

Sánchez C. C., Weber G. M., Gao G., Cleveland B. M., Yao J., Rexroad C. E. (2011). Generation of a Reference Transcriptome for Evaluating Rainbow Trout Responses to Various Stressors. BMC Genomics 12, 626. 10.1186/1471-2164-12-626 PubMed DOI PMC

Sakamoto T., Danzmann R. G., Gharbi K., Howard P., Ozaki A., Khoo S. K., et al. (2000). A Microsatellite Linkage Map of Rainbow Trout (Oncorhynchus Mykiss) Characterized by Large Sex-specific Differences in Recombination Rates. Genetics 155, 1331–1345. 10.1093/genetics/155.3.1331 PubMed DOI PMC

Sandor C., Li W., Coppieters W., Druet T., Charlier C., Georges M. (2012). Genetic Variants in REC8, RNF212, and PRDM9 Influence Male Recombination in Cattle. PLoS Genet. 8, e1002854. 10.1371/journal.pgen.1002854 PubMed DOI PMC

Santiago E., Novo I., Pardiñas A. F., Saura M., Wang J., Caballero A. (2020). Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium. Mol. Biol. Evol. 37, 3642–3653. 10.1093/molbev/msaa169 PubMed DOI

Schweizer R. M., VonHoldt B. M., Harrigan R., Knowles J. C., Musiani M., Coltman D., et al. (2016). Genetic Subdivision and Candidate Genes under Selection in North American Grey Wolves. Mol. Ecol. 25, 380–402. 10.1111/mec.13364 PubMed DOI

Silió L., Rodríguez M. C., Fernández A., Barragán C., Benítez R., Óvilo C., et al. (2013). Measuring Inbreeding and Inbreeding Depression on Pig Growth from Pedigree or SNP-Derived Metrics. J. Anim. Breed. Genet. 130, 349–360. 10.1111/jbg.12031 PubMed DOI

Stapley J., Feulner P. G. D., Johnston S. E., Santure A. W., Smadja C. M. (2017). Variation in Recombination Frequency and Distribution across Eukaryotes: Patterns and Processes. Phil. Trans. R. Soc. B 372, 20160455. 10.1098/rstb.2016.0455 PubMed DOI PMC

Sved J. A. (1971). Linkage Disequilibrium and Homozygosity of Chromosome Segments in Finite Populations. Theor. Popul. Biol. 2, 125–141. 10.1016/0040-5809(71)90011-6 PubMed DOI

Talbert P. B., Henikoff S. (2010). Centromeres Convert but Don't Cross. PLoS Biol. 8, e1000326. 10.1371/journal.pbio.1000326 PubMed DOI PMC

Thorgaard G. H., Allendorf F. W., Knudsen K. L. (1983). Gene-Centromere Mapping in Rainbow Trout: High Interference over Long Map Distances. Genetics 103, 771–783. 10.1093/genetics/103.4.771 PubMed DOI PMC

Thorgaard G. H., Bailey G. S., Williams D., Buhler D. R., Kaattari S. L., Ristow S. S., et al. (2002). Status and Opportunities for Genomics Research with Rainbow Trout. Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 133, 609–646. 10.1016/s1096-4959(02)00167-7 PubMed DOI

Vallejo R. L., Leeds T. D., Gao G., Parsons J. E., Martin K. E., Evenhuis J. P., et al. (2017). Genomic Selection Models Double the Accuracy of Predicted Breeding Values for Bacterial Cold Water Disease Resistance Compared to a Traditional Pedigree-Based Model in Rainbow Trout Aquaculture. Genet. Sel. Evol. 49, 17. 10.1186/s12711-017-0293-6 PubMed DOI PMC

Vallejo R. L., Silva R. M. O., Evenhuis J. P., Gao G., Liu S., Parsons J. E., et al. (2018). Accurate Genomic Predictions for BCWD Resistance in Rainbow Trout are Achieved Using Low Density SNP Panels: Evidence that Long Range LD is a Major Contributing Factor. J. Anim. Breed. Genet. 135, 263–274. 10.1111/jbg.12335 PubMed DOI

Vallejo R. L., Cheng H., Fragomeni B. O., Shewbridge K. L., Gao G., MacMillan J. R., et al. (2019). Genome-wide Association Analysis and Accuracy of Genome-Enabled Breeding Value Predictions for Resistance to Infectious Hematopoietic Necrosis Virus in a Commercial Rainbow Trout Breeding Population. Genet. Sel. Evol. 51, 47. 10.1186/s12711-019-0489-z PubMed DOI PMC

Vallejo R. L., Fragomeni B. O., Cheng H., Gao G., Long R. L., Shewbridge K. L., et al. (2020). Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus with Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population. Front. Vet. Sci. 7, 590048. 10.3389/fvets.2020.590048 PubMed DOI PMC

Yáñez J. M., Naswa S., López M. E., Bassini L., Correa K., Gilbey J., et al. (2016). Genomewide Single Nucleotide Polymorphism Discovery in Atlantic Salmon (Salmo Salar): Validation in Wild and Farmed American and European Populations. Mol. Ecol. Resour. 16, 1002–1011. 10.1111/1755-0998.12503 PubMed DOI

Yoshida G. M., Carvalheiro R., Rodríguez F. H., Lhorente J. P., Yáñez J. M. (2019). Single-step Genomic Evaluation Improves Accuracy of Breeding Value Predictions for Resistance to Infectious Pancreatic Necrosis Virus in Rainbow Trout. Genomics 111, 127–132. 10.1016/j.ygeno.2018.01.008 PubMed DOI

Young W. P., Wheeler P. A., Fields A. D., Thorgaard G. H., Vrijenhoek R. C. (1996). DNA Fingerprinting Confirms Isogenicity of Androgenetically Derived Rainbow Trout Lines. J. Hered. 87, 77–81. 10.1093/oxfordjournals.jhered.a022960 PubMed DOI

Zeng Q., Fu Q., Li Y., Waldbieser G., Bosworth B., Liu S., et al. (2017). Development of a 690 K SNP Array in Catfish and its Application for Genetic Mapping and Validation of the Reference Genome Sequence. Sci. Rep. 7, 40347. 10.1038/srep40347 PubMed DOI PMC

Zhao Z., Fu Y.-X., Hewett-Emmett D., Boerwinkle E. (2003). Investigating Single Nucleotide Polymorphism (SNP) Density in the Human Genome and its Implications for Molecular Evolution. Gene 312, 207–213. 10.1016/S0378-1119(03)00670-X PubMed DOI

Zhou T., Chen B., Ke Q., Zhao J., Pu F., Wu Y., et al. (2020). Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys Crocea). Front. Genet. 11, 571751. 10.3389/fgene.2020.571751 PubMed DOI PMC

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