Accuracy of Genomic Evaluations of Juvenile Growth Rate in Common Carp (Cyprinus carpio) Using Genotyping by Sequencing

. 2018 ; 9 () : 82. [epub] 20180313

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

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid29593780

Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key production traits. In the current study, a population of 1,425 carp juveniles, originating from a partial factorial cross between 40 sires and 20 dams, was used for investigating the potential of genomic selection (GS) for juvenile growth, an exemplar polygenic production trait. RAD sequencing was used to identify and genotype SNP markers for subsequent parentage assignment, construction of a medium density genetic map (12,311 SNPs), genome-wide association study (GWAS), and testing of GS. A moderate heritability was estimated for body length of carp at 120 days (as a proxy of juvenile growth) of 0.33 (s.e. 0.05). No genome-wide significant QTL was identified using a single marker GWAS approach. Genomic prediction of breeding values outperformed pedigree-based prediction, resulting in 18% improvement in prediction accuracy. The impact of reduced SNP densities on prediction accuracy was tested by varying minor allele frequency (MAF) thresholds, with no drop in prediction accuracy until the MAF threshold is set <0.3 (2,744 SNPs). These results point to the potential for GS to improve economically important traits in common carp breeding programs.

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Aguilar I., Misztal I., Legarra A., Tsuruta S. (2011). Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation. J. Anim. Breed. Genet. 128 422–428. 10.1111/j.1439-0388.2010.00912.x PubMed DOI

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

Balon E. K. (1995). Origin and domestication of the wild carp, Cyprinus carpio: from Roman gourmets to the swimming flowers. Aquaculture 129 3–48. 10.1016/0044-8486(94)00227-F DOI

Barría A., Christensen K. A., Yoshida G. M., Correa K., Jedlicki A., Lhorente J. P., et al. (2017). Genomic predictions and genome-wide association study of resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAD sequencing. G3. 10.1534/g3.118.200053 [Epub ahead of print]. PubMed DOI PMC

Baxter S. W., Davey J. W., Johnston J. S., Shelton A. M., Heckel D. G., Jiggins C. D., et al. (2011). Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One 6:e19315. 10.1371/journal.pone.0019315 PubMed DOI PMC

Campbell N. R., LaPatra S. E., Overturf K., Towner R., Narum S. R. (2014). Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing. G3 4 2473–2481. 10.1534/g3.114.014621 PubMed DOI PMC

Catchen J. M., Amores A., Hohenlohe P., Cresko W., Postlethwait J. H. (2011). Stacks: building and genotyping Loci de novo from short-read sequences. G3 1 171–182. 10.1534/g3.111.000240 PubMed DOI PMC

Daetwyler H. D., Calus M. P. L., Pong-Wong R., de los Campos G., Hickey J. M. (2013). Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking. Genetics 193 347–365. 10.1534/genetics.112.147983 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 los Campos G., Hickey J. M., Pong-Wong R., Daetwyler H. D., Calus M. P. L. (2013). Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 193 327–345. 10.1534/genetics.112.143313 PubMed DOI PMC

Dong Z., Nguyen N. H., Zhu W. (2015). Genetic evaluation of a selective breeding program for common carp Cyprinus carpio conducted from 2004 to 2014. BMC Genet. 16:94. 10.1186/s12863-015-0256-2 PubMed DOI PMC

Etter P. D., Bassham S., Hohenlohe P. A., Johnson E. A., Cresko W. A. (2011). SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods Mol. Biol. 772 157–178. 10.1007/978-1-61779-228-1-9 PubMed DOI PMC

FAO (2015). FishStat Database. Available at: http://faostat.fao.org/site/629/default.aspx

Ferdosi M. H., Kinghorn B. P., van der Werf J. H. J., Lee S. H., Gondro C. (2014). hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. BMC Bioinformatics 15:172. 10.1186/1471-2105-15-172 PubMed DOI PMC

Gjedrem T. (2000). Genetic improvement of cold-water fish species. Aquac. Res. 31 25–33. 10.1046/j.1365-2109.2000.00389.x DOI

Goddard M. E., Hayes B. J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10 381–391. 10.1038/nrg2575 PubMed DOI

Henderson C. R. (1975). Best linear unbiased estimation and prediction under a selection model. Biometrics 31 423–447. 10.2307/2529430 PubMed DOI

Hervé P., Dandine-Roulland C. (2018). Gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models Version 1.5 from CRAN. Available at: https://rdrr.io/cran/gaston/

Hickey J. M., Chiurugwi T., Mackay I., Powell W., Implementing Genomic Selection in CGIAR Breeding Programs Workshop Participants. (2017). Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nat. Genet. 49 1297–1303. 10.1038/ng.3920 PubMed DOI

Houston R. D., Davey J. W., Bishop S. C., Lowe N. R., Mota-Velasco J. C., Hamilton A., et al. (2012). Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics 13:244. 10.1186/1471-2164-13-244 PubMed DOI PMC

Houston R. D., Haley C. S., Hamilton A., Guy D. R., Tinch A. E., Taggart J. B., et al. , (2008). Major quantitative trait loci affect resistance to infectious pancreatic necrosis in atlantic salmon (Salmo salar). Genetics 178 1109–1115. 10.1534/genetics.107.082974 PubMed DOI PMC

Hu X., Li C., Shang M., Ge Y., Jia Z., Wang S., et al. (2017). Inheritance of growth traits in Songpu mirror carp (Cyprinus carpio L.) cultured in Northeast China. Aquaculture 477 1–5. 10.1016/j.aquaculture.2017.04.031 DOI

Hulata G. (1995). A review of genetic improvement of the common carp (Cyprinus carpio L.) and other cyprinids by crossbreeding, hybridization and selection. Aquaculture 129 143–155. 10.1016/0044-8486(94)00244-I DOI

Janssen K., Chavanne H., Berentsen P., Komen H. (2017). Impact of selective breeding on European aquaculture. Aquaculture 472 8–16. 10.1016/j.aquaculture.2016.03.012 DOI

Kocour M., Mauger S., Rodina M., Gela D., Linhart O., Vandeputte M. (2007). Heritability estimates for processing and quality traits in common carp (Cyprinus carpio L.) using a molecular pedigree. Aquaculture 270 43–50. 10.1016/j.aquaculture.2007.03.001 DOI

Langmead B., Salzberg S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 357–359. 10.1038/nmeth.1923 PubMed DOI PMC

Lillehammer M., Meuwissen T. H. E., Sonesson A. K. (2013). A low-marker density implementation of genomic selection in aquaculture using within-family genomic breeding values. Genet. Sel. Evol. 45:39. 10.1186/1297-9686-45-39 PubMed DOI PMC

Lv W., Zheng X., Kuang Y., Cao D., Yan Y., Sun X. (2016). QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio). BMC Genet. 17:65. 10.1186/s12863-016-0370-9 PubMed DOI PMC

Meuwissen T., Hayes B., Goddard M. (2013). Accelerating improvement of livestock with genomic selection. Annu. Rev. Anim. Biosci. 1 221–237. 10.1146/annurev-animal-031412-103705 PubMed DOI

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. PubMed PMC

Misztal I., Tsuruta S., Strabel T., Auvray B., Druet T., Lee D. H. (2002). “BLUPF90 and related programs (BGF90),” in Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier 21–22.

Moav R., Wohlfarth G. (1976). Two-way selection for growth rate in the common carp (Cyprinus carpio L.). Genetics 82 83–101. PubMed PMC

Moen T., Baranski M., Sonesson A. K., Kjøglum S. (2009). Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in atlantic salmon (Salmo salar): population-level associations between markers and trait. BMC Genomics 10:368. 10.1186/1471-2164-10-368 PubMed DOI PMC

Nielsen H. M., Ødegård J., Olesen I., Gjerde B., Ardo L., Jeney G., et al. (2010). Genetic analysis of common carp (Cyprinus carpio) strains. I: genetic parameters and heterosis for growth traits and survival. Aquaculture 304 14–21. 10.1016/j.aquaculture.2010.03.016 DOI

Ninh N. H., Ponzoni R. W., Nguyen N. H., Woolliams J. A., Taggart J. B., McAndrew B. J., et al. (2013). A comparison of communal and separate rearing of families in selective breeding of common carp (Cyprinus carpio): responses to selection. Aquaculture 40 152–159. 10.1016/j.aquaculture.2013.06.005 DOI

Odegård J., Moen T., Santi N., Korsvoll S. A., Kjøglum S., Meuwissen T. H. E. (2014). Genomic prediction in an admixed population of Atlantic salmon (Salmo salar). Front. Genet. 5:402. 10.3389/fgene.2014.00402 PubMed DOI PMC

Palaiokostas C., Ferraresso S., Franch R., Houston R. D., Bargelloni L. (2016). Genomic prediction of resistance to Pasteurellosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. G3 58 3693–3700. 10.1534/g3.116.035220 PubMed DOI PMC

Palti Y., Vallejo R. L., Gao G., Liu S., Hernandez A. G., Rexroad C. E., et al. (2015). Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing. PLoS One 10:e0138435. 10.1371/journal.pone.0138435 PubMed DOI PMC

Peng W., Xu J., Zhang Y., Feng J., Dong C., Jiang L., et al. (2016). An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio). Sci. Rep. 6:26693. 10.1038/srep26693 PubMed DOI PMC

Rastas P., Paulin L., Hanski I., Lehtonen R., Auvinen P. (2013). Lep-MAP: fast and accurate linkage map construction for large SNP datasets. Bioinformatics 29 3128–3134. 10.1093/bioinformatics/btt563 PubMed DOI PMC

Robledo D., Palaiokostas C., Bargelloni L., Martínez P., Houston R. (2017). Applications of genotyping by sequencing in aquaculture breeding and genetics. Rev. Aquac. 10.1111/raq.12193 [Epub ahead of print]. PubMed DOI PMC

Sargolzaei M., Chesnais J. P., Schenkel F. S. (2014). A new approach for efficient genotype imputation using information from relatives. BMC Genomics 15:478. 10.1186/1471-2164-15-478 PubMed DOI PMC

Sonesson A. K., Meuwissen T. H. E. (2009). Testing strategies for genomic selection in aquaculture breeding programs. Genet. Sel. Evol. 41:37. 10.1186/1297-9686-41-37 PubMed DOI PMC

Tsai H.-Y., Hamilton A., Tinch A. E., Guy D. R., Bron J. E., Taggart J. B., et al. (2016). Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations. Genet. Sel. Evol. 48:47. 10.1186/s12711-016-0226-9 PubMed DOI PMC

Tsai H.-Y., Hamilton A., Tinch A. E., Guy D. R., Gharbi K., Stear M. J., et al. (2015). Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array. BMC Genomics 16:969. 10.1186/s12864-015-2117-9 PubMed DOI PMC

Tsai H.-Y., Matika O., Edwards S. M., Antolín-Sánchez R., Hamilton A., Guy D. R., et al. (2017). Genotype imputation to improve the cost-efficiency of genomic selection in farmed Atlantic salmon. G3, 1377–1383. 10.1534/g3.117.040717 PubMed DOI PMC

Vallejo R. L., Leeds T. D., Fragomeni B. O., Gao G., Hernandez A. G., Misztal I., et al. (2016). Evaluation of genome-enabled selection for bacterial cold water disease resistance using progeny performance data in rainbow trout: insights on genotyping methods and genomic prediction models. Front. Genet. 7:96. 10.3389/fgene.2016.00096 PubMed DOI PMC

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

Vandeputte M. (2003). Selective breeding of quantitative traits in the common carp (Cyprinus carpio): a review. Aquat. Living Resour. 16 399–407. 10.1016/S0990-7440(03)00056-1 DOI

Vandeputte M., Haffray P. (2014). Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals. Front. Genet. 5:432. 10.3389/fgene.2014.00432 PubMed DOI PMC

Vandeputte M., Kocour M., Mauger S., Dupont-Nivet M., De Guerry D., Rodina M., et al. (2004). Heritability estimates for growth-related traits using microsatellite parentage assignment in juvenile common carp (Cyprinus carpio L.). Aquaculture 235 223–236. 10.1016/j.aquaculture.2003.12.019 DOI

Vandeputte M., Kocour M., Mauger S., Rodina M., Launay A., Gela D., et al. (2008). Genetic variation for growth at one and two summers of age in the common carp (Cyprinus carpio L.): heritability estimates and response to selection. Aquaculture 277 7–13. 10.1016/j.aquaculture.2008.02.009 DOI

VanRaden P. M. (2008). Efficient methods to compute genomic predictions. J. Dairy Sci. 91 4414–4423. 10.3168/jds.2007-0980 PubMed DOI

Xu P., Zhang X., Wang X., Li J., Liu G., Kuang Y., et al. (2014). Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat. Genet. 46 1212–1219. 10.1038/ng.3098 PubMed DOI

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