Development of genomic predictions for harvest and carcass weight in channel catfish

Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Garcia, Andre L. S. [verfasserIn] Bosworth, Brian Waldbieser, Geoffrey Misztal, Ignacy Tsuruta, Shogo Lourenco, Daniela A. L.

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2018

Anmerkung:	© The Author(s) 2018

Übergeordnetes Werk:	Enthalten in: Genetics, selection, evolution - London : BioMed Central, 1989, 50(2018), 1 vom: 14. Dez.
Übergeordnetes Werk:	volume:50 ; year:2018 ; number:1 ; day:14 ; month:12

Links:	Volltext

DOI / URN:	10.1186/s12711-018-0435-5

Katalog-ID:	SPR026812282

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520			\|a Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families.
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700	1		\|a Lourenco, Daniela A. L. \|4 aut
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allfields	10.1186/s12711-018-0435-5 doi (DE-627)SPR026812282 (SPR)s12711-018-0435-5-e DE-627 ger DE-627 rakwb eng Garcia, Andre L. S. verfasserin (orcid)0000-0001-9778-7978 aut Development of genomic predictions for harvest and carcass weight in channel catfish 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2018 Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. Bosworth, Brian aut Waldbieser, Geoffrey aut Misztal, Ignacy aut Tsuruta, Shogo aut Lourenco, Daniela A. L. aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 50(2018), 1 vom: 14. Dez. (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:50 year:2018 number:1 day:14 month:12 https://dx.doi.org/10.1186/s12711-018-0435-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 50 2018 1 14 12
spelling	10.1186/s12711-018-0435-5 doi (DE-627)SPR026812282 (SPR)s12711-018-0435-5-e DE-627 ger DE-627 rakwb eng Garcia, Andre L. S. verfasserin (orcid)0000-0001-9778-7978 aut Development of genomic predictions for harvest and carcass weight in channel catfish 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2018 Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. Bosworth, Brian aut Waldbieser, Geoffrey aut Misztal, Ignacy aut Tsuruta, Shogo aut Lourenco, Daniela A. L. aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 50(2018), 1 vom: 14. Dez. (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:50 year:2018 number:1 day:14 month:12 https://dx.doi.org/10.1186/s12711-018-0435-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 50 2018 1 14 12
allfields_unstemmed	10.1186/s12711-018-0435-5 doi (DE-627)SPR026812282 (SPR)s12711-018-0435-5-e DE-627 ger DE-627 rakwb eng Garcia, Andre L. S. verfasserin (orcid)0000-0001-9778-7978 aut Development of genomic predictions for harvest and carcass weight in channel catfish 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2018 Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. Bosworth, Brian aut Waldbieser, Geoffrey aut Misztal, Ignacy aut Tsuruta, Shogo aut Lourenco, Daniela A. L. aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 50(2018), 1 vom: 14. Dez. (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:50 year:2018 number:1 day:14 month:12 https://dx.doi.org/10.1186/s12711-018-0435-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 50 2018 1 14 12
allfieldsGer	10.1186/s12711-018-0435-5 doi (DE-627)SPR026812282 (SPR)s12711-018-0435-5-e DE-627 ger DE-627 rakwb eng Garcia, Andre L. S. verfasserin (orcid)0000-0001-9778-7978 aut Development of genomic predictions for harvest and carcass weight in channel catfish 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2018 Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. Bosworth, Brian aut Waldbieser, Geoffrey aut Misztal, Ignacy aut Tsuruta, Shogo aut Lourenco, Daniela A. L. aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 50(2018), 1 vom: 14. Dez. (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:50 year:2018 number:1 day:14 month:12 https://dx.doi.org/10.1186/s12711-018-0435-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 50 2018 1 14 12
allfieldsSound	10.1186/s12711-018-0435-5 doi (DE-627)SPR026812282 (SPR)s12711-018-0435-5-e DE-627 ger DE-627 rakwb eng Garcia, Andre L. S. verfasserin (orcid)0000-0001-9778-7978 aut Development of genomic predictions for harvest and carcass weight in channel catfish 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2018 Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. Bosworth, Brian aut Waldbieser, Geoffrey aut Misztal, Ignacy aut Tsuruta, Shogo aut Lourenco, Daniela A. L. aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 50(2018), 1 vom: 14. Dez. (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:50 year:2018 number:1 day:14 month:12 https://dx.doi.org/10.1186/s12711-018-0435-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 50 2018 1 14 12
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S.</subfield><subfield code="e">verfasserin</subfield><subfield code="0">(orcid)0000-0001-9778-7978</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Development of genomic predictions for harvest and carcass weight in channel catfish</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2018</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">© The Author(s) 2018</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Bosworth, Brian</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Waldbieser, Geoffrey</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Misztal, Ignacy</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Tsuruta, Shogo</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Lourenco, Daniela A. 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author	Garcia, Andre L. S.
spellingShingle	Garcia, Andre L. S. Development of genomic predictions for harvest and carcass weight in channel catfish
authorStr	Garcia, Andre L. S.
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topic_title	Development of genomic predictions for harvest and carcass weight in channel catfish
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title	Development of genomic predictions for harvest and carcass weight in channel catfish
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title_full	Development of genomic predictions for harvest and carcass weight in channel catfish
author_sort	Garcia, Andre L. S.
journal	Genetics, selection, evolution
journalStr	Genetics, selection, evolution
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author_browse	Garcia, Andre L. S. Bosworth, Brian Waldbieser, Geoffrey Misztal, Ignacy Tsuruta, Shogo Lourenco, Daniela A. L.
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title_sort	development of genomic predictions for harvest and carcass weight in channel catfish
title_auth	Development of genomic predictions for harvest and carcass weight in channel catfish
abstract	Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. © The Author(s) 2018
abstractGer	Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. © The Author(s) 2018
abstract_unstemmed	Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). Conclusions Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families. © The Author(s) 2018
collection_details	GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700
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title_short	Development of genomic predictions for harvest and carcass weight in channel catfish
url	https://dx.doi.org/10.1186/s12711-018-0435-5
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author2	Bosworth, Brian Waldbieser, Geoffrey Misztal, Ignacy Tsuruta, Shogo Lourenco, Daniela A. L.
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up_date	2024-07-03T22:52:05.759Z
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S.</subfield><subfield code="e">verfasserin</subfield><subfield code="0">(orcid)0000-0001-9778-7978</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Development of genomic predictions for harvest and carcass weight in channel catfish</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2018</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">© The Author(s) 2018</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Background Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. 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Results Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). 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Development of genomic predictions for harvest and carcass weight in channel catfish

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