Animal Science Publications Animal Science 9-1-2013 Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens Anna Wolc Iowa State University, [email protected] Jesus Arango Hy-Line International Tomasz Jankowski Poznan Supercomputing and Networking Center Petek Settar Hy-Line International Janet E. Fulton Hy-Line International See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/ans_pubs Part of the Genetics and Genomics Commons, and the Poultry or Avian Science Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ ans_pubs/649. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens Abstract Efficiency of oductionpr is increasingly important with the current escalation of feed costs and demands to minimize the environmental footprint. The objectives of this study were 1) to estimate heritabilities for daily feed consumption and residual feed intake and their genetic correlations with production and egg- quality traits; 2) to evaluate accuracies of estimated breeding values from pedigree- and marker-based prediction models; and 3) to localize genomic regions associated with feed efficiency in a ownbr egg layer line. Individual feed intake data collected over 2-wk trial periods were available for approximately 6,000 birds from 8 generations. Genetic parameters were estimated with a multitrait animal model; methods BayesB and BayesCπ were used to estimate marker effects and find genomic egionsr associated with feed efficiency. Using pedigree information, feed efficiency was foundo t be moderately heritable (h2 = 0.46 for daily feed consumption and 0.47 for residual feed intake). Hens that consumed more feed and had greater residual feed intake (lower efficiency) had a genetic tendencyo t lay slightly more eggs with greater yolk weights and albumen heights. Regions on chromosomes 1, 2, 4, 7, 13, and Z were found to be associated with feed intake and efficiency. The accuracy from genomic prediction was higher and more persistent (better maintained across generations) than that from pedigree-based prediction. These results indicate that genomic selection can be used to improve feed efficiency in yla ers. Keywords feed efficiency, layer, quantitative trait loci, genomic breeding value Disciplines Animal Sciences | Genetics and Genomics | Poultry or Avian Science Comments This article is published as Wolc, Anna, Jesus Arango, Tomasz Jankowski, Petek Settar, Janet E. Fulton, Neil P. O'Sullivan, Rohan Fernando, Dorian J. Garrick, and Jack CM Dekkers. "Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens." Poultry science 92, no. 9 (2013): 2270-2275. doi: 10.3382/ps.2013-03085. Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License. Authors Anna Wolc, Jesus Arango, Tomasz Jankowski, Petek Settar, Janet E. Fulton, Neil P. O'Sullivan, Rohan Fernando, Dorian J. Garrick, and Jack C. M. Dekkers This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/ans_pubs/649 GENETICS Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens Anna Wolc ,*†1 Jesus Arango ,† Tomasz Jankowski ,‡ Petek Settar ,† Janet E. Fulton ,† Neil P. O’Sullivan ,† Rohan Fernando ,* Dorian J. Garrick ,* and Jack C. M. Dekkers * * Department of Animal Science, Iowa State University, Ames 50011-3150; † Hy-Line International, Dallas Center, IA 50063; and ‡ Poznan Supercomputing and Networking Center, Noskowskiego10, 61-704 Poznan, Poland ABSTRACT Efficiency of production is increasingly find genomic regions associated with feed efficiency. important with the current escalation of feed costs and Using pedigree information, feed efficiency was found demands to minimize the environmental footprint. The to be moderately heritable (h2 = 0.46 for daily feed objectives of this study were 1) to estimate heritabili- consumption and 0.47 for residual feed intake). Hens ties for daily feed consumption and residual feed intake that consumed more feed and had greater residual feed and their genetic correlations with production and egg- intake (lower efficiency) had a genetic tendency to lay quality traits; 2) to evaluate accuracies of estimated slightly more eggs with greater yolk weights and albu- breeding values from pedigree- and marker-based pre- men heights. Regions on chromosomes 1, 2, 4, 7, 13, diction models; and 3) to localize genomic regions as- and Z were found to be associated with feed intake and sociated with feed efficiency in a brown egg layer line. efficiency. The accuracy from genomic prediction was Individual feed intake data collected over 2-wk trial higher and more persistent (better maintained across periods were available for approximately 6,000 birds generations) than that from pedigree-based prediction. from 8 generations. Genetic parameters were estimat- These results indicate that genomic selection can be ed with a multitrait animal model; methods BayesB used to improve feed efficiency in layers. and BayesCπ were used to estimate marker effects and Key words: feed efficiency , layer , quantitative trait loci , genomic breeding value 2013 Poultry Science 92 :2270–2275 http://dx.doi.org/ 10.3382/ps.2013-03085 INTRODUCTION with production and egg-quality traits; 2) to evaluate accuracies of estimated breeding values (EBV) from The long-term challenge for animal breeders is to im- pedigree- and marker-based prediction models; and 3) prove the productivity of the major livestock species to to localize genomic regions associated with feed effi- feed the growing human population while at the same ciency in a brown egg layer line. time minimizing the environmental impact (Hume et al., 2011; Van Arendonk, 2011). Feed efficiency has for MATERIALS AND METHODS many years been included in selection objectives for layer chickens (see review by Flock, 1998), which has Individual feed-intake data on approximately 6,000 resulted in a substantial reduction in emission of green- hens from an experimental brown-egg pure line layer house gases (Hume et al., 2011), as well as an improve- population were available for this study. Prior to and ment of economic efficiency by reducing feed required during the experiment, the line was selected on an in- per unit of product. Development of high-density SNP dex combining 16 production and egg-quality traits. In genotyping has provided tools to obtain further insights generation 5, full-sib families were split into 2 lines: into the genetic basis of variation in feed efficiency and a line that continued under conventional selection us- to improve accuracy of selection. ing phenotypic and pedigree information with a 13-mo The objectives of this study were 1) to estimate heri- generation interval; a line that was under genomic se- tabilities for daily feed consumption (DFC) and re- lection, with a shorter generation interval (around 6 sidual feed intake (RFI) and their genetic correlations mo). In the pedigree-selected subline, ~60 males were mated to 360 females, producing 4,000 selection candi- dates per generation; in the genomic subline, 50 males © 2013 Poultry Science Association Inc. were mated to 50 females, producing only 600 selection Received January 31, 2013. Accepted May 19, 2013. candidates to reduce genotyping cost. In the conven- 1 Corresponding author: [email protected] tional selection line, data were collected for one more 2270 FEED EFFICIENCY IN LAYERS 2271 Table 1. Number of records, means, SD, and ranges of the traits analyzed1 for animals used in pedigree-based analyses (All) and in marker-based analysis, separated by animals with own genotypes and phenotypes (Own) and animals that were included into progeny means of genotyped individuals (Progeny) All Own Progeny Trait N Mean SD Minimum Maximum N Mean SD N Mean SD RFI 6,088 0.0 22.5 −170.5 109.7 1,555 1.0 16.3 2,449 −0.6 16.8 DFC 6,088 145.4 55.4 15.6 375.7 1,555 123.9 20.7 2,449 122.9 21.8 PD 4,817 80.4 10.6 27.5 106.1 SM 6,072 149.4 9.7 121.0 199.0 EW 6,034 62.4 4.7 47.5 82.0 PS 6,037 1,461.4 55.4 1,228.9 1,640.5 AH 6,040 7.4 1.1 3.6 11.5 CO 6,040 73.2 9.1 35.4 101.6 YW 6,007 17.7 1.4 11.8 23.3 1Residual feed intake (RFI, g), average feed consumption (DFC, g), egg production rate (PD, %), age at sexual maturity (SM, d). Egg-quality traits recorded at 42 to 46 wk of life: egg weight (EW, g), shell quality (PS, N), albumen height (AH, mm), egg color (CO, index units), and yolk weight (YW, g). generation (generation 6). In the genomic selection line, traits were analyzed in a separate bivariate analysis feed-intake data were collected in generations 7 and 8 because of slow convergence with more traits. Produc- but not in generations 5 and 6 because of technical is- tion traits analyzed were egg production (number of sues arising from shortened generation interval. Data saleable eggs/number of days × 100 during 38–47 wk and genotypes from the 2 lines were combined for the of age); age at sexual maturity