Skip to main content Accessibility help

Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line

  • J. A. P. Marchesi (a1), M. E. Buzanskas (a2), M. E. Cantão (a3), A. M. G. Ibelli (a3), J. O. Peixoto (a3), L. B. Joaquim (a1), G. C. M. Moreira (a4), T. F. Godoy (a4), A. P. Sbardella (a1), E. A. P. Figueiredo (a3), L. L Coutinho (a4), D. P. Munari (a1) and M. C. Ledur (a3)...


Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.


Corresponding author


Hide All

Present address: Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bairro Vila Monte Alegre, 14049-900, Ribeirão Preto, São Paulo, Brazil.



Hide All
Aengwanich, W 2008. Pathological changes and the effects of ascorbic acid on lesion scores of bursa of fabricius in broilers under chronic heat stress. Research Journal of Veterinary Sciences 1, 6266.
Andreescu, C, Avendano, S, Brown, SR, Hassen, A, Lamont, SJ and Dekkers, JCM 2007. Linkage disequilibrium in related breeding lines of chickens. Genetics 177, 21612169.
Anwar, B, Khan, SA, Aslam, A, Maqbool, A and Khan, KA 2008. Effects of ascorbic acid and acetylsalicylic acid supplementation on the performance of broiler chicks exposed to heat stress. Pakistan Veterinary Journal 24, 109112.
Arras, LD, Laws, R, Leach, SM, Pontis, K, Freedman, JH, Schwartz, DA and Alper, S 2014. Comparative genomics RNAi screen identifies Eftud2 as a novel regulator of innate immunity. Genetics of Immunity 197, 485496.
Badyaev, AV 2005. Stress-induced variation in evolution: from behavioural plasticity to genetic assimilation. Proceedings of the Royal Society B 272, 877886.
Balboa, MA and Balsinde, J 2006. Oxidative stress and arachidonic acid mobilization. Biochimica et Biophysica Acta 1761, 385391.
Bosse, M, Megens, H-J, Madsen, O, Paudel, Y, Frantz, LAF, Schook, LB, Crooijmans, RPMA and Groenen, MAM 2012. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genetics 8, e1003100.
Carothers, AD, Rudan, I, Kolcic, I, Polasek, O, Hayward, C, Wright, AF, Campbell, H, Teague, P, Hastie, ND and Weber, JL 2006. Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. Annals of Human Genetics 70, 666676.
Curik, I, Sölkner, J and Stipic, N 2002. Effects of models with finite loci, selection, dominance, epistasis and linkage on inbreeding coefficients based on pedigree and genotypic information. Journal of Animal Breeding and Genetics 119, 101115.
Donalies, M, Cramer, M, Ringwald, M and Starzinski-Powitz, A 1991. Expression of M-cadherin, a member of the cadherin multigene family, correlates with differentiation of skeletal muscle cells. Proceedings of the National Academy of Sciences 88, 80248028.
Ferencakovic, M, Hamzic, E, Gredler, B, Solberg, TR, Klemetsdal, G, Curik, I and Sölkner, J 2012. Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. Journal of Animal Breeding and Genetics 130, 286293.
Figueiredo, EAP, Rosa, PS, Scheuermann, GN, Jaenisch, FRF, Schmidt, GS, Ledur, MC, Brentano, L and Costa, CAF 2003. Genetic gain in body weight, feed conversion, and carcass traits in White Plymouth Rock broiler strain Embrapa 021. Paper presented at the IX World Conference on Animal Production, 26–31 October, Porto Alegre, Brazil.
Fleming, DS, Koltes, JE, Markey, AD, Schmidt, CJ, Ashwell, CM, Rothschild, MF, Persia, ME, Reecy, JM and Lamont, SL 2016. Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 K genotyping array. BMC Genomics 17, 407.
Food and Agriculture Organization of the United Nations 2004. Secondary guidelines for development of national farm animal genetic resources management plans. FAO, Rome, Italy.
Fornari, MB, Zanella, R, Ibelli, AMG, Fernandes, LT, Cantão, ME, Thomaz-Soccol, V, Ledur, MC and Peixoto, JO 2014. Unraveling the associations of osteoprotegerin gene with production traits in a paternal broiler line. SpringerPlus 3, 682.
Fu, W, Dekkers, JCM, Lee, WR and Abasht, B 2015. Linkage disequilibrium in crossbred and pure line chickens. Genetics Selection Evolution 47, 112.
Fu, W, Lee, WR and Abasht, B 2016. Detection of genomic signatures of recent selection in commercial broiler chickens. BMC Genetics 17, 122.
Gorostizaga, A, Brion, L, Maloberti, P, Paz, C, Maciel, FC, Podestá, EJ and Paz, C 2005. Heat shock triggers MAPK activation and MKP-1 induction in Leydig testicular cells. Biochemical and Biophysical Research Communications 327, 2328.
Harada, Y, Tanaka, Y, Terasawa, M, Pieczyk, M, Habiro, K, Katakai, T, Hanawa-Suetsugu, K, Kukimoto-Niino, M, Nishizaki, T, Shirouzu, M, Duan, X, Uruno, T, Nishikimi, A, Sanematsu, F, Yokoyama, S, Stein, JV and Kinashi, T 2012. DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses. Blood 119, 44514461.
Hayes, BJ, Visscher, PM, Mcpartlan, HC and Goddard, ME 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research 13, 635643.
Hill, WG and Robertson, A 1968. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38, 226231.
International Chicken Genome Sequencing Consortium 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695716.
Julian, RJ 2005. Production and growth related disorders and other metabolic diseases of poultry – a review. The Veterinary Journal 169, 350369.
Ledur, MC, Peixoto, JO, Nones, K and Coutinho, LL 2012. Applied genomics: the Brazilian experience. In World’s Poultry Congress, 24., 2012, Salvador Abstract. Salvador: WSPA, 2012. 1 CD-ROM. Poultry Science Journal, 68, supl. 1, 2012.
Lin, H, Decuypere, E and Buyse, J 2006. Acute heat stress induces oxidative stress in broiler chickens. Comparative Biochemistry and Physiology 144, 1117.
McQuillan, R, Leutenegger, AL, Abdel-Rahman, R, Franklin, CS, Pericic, M, Barac-Lauc, L, Smolej-Narancic, N, Janicijevic, B, Polasek, O, Tenesa, A, MacLeod, AK, Farrington, SM, Rudan, P, Hayward, C, Vitart, V, Rudan, I, Wild, SH, Dunlop, MG, Wright, AF, Campbell, H and Wilson, JF 2008. Runs of homozygosity in European populations. The American Journal of Human Genetics 83, 359372.
Muir, WM, Wong, GK-S, Zhang, Y, Wang, J, Groenen, MAM, Crooijmans, RPMA, Megens, H-J, Zhang, H, Okimoto, R, Vereijken, A, Jungerius, A, Albers, GAA, Lawley, CT, Delany, ME, MacEachern, S and Cheng, HH 2008. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proceedings of the National Academy of Sciences 105, 1731217317.
Mujahid, A, Sato, K, Akiba, Y and Toyomizu, M 2006. Acute heat stress stimulates mitochondrial superoxide production in broiler skeletal muscle, possibly via downregulation of uncoupling protein content. Poultry Science 85, 12591265.
Mujahid, A, Yoshiki, Y, Akiba, Y, Toyomizu, M 2005. Superoxide radical production in chicken skeletal muscle induced by acute heat stress. Poultry Science 84, 307314.
Organisation for Economic Co-operation and Development (OECD)-Food and Agriculture Organization (FAO) 2015. OECD-FAO agricultural outlook 2015-2024. OECD Publishing, Paris, France.
Pamok, S, Aengwanich, W and Komutrin, T 2009. Adaptation to oxidative stress and impact of chronic oxidative stress on immunity in heat-stressed broilers. Journal of Thermal Biology 34, 353357.
Qanbari, S, Hansen, M, Weigend, S, Preisinger, R and Simianer, H 2010. Linkage disequilibrium reveals different demographic history in egg laying chickens. BMC genetics 11, 103.
Quinteiro-Filho, WM, Ribeiro, A, Ferraz-de-Paula, V, Pinheiro, ML, Sakai, M, , LRM, Ferreira, AJP and Palermo-Neto, J 2010. Heat stress impairs performance parameters, induces intestinal injury, and decreases macrophage activity in broiler chickens. Poultry Science 89, 19051914.
Rubin, C, Zody, MC, Eriksson, J, Meadows, JRS, Sherwood, E, Webster, MT, Jiang, L, Ingman, M, Sharpe, T, Ka, S, Hallbo, F, Besnier, F, Carlborg, O, Bed’hom, B, Tixier-Boichard, M, Jensen, P, Siegel, P, Lindblad-Toh, K, Andersson, L 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587591.
Sargolzaei, M 2014. SNP1101 User’s Guide. Version 1.0 Canada: University of Guelph.
Scheele, CW 1997. Pathological changes in metabolism of poultry related to increasing production levels. Veterinary Quarterly 19, 127130.
Sebzda, E, Bracke, M, Tugal, T, Hogg, N and Cantrell, DA 2002. Rap1A positively regulates T cells via integrin activation rather than inhibiting lymphocyte signaling. Nature Immunology 3, 252258.
Sun, L, Lamont, SJ, Cooksey, AM, Mccarthy, F, Tudor, CO, Derita, RM, Rothschild, M, Ashwell, C, Persia, ME and Schmidt, CJ 2015. Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line. Cell Stress and Chaperones 20, 939950.
Sved, JA 1971. Linkage disequilibrium of chromosome segments. Theoretical Population Biology 2, 125141.
Tsuji, T and Miypshi, M 2001. A scanning and transmission electron microscopic study of the lymphoreticular framework in the chicken fabricius’ bursa. Medical Bulletin of Fukuoka University 28, 6375.
Türkyilmaz, MK 2008. The effect of stocking density on stress reaction in broiler chickens during summer. Turkish Journal of Veterinary & Animal Sciences 32, 3136.
Zanella, R, Peixoto, JO, Cardoso, FF, Cardoso, LL, Biegelmeyer, P, Cantao, ME, Otaviano, A, Freitas, MS, Caetano, AR and Ledur, MC 2016. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. Genetics Selection Evolution 48, 24.
Zhang, Q, Guldbrandtsen, B, Bosse, M, Lund, MS and Sahana, G 2015. Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genomics 16, 542.
Zhang, S, Lillehoj, HS, Kim, C-H, Keeler, CL, Babu, JU and Zhang, MZ 2008. Transcriptional response of chicken macrophages to Salmonella enterica serovar enteritidis infection. Animal Genomics for Animal Health 132, 141151.
Zhu, M, Zhu, B, Wang, YH, Wu, Y, Xu, L, Guo, LP, Yuan, ZR, Zhang, LP, Gao, X, Gao, HJ, Xu, SZ and Li, JY 2013. Linkage disequilibrium estimation of Chinese beef simmental cattle using high-density SNP panels. Asian-Australasian Journal of Animal Sciences 26, 772779.


Type Description Title
Supplementary materials

Marchesi et al supplementary material 1
Marchesi et al supplementary material

 Unknown (32 KB)
32 KB
Supplementary materials

Marchesi et al supplementary material 2
Supplementary Table

 Word (21 KB)
21 KB
Supplementary materials

Marchesi et al supplementary material 3
Supplementary Table

 Word (18 KB)
18 KB


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed