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2016
L. Grigoletto, Mattos, E. C., Santana, M. H. A., Baldi, F., Eler, J. P., Ferraz, J. B. S., Grigoletto, L., Mattos, E. C., Santana, M. H. A., Baldi, F., Eler, J. P., and Ferraz, J. B. S., Inclusion of cytoplasmic lineage effect and direct-maternal genetic covariance for genetic evaluation of growth traits in Nellore cattle, vol. 15, p. -, 2016.
L. Grigoletto, Mattos, E. C., Santana, M. H. A., Baldi, F., Eler, J. P., Ferraz, J. B. S., Grigoletto, L., Mattos, E. C., Santana, M. H. A., Baldi, F., Eler, J. P., and Ferraz, J. B. S., Inclusion of cytoplasmic lineage effect and direct-maternal genetic covariance for genetic evaluation of growth traits in Nellore cattle, vol. 15, p. -, 2016.
A. L. Bocchi, Oliveira, H. N., Ferraz, J. B. S., Eler, J. P., Bocchi, A. L., Oliveira, H. N., Ferraz, J. B. S., and Eler, J. P., Multibreed genetic evaluation in bovines using simulated data employing a composite population, vol. 15, p. -, 2016.
A. L. Bocchi, Oliveira, H. N., Ferraz, J. B. S., Eler, J. P., Bocchi, A. L., Oliveira, H. N., Ferraz, J. B. S., and Eler, J. P., Multibreed genetic evaluation in bovines using simulated data employing a composite population, vol. 15, p. -, 2016.
M. H. A. Santana, Freua, M. C., Do, D. N., Ventura, R. V., Kadarmideen, H. N., and Ferraz, J. B. S., Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle, vol. 15, no. 4, p. -, 2016.
Conflicts of interestThe authors declare no conflict of interest.ACKNOWLEDGMENTSThe contributions of Núcleo de Criadores de Nelore do Norte do Paraná, Luciano Borges (Rancho da Matinha), and Eduardo Penteado Cardoso (Fazenda Mundo Novo) are gratefully acknowledged. We would like to thank Dr. Zhong Wang for help with the gwas.lasso package. Research supported in part by São Paulo Research Foundation (FAPESP, #2012/02039-9, #2013/26902-0, #2014/14121-7, #2013/20571-2, and #2014/07566-2) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, #473249/2013-8 and #442345/2014-3). REFERENCESAlexandre PA, Kogelman LJA, Santana MHA, Passarelli D, et al (2015). Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle. BMC Genomics 16: 1073. http://dx.doi.org/10.1186/s12864-015-2292-8 Anderson RV, Rasby RJ, Klopfenstein TJ and RT Clark. (2005). An evaluation of production and economic efficiency of two beef systems from calving to slaughter. J. Anim. Sci. 83: W 694-704. Chen Y, Gondro C, Quinn K, Herd RM, et al (2011). Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake. Anim. Genet. 42: 475-490. http://dx.doi.org/10.1111/j.1365-2052.2011.02182.x Das K, Li J, Wang Z, Tong C, et al (2011). A dynamic model for genome-wide association studies. Hum. Genet. 129: 629-639. http://dx.doi.org/10.1007/s00439-011-0960-6 Do DN, Ostersen T, Strathe AB, Mark T, et al (2014). Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs. BMC Genet. 15: 27. http://dx.doi.org/10.1186/1471-2156-15-27 Do DN, Janss LLG, Jensen J, Kadarmideen HN, et al (2015). SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs. J. Anim. Sci. 93: 2056-2063. http://dx.doi.org/10.2527/jas.2014-8640 Gantz I, Fong TM, et al (2003). The melanocortin system. Am. J. Physiol. Endocrinol. Metab. 284: E468-E474. http://dx.doi.org/10.1152/ajpendo.00434.2002 Gomes RC, Silva SL, Carvalho ME, Rezende FM, et al (2013). Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle. Genet. Mol. Res. 12: 2923-2936. http://dx.doi.org/10.4238/2013.August.12.8 Havlík P, Valin H, Herrero M, Obersteiner M, et al (2014). Climate change mitigation through livestock system transitions. Proc. Natl. Acad. Sci. USA 111: 3709-3714. http://dx.doi.org/10.1073/pnas.1308044111 Hoti F, Sillanpää MJ, et al (2006). Bayesian mapping of genotype x expression interactions in quantitative and qualitative traits. Heredity (Edinb) 97: 4-18. http://dx.doi.org/10.1038/sj.hdy.6800817 Huang W, Sherman BT, Lempicki RA, et al (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4: 44-57. http://dx.doi.org/10.1038/nprot.2008.211 Ji JD, Lee WJ, Kong KA, Woo JH, et al (2010). Association of STAT4 polymorphism with rheumatoid arthritis and systemic lupus erythematosus: a meta-analysis. Mol. Biol. Rep. 37: 141-147. http://dx.doi.org/10.1007/s11033-009-9553-z Kadarmideen HN, von Rohr P, Janss LLG, et al (2006). From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mamm. Genome 17: 548-564. http://dx.doi.org/10.1007/s00335-005-0169-x Kies AK, Gerrits WJ, Schrama JW, Heetkamp MJ, et al (2005). Mineral absorption and excretion as affected by microbial phytase, and their effect on energy metabolism in young piglets. J. Nutr. 135: 1131-1138. Kindt ASD, Navarro P, Semple CA, Haley CS, et al (2013). The genomic signature of trait-associated variants. BMC Genomics 14: 108. http://dx.doi.org/10.1186/1471-2164-14-108 Koufariotis L, Chen YP, Bolormaa S, Hayes BJ, et al (2014). Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics 15: 436. http://dx.doi.org/10.1186/1471-2164-15-436 Li J, Das K, Fu G, Li R, et al (2011). The Bayesian lasso for genome-wide association studies. Bioinformatics 27: 516-523. http://dx.doi.org/10.1093/bioinformatics/btq688 Lkhagvadorj S, Qu L, Cai W, Couture OP, et al (2010). Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. Am. J. Physiol. Regul. Integr. Comp. Physiol. 298: R494-R507. http://dx.doi.org/10.1152/ajpregu.00632.2009 McBride BW, Kelly JM, et al (1990). Energy cost of absorption and metabolism in the ruminant gastrointestinal tract and liver: a review. J. Anim. Sci. 68: 2997-3010. http://dx.doi.org/10.2527/1990.6892997x Moore SS, Mujibi FD, Sherman EL, et al (2009). Molecular basis for residual feed intake in beef cattle. J. Anim. Sci. 87 (Suppl): E41-E47. http://dx.doi.org/10.2527/jas.2008-1418 Nkrumah JD, Basarab JA, Wang Z, Li C, et al (2007). Genetic and phenotypic relationships of feed intake and measures of efficiency with growth and carcass merit of beef cattle. J. Anim. Sci. 85: 2711-2720. http://dx.doi.org/10.2527/jas.2006-767 Richardson EC, Herd RM, et al (2004). Biological basis for variation in residual feed intake in beef cattle. 2. Synthesis of results following divergent selection. Aust. J. Exp. Agric. 44: 431-440. http://dx.doi.org/10.1071/EA02221 Richardson EC, Herd RM, Archer JA, Arthur PF, et al (2004). Metabolic differences in Angus steers divergently selected for residual feed intake. Aust. J. Exp. Agric. 44: 441-452. http://dx.doi.org/10.1071/EA02219 Rincon G, Farber EA, Farber CR, Nkrumah JD, et al (2009). Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattle. Anim. Genet. 40: 878-882. http://dx.doi.org/10.1111/j.1365-2052.2009.01934.x Rolf MM, Taylor JF, Schnabel RD, McKay SD, et al (2012). Genome-wide association analysis for feed efficiency in Angus cattle. Anim. Genet. 43: 367-374. http://dx.doi.org/10.1111/j.1365-2052.2011.02273.x Santana MHA, Rossi PJuniorAlmeidaR, Cucco DC, et al (2012). Feed efficiency and its correlations with carcass traits measured by ultrasound in Nellore bulls. Livest. Sci. 145: 252-257. http://dx.doi.org/10.1016/j.livsci.2012.02.012 Santana MHA, Utsunomiya YT, Neves HHR, Gomes RC, et al (2014). Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle. BMC Genet. 15: 21. http://dx.doi.org/10.1186/1471-2156-15-21 Sargolzaei M, Chesnais JP, Schenkel FS, et al (2014). A new approach for efficient genotype imputation using information from relatives. BMC Genomics 15: 478. http://dx.doi.org/10.1186/1471-2164-15-478 Serão NV, González-Peña D, Beever JE, Faulkner DB, et al (2013). Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle. BMC Genet. 14: 94. http://dx.doi.org/10.1186/1471-2156-14-94 Villa-Angulo R, Matukumalli LK, Gill CA, Choi J, et al (2009). High-resolution haplotype block structure in the cattle genome. BMC Genet. 10: 19. http://dx.doi.org/10.1186/1471-2156-10-19 Yang J, Manolio TA, Pasquale LR, Boerwinkle E, et al (2011). Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet. 43: 519-525. http://dx.doi.org/10.1038/ng.823 Zhang F, Huang J, Li Q, Ju Z, et al (2010). Novel single nucleotide polymorphisms (SNPs) of the bovine STAT4 gene and their associations with production traits in Chinese Holstein cattle. Afr. J. Biotechnol. 9: 4003-4008.  
2013
A. M. Felício, Boschiero, C., Balieiro, J. C. C., Ledur, M. C., Ferraz, J. B. S., T. Filho, M., Moura, A. S. A. M. T., and Coutinho, L. L., Identification and association of polymorphisms in CAPN1 and CAPN3 candidate genes related to performance and meat quality traits in chickens, vol. 12, pp. 472-482, 2013.
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A. M. Felício, Boschiero, C., Balieiro, J. C. C., Ledur, M. C., Ferraz, J. B. S., Moura, A. S. A. M. T., and Coutinho, L. L., Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens, vol. 12, pp. 208-222, 2013.
Aigner A, Butscheid M, Kunkel P, Krause E, et al. (2001). An FGF-binding protein (FGF-BP) exerts its biological function by parallel paracrine stimulation of tumor cell and endothelial cell proliferation through FGF-2 release. Int. J. Cancer 92: 510-517. http://dx.doi.org/10.1002/1097-0215(20010515)92:4<510::AID-IJC1227>3.0.CO;2-H   Ambo M, Moura AS, Ledur MC, Pinto LF, et al. (2009). Quantitative trait loci for performance traits in a broiler x layer cross. Anim. Genet. 40: 200-208. http://dx.doi.org/10.1111/j.1365-2052.2008.01824.x PMid:19170675   Ankra-Badu GA, Shriner D, Le Bihan-Duval E, Mignon-Grasteau S, et al. (2010). Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate. BMC Genomics 11: 107. http://dx.doi.org/10.1186/1471-2164-11-107 PMid:20149241 PMCid:2830984   Anthony NB (1998). A review of genetic practices in poultry: efforts to improve meat quality. J. Muscle Food 9: 25-33. http://dx.doi.org/10.1111/j.1745-4573.1998.tb00641.x   Barbut S (1997). Occurrence of pale soft exudative meat in mature turkey hens. Br. Poult. Sci. 38: 74-77. http://dx.doi.org/10.1080/00071669708417943 PMid:9088616   Baron EE, Moura AS, Ledur MC, Pinto LF, et al. (2010). QTL for percentage of carcass and carcass parts in a broiler x layer cross. Anim. Genet. [Ahead of Print]. PMid:20880336   Beer HD, Bittner M, Niklaus G, Munding C, et al. (2005). The fibroblast growth factor binding protein is a novel interaction partner of FGF-7, FGF-10 and FGF-22 and regulates FGF activity: implications for epithelial repair. Oncogene 24: 5269-5277. http://dx.doi.org/10.1038/sj.onc.1208560 PMid:15806171   Berri C, Le Bihan-Duval E, Debut M, Sante-Lhoutellier V, et al. (2007). Consequence of muscle hypertrophy on characteristics of Pectoralis major muscle and breast meat quality of broiler chickens. J. Anim. Sci. 85: 2005-2011. http://dx.doi.org/10.2527/jas.2006-398 PMid:17431054   Dekkers JC (2004). Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 82 (E-Suppl): E313-E328.   Dransfield E and Sosnicki AA (1999). Relationship between muscle growth and poultry meat quality. Poult. Sci. 78: 743-746. PMid:10228972   Ewing B and Green P (1998). Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186-194. PMid:9521922   Falconer DS and Mackay TFC (2001). Introducción a la Genética Cuantitativa. 4ª ed. Acribia, Zaragoza.   Gaya LG, Ferraz JB, Rezende FM, Mourao GB, et al. (2006). Heritability and genetic correlation estimates for performance and carcass and body composition traits in a male broiler line. Poult. Sci. 85: 837-843. PMid:16673760   Gaya LG, Mourão GB, Ferraz JBS, Mattos EC, et al. (2011). Estimates of heritability and genetic correlations for meat quality traits in broilers. Sci. Agric. 68: 620-625. http://dx.doi.org/10.1590/S0103-90162011000600002   Gibby KA, McDonnell K, Schmidt MO and Wellstein A (2009). A distinct role for secreted fibroblast growth factor-binding proteins in development. Proc. Natl. Acad. Sci. U. S. A. 106: 8585-8590. http://dx.doi.org/10.1073/pnas.0810952106 PMid:19433791 PMCid:2689014   Gordon D, Abajian C and Green P (1998). Consed: a graphical tool for sequence finishing. Genome Res. 8: 195-202. PMid:9521923   Kastner S, Elias MC, Rivera AJ and Yablonka-Reuveni Z (2000). Gene expression patterns of the fibroblast growth factors and their receptors during myogenesis of rat satellite cells. J. Histochem. Cytochem. 48: 1079-1096. http://dx.doi.org/10.1177/002215540004800805 PMid:10898801   Le Bihan-Duval E, Berri C, Baeza E, Sante V, et al. (2003). Genetic parameters of meat technological quality traits in a grand-parental commercial line of turkey. Genet. Sel. Evol. 35: 623-635. http://dx.doi.org/10.1186/1297-9686-35-7-623 PMid:14604511 PMCid:2698002   Le Bihan-Duval E, Debut M, Berri CM, Sellier N, et al. (2008). Chicken meat quality: genetic variability and relationship with growth and muscle characteristics. BMC Genet. 9: 53. http://dx.doi.org/10.1186/1471-2156-9-53 PMid:18706119 PMCid:2533670   Marie PJ, Debiais F and Hay E (2002). Regulation of human cranial osteoblast phenotype by FGF-2, FGFR-2 and BMP-2 signaling. Histol. Histopathol. 17: 877-885. PMid:12168799   Nassar MK, Goraga ZS and Brockmann GA (2012). Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition. Anim. Genet. [Ahead of Print].   Nones K, Ledur MC, Zanella EL, Klein C, et al. (2012). Quantitative trait loci associated with chemical composition of the chicken carcass. Anim. Genet. 43: 570-576. http://dx.doi.org/10.1111/j.1365-2052.2012.02321.x PMid:22497237   Park GB, Moon SS, Ko YD, Ha JK, et al. (2002). Influence of slaughter weight and sex on yield and quality grades of Hanwoo (Korean native cattle) carcasses. J. Anim. Sci. 80: 129-136. PMid:11831510   Rosário MF, Ledur MC, Moura ASAMT, Coutinho LL, et al. (2009). Genotypic characterization of microsatellite markers in broiler and layer selected chicken lines and their reciprocal F1s. Sci. Agric. 66: 150-158. http://dx.doi.org/10.1590/S0103-90162009000200002   SAS (2004). SAS/STAT User's Guide: Version 9.1. SAS Institute, Cary.   Schmid M, Nanda I, Hoehn H, Schartl M, et al. (2005). Second report on chicken genes and chromosomes. Cytogenet. Genome Res. 109: 415-479. http://dx.doi.org/10.1159/000084205 PMid:15905640   Stephens M, Smith NJ and Donnelly P (2001). A new statistical method for haplotype reconstruction from population data. Am. J. Hum. 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R. C. Gomes, Silva, S. L., Carvalho, M. E., Rezende, F. M., Pinto, L. F. B., Santana, M. H. A., Stella, T. R., Meirelles, F. V., P. Júnior, R., Leme, P. R., and Ferraz, J. B. S., Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle, vol. 12, pp. 2923-2936, 2013.
2012
R. C. G. da Silva, Ferraz, J. B. S., Meirelles, F. V., Eler, J. P., Balieiro, J. C. C., Cucco, D. C., Mattos, E. C., Rezende, F. M., and Silva, S. L., Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle, vol. 11, pp. 3721-3728, 2012.
Buchanan FC, Fitzsimmons CJ, Van Kessel AG, Thue TD, et al. (2002). Association of a missense mutation in the bovine leptin gene with carcass fat content and leptin mRNA levels. Genet. Sel. Evol. 34: 105-116. http://dx.doi.org/10.1186/1297-9686-34-1-105 PMid:11929627 PMCid:2705418   Choudhary V, Kumar P, Bhattacharya TK, Bhushan B, et al. (2005). DNA polymorphism of leptin gene in Bos indicus and Bos taurus cattle. Genet. Mol. Biol. 28: 740-742. http://dx.doi.org/10.1590/S1415-47572005000500014   Clarke IJ and Henry BA (1999). Leptin and reproduction. Rev. Reprod. 4: 48-55. http://dx.doi.org/10.1530/ror.0.0040048 PMid:10051102   Eler JP, Ferraz JB, Balieiro JC, Mattos EC, et al. (2006). Genetic correlation between heifer pregnancy and scrotal circumference measured at 15 and 18 months of age in Nellore cattle. Genet. Mol. Res. 5: 569-580. PMid:17183470   Falconer DS and Mackay TFC (1996). Introduction to Quantitative Genetics. 4th edn. Longman, London. 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