Aulchenko YS, Ripke S, Isaacs A, van Duijn CM (2007) GenABEL: an R library for genome-wide association analysis. J Bioinform 23, 1294–1296.
Bennett AK, Hester PY, Spurlock DE (2006) Polymorphisms in vitamin D receptor, osteopontin, insulin-like growth factor 1 and insulin, and their associations with bone, egg and growth traits in a layer-broiler cross in chickens. Anim Genet 37, 283-286.
Boschiero C, Moreira GCM, Gheyas AA et al. (2018) Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines. BMC Genomics 19, 83.
Braz CU, Taylor JF, Bresolin T et al. (2019) Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle. BMC Genet 20, 8.
Chen B, Xu J, He X et al. (2015) A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth. PLoS One 10, e0137087.
Clancey E, Kiser JN, Moraes JGN et al. (2019) Genome-wide association analysis and gene set enrichment analysis with SNP data identify genes associated with 305-day milk yield in Holstein dairy cows. Anim Genet 50, 254-258.
Darzi Niarami M, Masoudi AA, Vaez Torshizi R (2014) Association of single nucleotide polymorphism of GHSR and TGFB2 genes with growth and body composition traits in sire and dam lines of a broiler chicken. Anim Biotechnol 25, 13-22.
Dong X, Li J, Zhang Y et al. (2019) Genomic Analysis Reveals Pleiotropic Alleles at EDN3 and BMP7 Involved in Chicken Comb Color and Egg Production. Front Genet 10, 612.
Duan Z, Chen S, Sun C et al. (2015) Polymorphisms in Ion Transport Genes Are Associated with Eggshell Mechanical Property. PLoS One 10, e0130160.
Dunn IC, Joseph NT, Bain M et al. (2009) Polymorphisms in eggshell organic matrix genes are associated with eggshell quality measurements in pedigree Rhode Island Red hens. Anim Genet 40, 110-114.
Durinck S, Spellman PT, Birney E, Huber W (2009) Mapping identifiers for the integration of genomic datasets with the R/bioconductor package biomaRt. Nat Protoc 4, 1184–1191.
Huang S, He Y, Ye S et al. (2018) Genome-wide association study on chicken carcass traits using sequence data imputed from SNP array. J Appl Genet 59, 335-344.
Jebessa E, Ouyang H, Abdalla BA et al. (2017) Characterization of miRNA and their target gene during chicken embryo skeletal muscle development. Oncotarget 9, 17309-17324.
Li DF, Liu WB, Liu JF et al. (2012) Whole-genome scan for signatures of recent selection reveals loci associated with important traits in White Leghorn chickens. Poult Sci 91, 1804-1812.
Liu J, Liu R, Wang J et al. (2018) Exploring Genomic Variants Related to Residual Feed Intake in Local and Commercial Chickens by Whole Genomic Resequencing. Genes 9, 57-67.
Liu Z, Sun C, Yan Y, et al. (2018) Genome-wide association analysis of age-dependent egg weights in chickens. Front Genet 9, 128.
Liu Z, Yang N, Yan Y et al. (2019) Genome-wide association analysis of egg production performance in chickens across the whole laying period. BMC Genet 20, 67.
Lu Y, Chen SR, Liu WB et al. (2012) Polymorphisms in Wnt signaling pathway genes are significantly associated with chicken carcass traits. Poult Sci 91, 1299-307.
Moazeni SM, Mohammadabadi MR, Sadeghi M et al. (2016) Association of the melanocortin-3(MC3R) receptor gene with growth and reproductive traits in Mazandaran indigenous chicken. J Livest Sci Tech 4, 51-56.
Mohammadifar A, Mohammadabadi MR (2018) Melanocortin-3 receptor (mc3r) gene association with growth and egg production traits in Fars indigenous chicken. Malays Appl Biol 47, 85–90.
Mohammadifar A, Mohammadabadi MR )2017( The Effect of Uncoupling Protein Polymorphisms on Growth, Breeding Value of Growth and Reproductive Traits in the Fars Indigenous Chicken. Iran J Appl Anim Sci 7, 679-685.
Mooney MA, Wilmot B (2015) Gene Set Analysis: A Step-By-Step Guide. AM J MED GENET B 168, 517-527.
Nie Q, Lei M, Ouyang J et al. (2005) Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography. Genet Sel Evol 37, 339-60.
Peng G, Luo L, Siu H et al. (2010) Gene and pathway-based second wave analysis of genome-wide association studies. Eur J Hum Genet 18, 111–117.
Pértille F, Moreira GC, Zanella R et al. (2017) Genome-wide association study for performance traits in chickens using genotype by sequencing approach. Sci Rep 7, 41748.
Powell JA (2014) GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. BMC Bioinform 17, 146.
Rasal KD, Shah TM, Vaidya M et al. (2015) Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-β receptor type 3 gene in chicken. Meta Gene 4, 107-117.
Sah N, Mishra B (2018) Regulation of egg formation in the oviduct of laying hen. Poult Sci J 74, 1–13.
Sell-Kubiak E, Wimmers K, Reyer H, Szwaczkowski T (2017) Genetic aspects of feed efficiency and reduction of environmental footprint in broilers: a review. J Appl Genet 58, 487-498.
Shahdadnejad N, Mohammadabadi MR, Shamsadini M. 2016. Typing of Clostridium Perfringens Isolated from Broiler Chickens Using Multiplex PCR. Genet 3rd millennium 14, 4368-4374.
Tongsiri S, Jeyaruban MG, Van Der Werf JH (2015) Genetic Parameters for Egg Production Traits in Purebred and Hybrid Chicken in a Tropical Environment. Br Poult Sci 6, 613-20.
Walugembe M, Bertolini F, Dematawewa CMB et al. (2019) Detection of Selection Signatures among Brazilian, Sri Lankan, and Egyptian Chicken Populations under Different Environmental Conditions. Front Genet 9, 737.
Wang L, Jia P, Wolfinger RD et al. (2011) Gene set analysis of genome-wide association studies: Methodological issues and perspectives. Genomics 98, 1–8.
Wolc A, Arango J, Jankowski T et al. (2013) Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens. Poult Sci 92, 2270-2275.
Xu H, Zeng H, Luo C et al. (2011) Genetic effects of polymorphisms in candidate genes and the QTL region on chicken age at first egg. BMC Genet 15, 33.
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Method gene ontology analysis for RNA-seq: Accounting for selection bias. Genome Biol 11, 14-23.
Yousefi Zonuz A, Alijani A, Mohammadi H et al. (2013) Estimation of genetic parameters for productive and reproductive traits in Esfahan native chickens. J Livest Sci Tech 1, 36-40.
Zandi E, Mohammadabadi MR, Ezzatkhah M, Esmailizadeh AK (2014) Typing of Toxigenic Isolates of Clostridium Perfringens by Multiplex PCR in Ostrich. Iran J Appl Anim Sci 4, 509-514.
Zappaterra M (2017) Genomics and New Approaches to Study Complex Traits in Pigs and Other Livestock Species. A Focus on the Investigation of Gene Networks Related to Fat Quality and Deposition in Pigs and Preliminary Research to Study Factors Related to Performances in Piglets and Poultry, PhD thesis, Alma Mater Studiorum Università di Bologna.
Zhang GX, Fan QC, Zhang T et al. (2015) Genome-wide association study of growth traits in the Jinghai Yellow chicken. Genet Mol Res 14, 15331-15338.
Zhu G, Jiang Y (2014) Polymorphism, genetic effect and association with egg production traits of chicken matrix metalloproteinases 9 promoter. Asian-Australas J Anim Sci 27, 1526-1531.