Ai, H, Huang, L and Ren, J. 2013. Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers. PLoS ONE 8, e56001.
Bertolini, F, Galimberti, G, Calò, DG, Schiavo, G, Matassino, D and Fontanesi, L 2015. Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: application in cattle breeds. Journal of Animal Breeding and Genetics 132, 346–356.
Bertolini, F, Galimberti, G, Schiavo, G, Mastrangelo, S, Di Gerlando, R, Strillacci, MG, Bagnato, A, Portolano, B and Fontanesi, L 2018. Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochthonous cattle breeds. Animal 12, 12–19.
Bovo, S, Mazzoni, G, Bertolini, F, Schiavo, G, Galimberti, G, Gallo, M, Dall’Olio, S and Fontanesi, L 2019. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Scientific Reports 9, 7003.
Breiman, L 2001. Random forests. Machine Learning 45, 5–32.
Chang, CC, Chow, CC, Tellier, LC, Vattikuti, S, Purcell, SM and Lee, JJ 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, s13742–015–0047–8.
Fontanesi, L, Scotti, E, Gallo, M, Nanni Costa, L and Dall’Olio, S 2016. Authentication of “mono-breed” pork products: identification of a coat colour gene marker in Cinta Senese pigs useful to this purpose. Livestock Science 184, 71–77.
Genuer, R, Poggi, J-M and Tuleau-Malot, C 2015. VSURF: an R package for variable selection using random forests. The R Journal 7/2, 19–33.
Hastie, T, Tibshirani, R and Friedman, JH 2009. The elements of statistical learning, 2nd edition. Springer, New York, NY, USA.
Huisman, J 2017. Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond. Molecular Ecology Resources 17, 1009–1024.
Hulsegge, B, Calus, MP, Windig, JJ, Hoving-Bolink, AH, Eijndhoven, MH and Hiemstra, SJ 2013. Selection of SNPs from 50K and 777K arrays to predict breed-of-origin in cattle. Journal of Animal Science 91, 5128–5134.
Jacobs, A, De Noia, M, Praebel, K, Kanstad-Hanssen, Ø, Paterno, M, Jackson, D, McGinnity, P, Sturm, A, Elmer, KR and Llewellyn, MS 2018. Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach. Scientific Reports 8, 1203.
Jolliffe, IT and Cadima, J 2016. Principal component analysis: a review and recent developments. Philosophical Transactions of the Royal Society A 374, 20150202.
Kijas, JW, Serrano, M, McCulloch, R, Li, Y, Salces Ortiz, J, Calvo, JH, Pérez-Guzmán, MD and International Sheep Genomics Consortium 2013. Genome wide association for a dominant pigmentation gene in sheep. Journal of Animal Breeding and Genetics 130, 468–475.
Li, M, Tian, S, Jin, L, Zhou, G, Li, Y, Zhang, Y, Wang, T, Yeung, CK, Chen, L, Ma, J, Zhang, J, Jiang, A, Li, J, Zhou, C, Zhang, J, Liu, Y, Sun, X, Zhao, H, Niu, Z, Lou, P, Xian, L, Shen, X, Liu, S, Zhang, S, Zhang, M, Zhu, L, Shuai, S, Bai, L, Tang, G, Liu, H, Jiang, Y, Mai, M, Xiao, J, Wang, X, Zhou, Q, Wang, Z, Stothard, P, Xue, M, Gao, X, Luo, Z, Gu, Y, Zhu, H, Hu, X, Zhao, Y, Plastow, GS, Wang, J, Jiang, Z, Li, K, Li, N, Li, X and Li, R 2013 Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nature Genetics 45, 1431–1438.
Liaw, A and Wiener, M 2002. Classification and regression by random forest. R News 2, 18–22.
Ligges, U and Mächler, M 2013. Scatterplot3d - an R package for visualizing multivariate data. Journal of Statistical Software 8, 1–20.
Meng, YA, Yu, Y, Cupples, LA, Farrer, LA and Lunetta, KL 2009. Performance of random forest when SNPs are in linkage disequilibrium. BMC Bioinformatics 10, 78.
Naderi, S, Yin, T and König, S 2016. Random forest estimation of genomic breeding values for disease susceptibility over different disease incidences and genomic architectures in simulated cow calibration groups. Journal of Dairy Science 99, 7261–7273.
Paschou, P, Ziv, E, Burchard, EG, Choudhry, S, Rodriguez-Cintron, W, Mahoney, MW and Drineas, P 2007. PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genetics 9, 1672–1686.
Rothschild, M, Jacobson, C, Vaske, D, Tuggle, C, Wang, L, Short, T, Eckardt, G, Sasaki, S, Vincent, A, McLaren, D, Southwood, O, van der Steen, H, Mileham, A and Plastow, G 1996. The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proceedings of the National Academy of Sciences of the USA 93, 201–205.
Rubin, CJ, Megens, HJ., Martinez Barrio, A, Maqbool, K, Sayyab, S, Schwochow, D, Wang, C, Carlborg, Ö, Jern, P, Jørgensen, CB, Archibald, AL, Fredholm, M, Groenen, MA and Andersson, L 2012. Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences of the USA 109, 19529–19536.
Russo, V, Fontanesi, L, Davoli, R, Chiofalo, L, Liotta, L and Zumbo, A 2004. Analysis of single nucleotide polymorphisms in major and candidate genes for production traits in Nero Siciliano pig breed. Italian Journal of Animal Science 3, 19–29.
Schiavo, G, Galimberti, G, Calò, DG, Samorè, AB, Bertolini, F, Russo, V, Gallo, M, Buttazzoni, L and Fontanesi, L 2016. Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed. Animal Genetics 47, 181–191.
Takasuga, A 2016. PLAG1 and NCAPG-LCORL in livestock. Animal Science Journal 87, 159–167.
Wang, K, Wu, P, Yang, Q, Chen, D, Zhou, J, Jiang, A, Ma, J, Tang, Q, Xiao, W, Jiang, Y, Zhu, L, Li, X and Tang, G 2018. Detection of selection signatures in Chinese Landrace and Yorkshire pigs based on genotyping-by-sequencing data. Frontiers in Genetics 9, 119.
Weir, BS and Cockerham, CC 1984. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370.
Wilkinson, S, Archibald, AL, Haley, CS, Megens, HJ, Crooijmans, RP, Groenen, MA, Wiener, P and Ogden, R 2012. Development of a genetic tool for product regulation in the diverse British pig breed market. BMC Genomics 13, 580.
Wilkinson, S, Lu, ZH, Megens, HJ, Archibald, AL, Haley, C, Jackson, IJ, Groenen, MA, Crooijmans, RP, Ogden, R and Wiener, P 2013. Signatures of diversifying selection in European pig breeds. PLoS Genetics 9, e1003453.
Wilkinson, S, Wiener, P, Archibald, AL, Law, A, Schnabel, RD, McKay, SD, Taylor, JF and Ogden, R 2011. Evaluation of approaches for identifying population informative markers from high density SNP chips. BMC Genetics 12, 45.
Yang, B, Cui, L, Perez-Enciso, M, Traspov, A, Crooijmans, RPMA, Zinovieva, N, Schook, LB, Archibald, A, Gatphayak, K, Knorr, C, Triantafyllidis, A, Alexandri, P, Semiadi, G, Hanotte, O, Dias, D, Dovč, P, Uimari, P, Iacolina, L, Scandura, M, Groenen, MAM, Huang, L and Megens, HJ 2017. Genome-wide SNP data unveils the globalization of domesticated pigs. Genetics Selection Evolution 49, 71.
Yang, S, Li, X, Li, K, Fan, B and Tang, Z 2014. A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. BMC Genetics 15, 7.
Zhang, Z, Xiao, Q, Zhang, QQ, Sun, H, Chen, JC, Li, ZC, Xue, M, Ma, PP, Yang, HJ, Xu, NY, Wang, QS and Pan, YC 2018. Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds. Scientific Reports 8, 13352.