GenomicLand: Software for genome-wide association studies and genomic prediction

被引:11
作者
Azevedo, Camila Ferreira [1 ]
Nascimento, Moyses [1 ]
Fontes, Vitor Cunha [2 ]
Fonseca e Silva, Fabyano [3 ]
Vilela de Resende, Marcos Deon [4 ]
Cruz, Cosme Damiao [5 ]
机构
[1] Univ Fed Vicosa, Dept Estat, Lab Inteligencia Comp, Av PH Rolfs S-N,Campus Univ, BR-36570900 Vicosa, MG, Brazil
[2] Univ Fed Vicosa, Grp Pesquisa Interacao Atmosfera Biosfera, Dept Engn Agr, Vicosa, MG, Brazil
[3] Univ Fed Vicosa, Dept Zootecnia, Vicosa, MG, Brazil
[4] Univ Fed Vicosa, Embrapa Florestas, Dept Engn Florestal, Vicosa, MG, Brazil
[5] Univ Fed Vicosa, Dept Biol Geral, Lab Bioinformat, Vicosa, MG, Brazil
关键词
statistical analysis; genomic analysis; molecular markers; biometrics; CARCASS TRAITS; SELECTION; MARKERS; MODELS;
D O I
10.4025/actasciagron.v41i1.45361
中图分类号
S3 [农学(农艺学)];
学科分类号
0901 ;
摘要
GenomicLand is free software intended for prediction and genomic association studies based on the R software. This computational tool has an intuitive interface and supports large genomic databases, without requiring the user to use the command line. GenomicLand is available in English, can be downloaded from the Internet (https://licaeufv.wordpress.com/), and requires the Windows or Linux operating system. The software includes statistical procedures based on mixed models, Bayesian inference, dimensionality reduction and artificial intelligence. Examples of data files that can be processed by GenomicLand are available. The examples are useful to learn about the operation of the modules and statistical procedures.
引用
收藏
页数:7
相关论文
共 25 条
[1]   Comparison of dimensionality reduction methods to predict genomic breeding values for carcass traits in pigs [J].
Azevedo, C. F. ;
Nascimento, M. ;
Silva, F. F. ;
Resende, M. D. V. ;
Lopes, P. S. ;
Guimaraes, S. E. F. ;
Gloria, L. S. .
GENETICS AND MOLECULAR RESEARCH, 2015, 14 (04) :12217-12227
[2]   Supervised independent component analysis as an alternative method for genomic selection in pigs [J].
Azevedo, C. F. ;
Silva, F. F. ;
de Resende, M. D. V. ;
Lopes, M. S. ;
Duijvesteijn, N. ;
Guimaraes, S. E. F. ;
Lopes, P. S. ;
Kelly, M. J. ;
Viana, J. M. S. ;
Knol, E. F. .
JOURNAL OF ANIMAL BREEDING AND GENETICS, 2014, 131 (06) :452-461
[3]   Population structure correction for genomic selection through eigenvector covariates [J].
Azevedo, Camila Ferreira ;
Vilela de Resende, Marcos Deon ;
Fonseca e Silva, Fabyano ;
Nascimento, Moyses ;
Soriano Viana, Jose Marcelo ;
Ferreira Valente, Magno Savio .
CROP BREEDING AND APPLIED BIOTECHNOLOGY, 2017, 17 (04) :350-358
[4]   Ridge, Lasso and Bayesian additive-dominance genomic models [J].
Azevedo, Camila Ferreira ;
Vilela de Resende, Marcos Deon ;
Fonseca e Silva, Fabyano ;
Soriano Viana, Jose Marcelo ;
Ferreira Valente, Magno Savio ;
Ribeiro Resende, Marcio Fernando, Jr. ;
Munoz, Patricio .
BMC GENETICS, 2015, 16
[5]   Independent component regression applied to genomic selection for carcass traits in pigs [J].
Azevedo, Camila Ferreira ;
Vilela de Resende, Marcos Deon ;
Fonseca e Silva, Fabyano ;
Lopes, Paulo Savio ;
Facioni Guimaraes, Simone Eliza .
PESQUISA AGROPECUARIA BRASILEIRA, 2013, 48 (06) :619-626
[6]   Regularized quantile regression for SNP marker estimation of pig growth curves [J].
Barroso, L. M. A. ;
Nascimento, M. ;
Nascimento, A. C. C. ;
Silva, F. F. ;
Serao, N. V. L. ;
Cruz, C. D. ;
Resende, M. D. V. ;
Silva, F. L. ;
Azevedo, C. F. ;
Lopes, P. S. ;
Guimaraes, S. E. F. .
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, 2017, 8
[7]   Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree [J].
de los Campos, Gustavo ;
Naya, Hugo ;
Gianola, Daniel ;
Crossa, Jose ;
Legarra, Andres ;
Manfredi, Eduardo ;
Weigel, Kent ;
Cotes, Jose Miguel .
GENETICS, 2009, 182 (01) :375-385
[8]   Additive Genetic Variability and the Bayesian Alphabet [J].
Gianola, Daniel ;
de los Campos, Gustavo ;
Hill, William G. ;
Manfredi, Eduardo ;
Fernando, Rohan .
GENETICS, 2009, 183 (01) :347-363
[9]   Uses of genomics in livestock agriculture [J].
Goddard, M. E. .
ANIMAL PRODUCTION SCIENCE, 2012, 52 (2-3) :73-77
[10]   Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle [J].
Hayes, B. J. ;
Chamberlain, A. J. ;
McPartlan, H. ;
Macleod, I. ;
Sethuraman, L. ;
Goddard, M. E. .
GENETICS RESEARCH, 2007, 89 (04) :215-220