GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction

Genome-wide association study (GWAS) and genomic prediction/selection (GP/GS) are the two essential enterprises in genomic research. Due to the great magnitude and complexity of genomic and phenotypic data, analytical methods and their associated software packages are frequently advanced. GAPIT is a widely-used genomic association and prediction integrated tool as an R package. The first version was released to the public in 2012 with the implementation of the general linear model (GLM), mixed linear model (MLM), compressed MLM (CMLM), and genomic best linear unbiased prediction (gBLUP). The second version was released in 2016 with several new implementations, including enriched CMLM (ECMLM) and settlement of MLMs under progressively exclusive relationship (SUPER). All the GWAS methods are based on the single-locus test. For the first time, in the current release of GAPIT, version 3 implemented three multi-locus test methods, including multiple loci mixed model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK). Additionally, two GP/GS methods were implemented based on CMLM (named compressed BLUP; cBLUP) and SUPER (named SUPER BLUP; sBLUP). These new implementations not only boost statistical power for GWAS and prediction accuracy for GP/GS, but also improve computing speed and increase the capacity to analyze big genomic data. Here, we document the current upgrade of GAPIT by describing the selection of the recently developed methods, their implementations, and potential impact. All documents, including source code, user manual, demo data, and tutorials, are freely available at the GAPIT website (http://zzlab.net/GAPIT).