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Protocols

GAPIT specifications

Information


Unique identifier OMICS_08869
Name GAPIT
Alternative names Genome Association and Prediction Integrated Tool, SUPER (Settlement of MLM Under Progressively Exclusive Relationship)
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Zhiwu Zhang

Publications for Genome Association and Prediction Integrated Tool

GAPIT citations

 (176)
library_books

Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi Locus Genome Wide Association Studies

2018
Front Plant Sci
PMCID: 5933171
PMID: 29755499
DOI: 10.3389/fpls.2018.00561

[…] the five traits using mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB, respectively (Figure ; Tables –). However, only one and six significantly associated SNPs were detected when using MLM (R package GAPIT) and FarmCPU (R package FarmCPU; PCA+K, where PCA and K were calculated by GAPIT and SpAGeDi, respectively) models, respectively (P = 0.05/43427 = 1.15 × 10−6; Table ). This suggested that these […]

call_split

Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome Wide Association Analyses

2018
Sci Rep
PMCID: 5916932
PMID: 29695843
DOI: 10.1038/s41598-018-24946-3
call_split See protocol

[…] For QTN identification, 395,553 SNPs and 208 accessions were used to detect SNP-trait associations using GWAS. Marker-trait associations were conducted by compressed mixed linear model implemented in GAPIT with the default settings except for the PCA setting as 3. A threshold of p-value (1.0 × 10−5) was used to claim significant SNP-trait associations and significant SNPs in <200 kb distances were […]

library_books

Joint Exploration of Favorable Haplotypes for Mineral Concentrations in Milled Grains of Rice (Oryza sativa L.)

2018
Front Plant Sci
PMCID: 5906679
PMID: 29706977
DOI: 10.3389/fpls.2018.00447

[…] were conducted using SAS software (S. A. S. I. Inc., ). The basic scenario of a compressed mixed linear model (Zhang et al., ), implemented in the Genomic Association and Prediction Integrated Tool (GAPIT) Version 2 (Lipka et al., ), was adopted for association analysis between QTL-flanking markers and GMC traits for the pooled, the X-set, and the G-set. Parameters for GAPIT were set with referen […]

library_books

Genome wide association mapping for eyespot disease in US Pacific Northwest winter wheat

2018
PLoS One
PMCID: 5880388
PMID: 29608579
DOI: 10.1371/journal.pone.0194698

[…] Genome-wide association analysis was conducted using the compressed mixed linear model (CMLM) implemented in the GAPIT R package [–]. The CMLM approach accounts for population structure (Q) and relatedness among individuals [kinship matrix (K)] to reduce false discoveries []. The K and Q was calculated by princi […]

library_books

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

2018
Front Plant Sci
PMCID: 5869928
PMID: 29616069
DOI: 10.3389/fpls.2018.00362

[…] using r2 parameter with sliding windows size of 50 sites (bp) through the software Tassel v5.0 (Bradbury et al., ). Associations between molecular markers and phenotypic data were computed using the Genome Association and Prediction Integrated Tool—GAPIT (Lipka et al., ) based on the Mixed Linear Model (MLM) that controls the population structure and genetic relatedness among the individuals by i […]

library_books

Genetic Architecture and Candidate Genes for Deep Sowing Tolerance in Rice Revealed by Non syn GWAS

2018
Front Plant Sci
PMCID: 5864933
PMID: 29616055
DOI: 10.3389/fpls.2018.00332

[…] . A neighbor-joining (N-J) tree was generated from more than 75,000 randomly selected SNPs using Tassel 5 and Mega 6 software. Principal components (PC) and kinship matrix were calculated by software GAPIT to verify population structure using more than 3 million SNPs with minor allele frequency >0.05 and missing rates <0.5. LD heatmaps of two important QTLs identified in GWAS were generated using […]

Citations

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GAPIT institution(s)
College of Electrical and Information, Northeast Agricultural University, Harbin, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA; Department of Animal Science and Technology, North East Agricultural University, Harbin, China; Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Science, Harbin, China; College of Horticulture, Nanjing Agricultural University, Nanjing, China; School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China; National Maize Improvement Center of China, China Agricultural University, Beijing, China; Department of Crop Sciences, University of Illinois, Urbana, IL, USA; USDA- ARS, Ithaca, NY, USA; Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
GAPIT funding source(s)
Supported by NSF (0922493 and 1238014), USDA-ARS, an Emerging Research Issues Internal Competitive Grant from the Agricultural Research Center at Washington State University, College of Agricultural, Human, and Natural Resource Sciences, the Endowment and Research Project (No. 126593) from the Washington Grain Commission, the National Natural Science Foundation of China (Grant no. 31301748), and the China Postdoctoral Science Foundation (Grant no. 2014M551607).

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