The Intelligent Agricultural Solutions of Breeding (IASBreeding) is an analytical platform specifically designed for animal and crop breeding services. At present, the platform includes four functional modules: linear mixed model IASBLUP, machine learning model IASML, molecular phenotype tools (MPtools), breeding mating IASmating, and genotype imputation IASimpute. IASBLUP software provides three analysis versions: C++software, R package, and cloud platform. IASML software provides Python software and cloud platform services. MPtools provides software service. IASmating provides software and cloud platform services for breeding decisions, while IASimpute only provides cloud platform services.
Diverse software versions
Linux C++, R, Shiny web
Efficient computation
Fast C++ math library
User friendly
Interactive webpage and R version
Rich in features
Heritability and Breeding value estimation
Variance component
AI-REML
genetic parameter estimation
Heritability and genetic correlation
Pedigree BLUP
Linear mixed model
Genomic prediction
Genomic kinship matrix, linear mixed model
analysis result
Basic Phenotypic Statistics
Phenotypic distribution statistics
Variance component calculation
heritability
IASbreeding R Package
IASbreeding V0.1.0 can calculate kinship matrix, variance component analysis using linear mixed model, breeding value using BLUP. The core algorithm of IASbreeding is built using Rcpp and RcppEigen.
Install IAS-breeding software
Start an R session using RStudio and run these lines:
install.packages("IASbreeding_0.1.0.zip", repos = NULL)
install.packages("Rcpp","RcppEigen")
library(IASbreeding)
library(Rcpp)
library(RcppEigen)
How to using IAS-breeding software
phe_file <- system.file("extdata", "Phenotype.txt", package = "IASbreeding", mustWork = TRUE)
pheno <- read.table(phe_file,header=TRUE)
ped_file <- system.file("extdata", "Pedigree.txt", package = "IASbreeding", mustWork = TRUE)
ped <- read.table(ped_file,header=TRUE)
newped<-pedcheck(ped)
A<-Akin(newped)
Results <- IASBLUP(BW56 ~ 1 + Sex + Condition,random = "ID", kinship = A, max_iter = 20, data = pheno)
bed_file <- system.file("extdata", "Genotype.bed", package = "IASbreeding", mustWork = TRUE)
file_prefix <- sub("\\.bed$", "", bed_file)
Genotype <-read_bed(file_prefix)
kin<-Gkin(Genotype)
Results <- IASBLUP(BW56 ~ 1 + Sex + Condition,random = "ID", kinship = kin, max_iter = 20, data = pheno)
- Please read the instructions for the IAS-Breeding software for detailed usage.
IAS-Breeding C++ software
IASBreeding V1.1.0 can calculate kinship matrix, variance component, breeding value using linear mixed model.
Installing IAS-Breeding
You can directly use it after extraction:
tar -xzvf IASBreeding-1.1.0-Linux-x86_64.tar.gz
./IASBreeding
Using IAS-Breeding
- Build genomic relationship matrix : –kinship
–kin-method 1: sum[2p(1-p)](VanRaden et al 2008);
–kin-method 2: Independent 2p(1-p)(Yang et al 2010);
–kin-method 3: Independent variance(Cai et al., 2023)
--kin-method 1, 2 or 3. Choose a specific method for calculation (Default: --kin-method 1)
./IASBreeding --kinship --bedfile Genotype --kin-bin --threads 8 --out output --kin-method 1
--bedfile Perform calculations using the given genotype (the prefix of PLINK binary genotype file):
./IASBreeding --kinship --bedfile Genotype
--pedigree Perform calculations using the given pedigree (the pedigree file with three columns):
./IASBreeding --kinship --pedigree Pedigree.txt
--kin-bin Kinship saved for binary format(if not given, kinship saved for txt format):
./IASBreeding --kinship --bedfile Genotype --kin-bin
--threads Specify the number of threads used (default:1):
./IASBreeding --kinship --bedfile Genotype --kin-bin --threads 8
--out Specify the output prefix (default: Result):
./IASBreeding --kinship --bedfile Genotype --kin-bin --threads 8 --out output
--kin-lambda The power of Indipendent 2p(1-p) or variance (only useful for kin-method 2 or 3, default lambda = 1):
./IASBreeding --kinship --bedfile Genotype --pedigree Pedigree.txt --kin-bin --threads 8 --out output --kin-method 2 --kin-lambda 2
--kin-tau Scaling factor (tau) for G22 matrix (Default tau=1)
./IASBreeding --kinship --bedfile Genotype --pedigree Pedigree.txt --kin-bin --threads 8 --out output --kin-method 2 --kin-lambda 2 --kin-tau 1.1
--kin-omega Scaling factor (1-omega) for A22 matrix (Default omega=1)
./IASBreeding --kinship --bedfile Genotype --pedigree Pedigree.txt --kin-bin --threads 8 --out output --kin-method 2 --kin-lambda 2 --kin-tau 2 --kin-omega 0.5
- Variance component analysis using linear mixed model : –reml
Perform calculations using the given phenotype and kinship (relationship matrix built by --kinship):
--kin-file Specify the kinship txt file
--phefile Specify the phenotype file
--phe-pos Specify the column for phenotype data
./IASBreeding --reml --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4
--covar-pos Specify the columns for covariates, separated by commas:
./IASBreeding --reml --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3
--max-iter Specify the maximum iterations of REML:
./IASBreeding --reml --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3 --max-iter 50
- Perform prediction of breeding values : –predict
Perform calculations using the given phenotype and kinship (relationship matrix built by --kinship):
--kin-file Specify the kinship txt file
--phefile Specify the phenotype file
--phe-pos Specify the column for phenotype data
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4
--covar-pos Specify the columns for covariates, separated by commas:
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3
--max-iter Specify the maximum iterations of REML:
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3 --max-iter 50
--out Specify the output prefix (default: Result):
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3 --max-iter 50 --out output
./IASBreeding --kinship --pedigree Pedigree.txt --out output
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3 --out BLUP_bv
./IASBreeding --kinship --bedfile Genotype --out output
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3 --out GBLUP_bv
./IASBreeding --kinship --pedigree Pedigree.txt --bedfile Genotype --out output
./IASBreeding --predict --kin-file output.kinship.txt --phefile Phenotype.txt --phe-pos 4 --covar-pos 3 --out SSGBLUP_bv
About IAS-breeding
This app (IAS-breeding) was built by Wentao Cai(caiwentao@caas.cn).
The current release of IAS-breeding contains:
Use IAS-breeding online
