QUE about Heritability Estimation

[Yoledou]

Dear Dr. Gustavo
The heritability I calculated using BGLR is significantly lower than the heritability reported in the literature. And no errors were reported during the BGLR operation.
The following is my own code. Is there something wrong? ?
(In the ETA settings, I set 'flock' and 'sex' in my dataset as fixed factors)

GBLUP: Heritability Estimation
library(BGLR)
setwd('F:\GS2\demo\275demo')
##dataset of phenotype
Y<-read.table("wool_1_2.txt",sep="\t",header=TRUE)
Y$SEX <- as.factor(Y$SEX) ##set sex into factor
Y$FLOCK <- as.factor(Y$FLOCK) ##set flock into factor
y<-Y[,7] select the trait “diameter of wool (DIA)”
##red_ped
out=read_ped("AMS286_QC_impute.ped")
p=out$p
n=out$n
out=out$x
out[out==2]=NA
out[out==3]=2
X=matrix(out,nrow=p,ncol=n, byrow=TRUE)
X=t(X)
X<-scale(X,center=TRUE,scale=TRUE)
G=tcrossprod(X)/ncol(X)
fm1=BGLR( y=y,ETA=list(list(~factor(FLOCK)+factor(SEX),data=Y,model='FIXED'),
list(K=G,model='RKHS')),
nIter=12000,burnIn=2000,saveAt='eig_'
)

varE=scan( 'eig_varE.dat')
varU=scan('eig_ETA_G_varU.dat')
h2_2=varU/(varU+varE)
h2_2
mean(h2_2)

The heritability of the diameter of wool in the literature is 0.57 ~ 0.59, but the heritability of the calculation after running the above code is 0.19, please help me check where the above code problems occur, why the difference is so great
Thanks a lot !

[Yoledou]

Could you please help me to check the code ? Thanks a lot !