How to create genotype by trait (GT) Biplot in R software?

A genotype by trait biplot can help understand the relationships among traits (breeding objectives) and help identify traits that are positively or negatively associated, traits that are redundantly measured, and traits that can be used in indirect selection for another trait. It also helps to visualize the trait profiles (strength and weakness) of genotypes, which is important for parent as well as variety selection.
The code
How to compute GT Biplots in R ?
library(metan)
attach(data_ge2)
View(data_ge2)
mod =gtb(data_ge2, GEN, resp = contains("E"))
Basic Biplot
plot(mod,
type = 1,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)
#The Average Tester Coordination view for genotype-trait
plot(mod,
type = 2,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 3,repel=TRUE)
Which-won-where
plot(mod,
type = 3,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)
Discriminativeness vs. representativeness.
plot(mod,
type = 4,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)
Examine trait
plot(mod,
type = 5,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)# not worked
plot(mod,sel_env = "ENV")
#Ranking traits
plot(mod,
type = 6,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)
Examine a genotype
plot(mod,
type = 7,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)# not worked
plot(mod,sel_gen = "GEN")
#Ranking genotypes
plot(mod,
type = 8,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)
#Compare two genotypes
plot(mod,
type = 9,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)# not worked
plot(mod,sel_gen1 = "H1",sel_gen2 = "H10")
Relationship among traits
plot(mod,
type = 10,
col.gen = 'blue',
col.env = 'red',
size.text.gen = 4)

[@techalebirhan3704]

I love the prediction part! Also it's good if you try genomic prediction! Its very nice Wake!

[@wakjiratesfahun3682]

Okay Dr. I Will try

[@chekolenigus9868]

Wakjira could you help me on analysis for location grouping (LG) for mega environments and identifying target testing locations by biplot scripts. Which developed by Weikai Yan, 2019.Thank you

[@plantgenetics6405]

i run into the following error when running the code:Error in svd(gt_mat) : infinite or missing values in 'x'. How can I resolve it?

[@wakjiratesfahun3682]

It is better to check your data and impute the missing value.

[@sylwiajedzura7516]

Greate tutorial👍 thank you

[@wakjiratesfahun3682]

Thank you very much.

[@matinakand8874]

I am have a field data (single location) of three factor like 80% field capacity (no stress) 60% fc ( moderate stress) and 40% fc (sever stress) for evaluation of 20 genotype at rcbd design.. can i perform GT biplot by this data ?

[@wakjiratesfahun3682]

Yeah It is possible. You can do for single site. For more info please run the following word, ?gtb. Don't forget to run the metan package.

[@matinakand8874]

@@wakjiratesfahun3682 thanks

[@matinakand8874]

What is the difference between GT biplot vs GGE biplot??

[@wakjiratesfahun3682]

In GT there is inclusion of some traits and while the GGE focus on grain yield performance on the basis of genotype +genotype environmental interaction.

[@matinakand8874]

@@wakjiratesfahun3682 thanks