An example of GWAS applied to potato plants using the MultiGWAS tool for GWAS on polyploids using múltiple GWAS tools

1. Application of Bioinformatics in Plant Breeding
Case Potato Crops and late blight resistence
Luis Garreta
Postdoctoral Research Colciencias
AGROSAVIA - Corporación Colombiana para de Investigación Agropecuaria
April 18, 2020

2. Objective
I Identify of genomic associations between the tetraploid potato
and late blight resistence
I Implement a model for predicting breeding values in potatos

3. Methods
I Genome-Wide Association Studies (GWAS)
I Genomic Selection (GS)

4. Genotype and Phenotype

5. Single nucleotide polymorphisms (SNPs)
I The most common type of genetic variation among people.
I It is a substitution of a single nucleotide that occurs at a
specic position in the genome

6. SNPs in Whole Genomes

7. GWAS: Genome-Wide Association Studies
An approach used in ge-
netics research to asso-
ciate specic genetic vari-
ations (SNPs) with partic-
ular traits (e.g. diseases,
agronomic trait).
GWAS involves scanning
the genomes from many
dierent people and look-
ing for SNPs that can be
used to predict the pres-
ence of a disease.

8. SNP-chips (DNA microarray)
The DNA microarray is a tool used to determine whether the DNA
from a particular individual contains a mutation in genes

9. WGAS Process

10. GWAS Methods (Methods for test associations)
I Linear Models
I Linear Regression
I Logistic Regresion
I Linear Mixed Models
I Bayesian Mixed Models

11. Linear Models
where:
I y represents the n Ö 1 vector of phenotypes,
I
−
→
1 is an n Ö 1 vector of ones,
I xG is the n Ö 1 vector of the genotypes for a given SNP,
I β0, β1 ∈ R, are the oset and the genotype eects.

12. Linear Mixed Model

13. Genomic Data Tetraploid Potato
I Example of tetraploid potato (Four set of chromosomes):
I Humans are diploids (Father and Mother)
Phenotype Genotype

14. MultiGWAS: a tool for integrating multiple GWAS tools

15. Popular Tools for GWAS analysis
1. GWASPoly:
I Relatively new R library for GWAS in polyploid.
2. PLINK:
I Popular Program for GWAS in diploids
I Mainly used in humans.
3. TASSEL:
I Popular Java Package and program for GWAS in diploids
I Mainly use in plants.
4. SHEsis:
I Simple Program for GWAS analysis in polyploids.

16. MulitiGWAS: A tools for GWAS analysis integrating four
GWAS tools
Multi Analysis
Diploids
Polyploids
GWASpoly
Plink
Tassel
SHEsis

17. MulitiGWAS: A tools for GWAS analysis integrating four
GWAS tools
Multi Analysis
Diploids
Polyploids
Integration
Adjustment
Clean
Quality Control
Format
GWASpoly
Plink
Tassel
SHEsis
Scan
Summarize
Report
Read
Config File
Genotype file
Phenotype file
GWAS model
Significance
Correction
N associations
QC filters
Score tables
Venn diagrams
Manhattan plots
SNPs profiles

18. MultiGWAS outputs
file:///home/lg/agrosavia/docs/presentations/
biomedicine/multiGWAS-report.html

19. What next?
I Genomic Selection