Location: Plant Germplasm Introduction and Testing Research
Project Number: 2090-21000-037-004-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2022
End Date: Jul 31, 2024
Objective:
The funds will be used to pay a sub-award for part of the annual salary and benefits of a graduate student, under the supervision of the cooperator, to evaluate USDA 300 common bean germplasm accessions for ashy stem blight resistance, conduct GWAS and Genomic Prediction. Cooperator and other UPR faculty will supervise the analysis of genome wide association data set in common bean and find the best model to run genomic prediction.
Approach:
Objective 1. Evaluate USDA GRIN common bean germplasm accession for ashy stem blight resistance: The greenhouse experiments will be performed to evaluate ashy stem blight resistance in 300 common bean accessions using a M. phaseolina isolate PRI21. A randomized complete block design (RCBD) with three replications will be used for the experiment and two plants of each accession per replication will be planted in greenhouse trials in Lajas. Before inoculation, a 200-µL Eppendorf tip stacked with four mycelial plugs from 48 h old M. phaseolina culture. One inoculation will be carried out at the fourth internode by the cut-stem method and only resistant plants will be inoculated a second time 10 days later. Inoculated plants will be exposed to high mean day temperatures > 27 °C and moisture ranged from 50-70%. The disease severity will be evaluated at 35 d after inoculation using a 1-9 scale. Data will be analyzed using SAS 9.4 PROC GLM.
Objective 2. Conduct genome-wide association study (GWAS) and identify SNP markers for ashy stem blight resistance in common bean.
Using a filtered set of 24.4 million (M) SNPs among the 300 accessions previously identified, GWAS will be conducted with the mixed linear model (MLM) method as described in TASSEL 5 (Bradbury et al., 2007) and the analysis will be also performed in GAPIT 3 using FarmCPU and BLINK models (Wang and Zhang, 2021) (https://zzlab.net/GAPIT/index.html; https://github.com/jiabowang/GAPIT3), which will be run in R, to validate and identify more reliable SNP markers associated with ashy stem blight resistance.
Objective 3. Genomic prediction for ashy stem blight resistance in common bean
from the 300 common bean genotypes of the association panel, randomly the 240 accessions will be used as training set, which will estimate the marker effect. The marker effect will be used to predict the GEBV of the remaining 60 genotypes, which will be used as validation set. GEBV prediction: The GP will be conducted using BLUP methods (RR-BLUP, gBLUP, and cBLUP) and Bayesian methods (BayesA, BayesB, Bayes LASSO, and Bayes ridge regression) to predict genomic estimated breeding value (GEBV).
