Location: Sunflower and Plant Biology Research
Project Number: 3060-21220-031-011-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2015
End Date: Jun 30, 2020
Objective:
1. Identify, transfer and validate white mold (WM) resistance factors from P. coccineus and P. vulgaris in advanced snap bean breeding lines.
2. Examine phenotypic interaction among major QTL conferring partial resistance to WM in common bean.
3. Conduct genome-wide association (GWAS) mapping in Snap Bean, Middle American and Andean Diversity Panels using genotype-by-sequencing (GBS).
4. Correlate GWAS results with RNA-seq gene expression data.
5. Develop a WM-MAGIC (Multi-parent Advanced Generation Inter-Cross) population for future fine-mapping and improved germplasm development.
Approach:
Objective 1: Lines developed from inbred backcross populations from P. vulgaris //P. vulgaris x P. coccineus crosses will be used to identify QTL associated with WM resistance. Those QTL will be validated in separate populations and environments to determine if they are broadly expressed in multiple populations. The P. coccineus QTL will be transferred into advanced common bean breeding lines (both snap and dry beans) with stable fertility traits and adequate agronomic performance. New sources of resistance in P. vulgaris identified in the Snap Bean Diversity Panel (SBDP) through GWAS will be crossed to susceptible lines to create recombinant inbred (RI) populations to characterize potentially novel QTL for resistance.
Objective 2: A newly discovered QTL WM7.3 from I9365-31 black bean breeding line will be remapped in the originating recombinant inbred population (Raven/I9365-31 – 105 RILs) using the Ilumina 6000 SNP chip. The introgression and effect of WM7.3 in susceptible great northern bean will be examined using inbred backcross populations genotyped by the SNP chip.
Objective 3: Genotype-by-sequencing (GBS) will increase the genome-wide association (GWAS) mapping resolution for Snap Bean, Mesoamerican (syn Middle American), and Andean Diversity Panels (SBDP, MDP, and ADP), respectively. The three association mapping populations represent accessions grouped by origin, (MDP representing pinto, Great Northern, medium red, pink, navy, and black market classes; ADP representing kidney, cranberry) and utilization (snap beans). Additional white mold disease reaction data from greenhouse and field trials will be collected on the populations across locations and years, and GWAS analysis will discover significant QTL by association with high resolution (<50 kb).
Objective 4: Fine-structure mapping and candidate gene discovery will focus on major WM resistance QTL pyramided into individual lines. Highly divergent lines with combinations of WM QTL will be evaluated by RNA-seq. These lines will be infected and next generation sequencing data (Illumina HiSeq2000) will be generated for each tissue source. Comparisons will be made with GWAS peaks to identify candidate genes.
Objective 5: A MAGIC (Multi-parent Advanced Generation Inter-Cross) population obtained from crosses among eight parents representing diverse sources of white mold resistance will generate a large segregating population for multiple WM resistance QTL. This MAGIC population will provide a) a high resolution mapping population that will augment the GWAS analysis; and b) a new source of germplasm for future cultivar development.
