Location: Sunflower Improvement Research
Project Number: 3060-21000-047-017-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2023
End Date: Dec 31, 2027
Objective:
Objective 1: Develop short read sequence resources for USDA sunflower breeding lines with performance data for marker-based trait prediction
Objective 2: Develop mapping resources to detect genes involved with the Red Sunflower Seed Weevil resistance response sourced from USDA line HA 488.
Approach:
Objective 1: Fourteen F4 and later sunflower breeding and mapping populations with no conscious selection imposed (n=28 to 192 for each) have been selected for this portion of the work. These populations are a random sample from the current and recent USDA breeding materials. The progeny lines, 613 in total, will need to be sequenced to an approximately 1x depth and variants called across the entire set of populations to derive a consistent set of markers for the entire panel. Missing markers will be imputed using BEAGLE 5.4 software (Browning et al., 2021), and the resulting marker data set filtered to include only markers that are monomorphic in individual populations OR segregate in a Mendelian manner in each population using a custom data filter script that includes only markers where the Chi-square ratio does not deviate from a 1:2:1 ratio with 90% confidence. This was found to be necessary despite using GATK best practices in previous datasets (Barstow et al., 2022). The physical sites of variant polymorphisms from the GWAS studies of Pogoda et al. (2020) and Guidini et al. (2022) will be translated to the polymorphic sites in the panel of unselected breeding populations, and diagnostic markers verified. Haplotypes associated with Sclerotinia and Phomopsis resistance loci (necrotrophic resistance traits with notable covariance) will be determined using Haploview software (Broad Institute) or a similar tool for inferring haplotypes from multi-marker data. Haplotypes will be compared to the annotated sunflower genome to catalogue genes existing in these regions.
Objective 2: Four populations have been developed that are segregating for resistance to Red Sunflower Seed Weevil sourced from HA 488. One of these populations has been resequenced, while the other three still require sequencing. We will sequence the lines of the remaining populations at an approximately 1x depth of coverage, and call variants using the protocols from Objective 1. Additionally, the parental lines and/or bulks of resistant and susceptible materials will be sequenced using long-read sequencing protocols. Phenotypic data from our field experiments will be used with this genotypic data to find the genetic loci (or genes) responsible for the resistance.
