| dc.description.abstract | A dry edible bean MAGIC population was generated to map genes for resistance to white mold and to produce inbred lines with improved white mold (WM) resistance combined with good agronomic performance for primarily the pinto bean market class.
Eight founding parents were crossed to develop a modified MAGIC population. PT7-2 was intermated with Powderhorn (cross A). ID14-4 was intermated with CO16079 (cross B). La Paz was intermated with Lariat (cross C). USPT-WM_12 was intermated with El Dorado (cross D). Subsequently, F1 plants of each initial cross were intermated using a one-way funnel, F1 from cross A was mated with F1 from cross B and F1 from cross C was mated with F1 from cross D meaning that not every possible cross combination was conducted. The next cycle consisted of intermating F1 from the AxB cross with F1 from the CxD cross. For each cycle reciprocal crosses were conducted to offset potential maternal effects and maternal inheritance. After the final crosses, the F1 were planted to produce the F2 generation which then went through three rounds of single seed descent from F2 to F5. A total of 1,050 F2-derived F5 inbred lines were developed for this WM-MAGIC population.
A total of 428 lines representing each of the crosses were assigned to the training population. The remaining lines were assigned to the validation population. The training population has been genotyped. Briefly, the DNA was isolated from each line and sequenced using a single-end Illumina platform. Sequences were quality trimmed using SICKLE and then aligned to the Phaseolus vulgaris v2.1 reference sequence (DOE-JGI and USDA-NIFA, http://phytozome.jgi.doe.gov) or the UI111 v1.0 reference sequence, indexed and sorted using BWA-MEMB and SAMtools. Read groups including library ID, platform and platform unit were added to each alignment within the BAM files using Picard. Unifiedgenotyper from GATK3.6 (DePristo et al. 2011) was used to call variants with quality scores above 10. Quality scores between 10 and 30 were marked as low quality. Variants with a read depth of less than two were filtered using GATK3.6 variantfiltration and subsequently replaced as missing data. Low quality variants were removed via hard filtering when variants contained more than 25% missing data, more than one nucleotide, or the minor allele was less than 1%. Genotypes with more than 90% missing data were removed. SNPs with missing data were imputed using fastPHASE. The output file was converted to a hmp file for distribution.
Lines were phenotyped using the seedling straw test method proposed by Arkwazee and Myers (2017). The plants were scored four days after inoculation using the disease severity scale described in the protocol. Lines were considered resistant with values from 1 to 3, intermediate with a value of 4, and susceptible with values from 5 to 9. Adjusted means (least square means) were calculated using a linear mixed model in which genotypes were considered fixed effects and reps, blocks, and samples were considered random effects. | en_US |
