Epub 2015 Sep 28. The Sequence alignment/map (SAM) format and SAMtools. 2014; Lobaton et al; 2018). A. Again, because the trials were under two stress conditions, Z transform data were evaluated. Previously, the ADP had only been genotyped with the ∼6k SNPs from the BARCBean 6K_3 BeadChip (Song et al. Single-trait and multi-trait meta-analysis genome-wide association study (GWAS) results Study-specific genomic-control inflation ranged from 0.98â1.06 ( S3 Table , S1 Fig ) and the linkage disequilibrium (LD) score regression intercepts of the single-trait BP meta-analyses calculated by the LD score regression approach ranged from 1.02â1.04. 2013). Many genetic variants identified in genome-wide association studies (GWAS) are associated with multiple, sometimes seemingly unrelated, traits. Leveraging GWAS for complex traits to detect signatures of natural selection in humans. 5. GWAS were performed for each trait in each location under different stress conditions using untransformed data. Genetic analysis of flooding tolerance in an Andean Diversity Panel of dry bean (Phaseolus vulgaris L.). The regulation depends on the perception of a hormone peptide called RALF. Thank you for sharing this G3: Genes | Genomes | Genetics article. The BASE_Meso and BASE_Andean are located within their correct gene pools in the tree demonstrating they are appropriate genotypes to study phenotypic responses in the two gene pools. 2012) is demonstrated as a method to identify statistically robust genetic factors in smaller-sized populations. Affiliations. With these considerations in mind, the three panels of ∼120 individuals were phenotyped in replicated trials in multiple abiotic stress conditions. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Cells. The 1,882 SNPs were also used to develop a bifurcated ML phylogenic tree that demonstrated the two populations were clustered into two separate clades (Figure 2B). This tree was developed with the 5,637 SNPs shared between the MA and Andean SNP data sets. (2012). Since the three locations were considered different environments with potentially different heat stress conditions, the phenotypic data were transformed using the Z transformation, and the data were combined into a single MLM GWAS analysis (Figure 3A). 2018). Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. The un-imputed HapMap data for each gene pool can be found in S4 and S5 text files. The P value cutoff for the two GWAS, as determined using the Bonferroni test based on the effective number of SNPs was –log10(P)=4.10. Oxidative Stress Responses and Nutrient Starvation in MCHM Treated, http://phaseolusgenes.bioinformatics.ucdavis.edu/, https://plantscience.psu.edu/research/labs/roots/projects/usaid-crb, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris, http://creativecommons.org/licenses/by/4.0/, Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments. For converting data from other formats, see This report also describes the utility of those SNP collections and the new association panels to map genetic factors controlling important production related traits under heat and drought conditions. Func. HHS The effect of heat stress on yield and DTF was assessed on the BASE_Meso population genotypes evaluated in PR in 2015 and 2016, and HN in 2016 (Table S2). MultiABEL does NOT require different single-trait GWAS having been performed in exactly the same individuals. 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