*2.8. QTL Mapping of P. capsici Resistance and Candidate Gene Prediction*

QTL analysis was identified by r/QTL software using CIM methods [47,48]. The LOD score thresholds for evaluating the statistical significance of the QTL effects were established using 1000 permutations (*p* < 0.05). The predicted genes within the target QTL interval were determined by comparison with the annotated Zunla-1 and CM334 reference genomes (http://peppersequence.genomics.cn, accessed on: 20 January 2019). The function of genes identified in the candidate regions was manually determined by BLASTX (https://blast.ncbi.nlm.nih.gov/, accessed on: 20 January 2019). In addition, the predicted genes were further annotated based on KEGG (https://www.kegg.jp/kegg/, accessed on: 20 January 2019), COG (http://www.ncbi.nlm.nih.gov/COG/, accessed on: 20 January 2019), Swiss-Prot (http://www.ebi.ac.uk/uniprot/ accessed on: 20 January 2019), and NR (https://blast.ncbi.nlm.nih.gov/ accessed on: 20 January 2019) databases.
