Idate gene association mapping Linkage disequilibrium was estimated because the correlation between all pairs of SNPs in individual candidate genes by use in the SNP & Variation Suite v7.7.6. Haplotype blocks were computed with the default settings for the Gabriel et al. algorithm imbedded in SVS v7.7.6. Haplotype frequencies for each defined haplotype block in all three genes were calculated by the estimation maximization method, with a 1676428 frequency threshold of 0.01. Only SNPs with a minimum minor allele frequency. 0.1 were considered for LD studies and candidate gene association mapping. To visualize LD throughout the gene, heat maps were produced on the basis of pair-wise correlation estimates of all marker pairs. The Q and K matrices were adapted from previously performed simple sequence repeat analysis. Q matrix was adapted from K-5 cluster of SSR data obtained by use of Structure v2.2. The Mixed Linear Model of TASSEL v3.0 was used for association mapping for Pun1, KAS1 and CCR. HCT did not undergo association mapping because of minimum minor allele frequency, 0.1 for SNPs discovered in this gene. The SNP P-values obtained were not subjected to sequential Bonferroni correction or FDR. Considering the sample size and number of polymorphisms used in our study, corrections for population structure and kinship were 25837696 sufficient for association tests. Principal component analysis Numeric principal component analysis with the metabolic profiles involved use of SVS v7.7.6. Before PCA, concentrations of metabolites directly or indirectly involved in the capsaicinoid Polymorphisms among Capsaicin Pathway Genes Season 1 Log2 total capsaicinoids 18.5616094 18.51012019 17.37448703 17.04109434 16.79526245 16.2388068 16.23223184 16.21818292 16.11034879 15.84204851 doi:10.1371/journal.pone.0086393.t001 Accession H114 H110 H106 H072 H141 H077 H138 H102 H067 H105 Season 2 Log2 total capsaicinoids 4.660259827 4.469676922 4.278490915 4.231831093 4.203551229 4.000636899 3.920554658 3.806494182 3.765499939 3.757719495 Accession CA05 H114 H102 H138 H077 CA14 H106 H119 H035 CA17 Alignment of exons from the cDNA sequence of Pun1 to the Capsicum BIBS39 site genome draft showed that Pun1 is on the negative strand of chromosome 2. A total of 36 polymorphisms were identified in Pun1: 19 were localized in the promoter, seven in the first exon, seven in the intron and three in the second exon: 20 were transversions, 15 were transitions and one was an indel of two nucleotides. SNP positions are numbered by orientation and Z-360 web position from the transcription start site. Annotations of Cis regulatory elements for various SNP positions are presented in Four haplotype blocks were defined in Pun1. Markers contained in each block and haplotype frequencies calculated with the EM method are in 4 Polymorphisms among Capsaicin Pathway Genes Gene region Pun1 Exon 1 Intron 1 Exon 2 CCR Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 Intron 3 Exon 4 Intron 4 Exon 5 HCT Exon 1 Intron 1 Exon 2 Chromosome Starting genome position Ending genome position Starting gene position Ending gene position chr02 chr02 chr02 120715906 120715132 120714793 120715133 120714794 120714019 1 773 1112 772 1111 1886 chr03 chr03 chr03 chr03 chr03 chr03 chr03 chr03 chr03 233893926 233894047 233894334 233894490 233895068 233895253 233895344 233895699 233896502 233894046 233894333 233894489 233895067 233895252 233895343 233895698 233896501 233896689 1 122 409 565 1143 1328 1419 1774 2577 121 408 564 1142 1327 1418 1773 2576 2764 chr07.Idate gene association mapping Linkage disequilibrium was estimated because the correlation involving all pairs of SNPs in person candidate genes by use in the SNP & Variation Suite v7.7.6. Haplotype blocks were computed with the default settings for the Gabriel et al. algorithm imbedded in SVS v7.7.6. Haplotype frequencies for each defined haplotype block in all three genes were calculated by the estimation maximization method, with a 1676428 frequency threshold of 0.01. Only SNPs with a minimum minor allele frequency. 0.1 were considered for LD studies and candidate gene association mapping. To visualize LD throughout the gene, heat maps were produced on the basis of pair-wise correlation estimates of all marker pairs. The Q and K matrices were adapted from previously performed simple sequence repeat analysis. Q matrix was adapted from K-5 cluster of SSR data obtained by use of Structure v2.2. The Mixed Linear Model of TASSEL v3.0 was used for association mapping for Pun1, KAS1 and CCR. HCT did not undergo association mapping because of minimum minor allele frequency, 0.1 for SNPs discovered in this gene. The SNP P-values obtained were not subjected to sequential Bonferroni correction or FDR. Considering the sample size and number of polymorphisms used in our study, corrections for population structure and kinship were 25837696 sufficient for association tests. Principal component analysis Numeric principal component analysis of your metabolic profiles involved use of SVS v7.7.6. Before PCA, concentrations of metabolites directly or indirectly involved in the capsaicinoid Polymorphisms among Capsaicin Pathway Genes Season 1 Log2 total capsaicinoids 18.5616094 18.51012019 17.37448703 17.04109434 16.79526245 16.2388068 16.23223184 16.21818292 16.11034879 15.84204851 doi:10.1371/journal.pone.0086393.t001 Accession H114 H110 H106 H072 H141 H077 H138 H102 H067 H105 Season 2 Log2 total capsaicinoids 4.660259827 4.469676922 4.278490915 4.231831093 4.203551229 4.000636899 3.920554658 3.806494182 3.765499939 3.757719495 Accession CA05 H114 H102 H138 H077 CA14 H106 H119 H035 CA17 Alignment of exons from the cDNA sequence of Pun1 to the Capsicum genome draft showed that Pun1 is on the negative strand of chromosome 2. A total of 36 polymorphisms were identified in Pun1: 19 were localized in the promoter, seven in the first exon, seven in the intron and three in the second exon: 20 were transversions, 15 were transitions and one was an indel of two nucleotides. SNP positions are numbered by orientation and position from the transcription start site. Annotations of Cis regulatory elements for various SNP positions are presented in Four haplotype blocks were defined in Pun1. Markers contained in each block and haplotype frequencies calculated with the EM method are in 4 Polymorphisms among Capsaicin Pathway Genes Gene region Pun1 Exon 1 Intron 1 Exon 2 CCR Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 Intron 3 Exon 4 Intron 4 Exon 5 HCT Exon 1 Intron 1 Exon 2 Chromosome Starting genome position Ending genome position Starting gene position Ending gene position chr02 chr02 chr02 120715906 120715132 120714793 120715133 120714794 120714019 1 773 1112 772 1111 1886 chr03 chr03 chr03 chr03 chr03 chr03 chr03 chr03 chr03 233893926 233894047 233894334 233894490 233895068 233895253 233895344 233895699 233896502 233894046 233894333 233894489 233895067 233895252 233895343 233895698 233896501 233896689 1 122 409 565 1143 1328 1419 1774 2577 121 408 564 1142 1327 1418 1773 2576 2764 chr07.

Idate gene association mapping Linkage disequilibrium was estimated as the correlation

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