FA07 genetic map: Pepper genetic map of Capsicum frutescens accession BG2814-6 x C. annuum cv. 'NuMex RNaky' F7:F8 RIL population (119 RILs) Sixth Release 

The current version of the C. frutescens acc. BG2814-6 X C. annuum 'NuMex RNaky' map (v06) is based on the Pepper Chip assembly
unigene haplotypes (Ashrafi et al., 2012, Hill et al., 2013). The haplotypes were generated by summarizing
multiple polymorphic positions (SPPs) of the same EST unigene into consensus haplotypes for mapping, which we refer to as markers.
Therefore, SPP positions within unigenes are not included in the mapped marker names. The map was generated with RECORD_Win. Four
of the original 123 F7:F8 RILs were removed due to high number of double cross-oversand missing data. Thirteen contigs with
multiple haplotypes (accounting for 26 markers) were included in the map, these can be identified by an ID_1 or ID_2 in the
marker designation, all single haplotype contigs have four letter ID marker designations (see Table 6).

The linkage group assignation was based on conserved ortholog set II (COSII) markers between the parental lines C. frutescence
acc BG2814-6 X C. annuum 'NuMex RNaky' that were previously assayed on the pepper genome.
The Linkage Groups P1 and P8 are refered to as P1 Wild and P8 Wild to acknowledge the differences between the wild and cultivated
chromosomes as in the pepper COSII map.

Note:  In the haplotype table(s) C. frutescens is designated with B allele and C. annuum is designated as A allele. 

FA07 Table 1. C. frutescence BG2814-6 X C. annuum NuMex RNaky Bin Map.

FA07 Table 2. Consensus haplotype for each mapped bin.

FA07 Table 3. C. frutescens BG2814-6 X C. annuum NuMex RNaky map including all mapped markers. 

FA07 Table 4. Consensus haplotype for each mapped marker. 

FA07 Table 5. All polymorphic positions (SPPs) file.

Table 6. Table of conversion of four letter IDs to original contig namesFour letter codes were used for mapping to shorten IDs and allow for easy alignment on graphical map and genotype images.

FA07 Table 7. Cross reference of column numbers to RIL IDs in mapping files. 

FA07 Table 8. Summary table of the linkage groups. 

FA07 Table 9. Contigs with multiple haplotypes/markers where 2 markers were mapped. 

Definition of Column Names:
Chr = Pepper chromosome designaiton according to Wu et al.
LG# = Linkage group number based on pepper chromosome number.
Pos(cM) = Position in cM on linkage group (linkage groups oriented based on the Wu et al., 2009 pepper COSII map).
BinID = Four letter code for the contig selected to repersent a mapped bin followed by _C to indicate that the actual haplotype is based on the consensus haplotype of all markers within that genetic bin.
ContigName = Original contig designation created during EST assembly in Ashrafi et al. 
ContigID = Four letter code assigned to contigs.
Marker = Designation for consensus contig haplotypes used to generate the map. This designation consists of: ContigID_Haplotype#. 


Wu, F., Eannetta, N. T., Xu, Y., Durrett, R., Mazourek, M., Jahn, M. M., & Tanksley, S. D. (2009). A COSII genetic map of the
pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus
Capsicum. Theoretical and applied genetics, 118(7), 1279-1293.

Ashrafi, H., Hill, T., Stoffel, K., Kozik, A., Yao, J., Chin-Wo, S. R., & Van Deynze, A. (2012). De novo assembly of the pepper
transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC genomics, 13(1), 571.

Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, Truco M-J, et al. (2013). Characterization of Capsicum annuum Genetic
Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip. PLoS ONE 8(2):
e56200. doi:10.1371/journal.pone.0056200
