NM06 genetic map: Pepper genetic map of C. annuum Criollo de Morelos 334 (CM334) X C. annuum Early Jalapeno F6:F7 RIL population
(63 RILs) Second Release (Nov 2014)

The current version of the Capsicum annuum 'Criollo de Morelos 334' (CM334) X C. annuum 'Early Jalapeno' F6:F7 RIL population
map (v03)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. This map was generated with RECORD_Win.  The linkage group
assignment was based on common markers between this population and the FA07 genetic map.

In the haplotype table(s) C. annuum 'Early Jalapeno' is designated with A allele and C. annuum 'CM334' is designated as B allele.

NM06 Table 1. Capsicum annuum Criollo de Morelos 334 (CM334) X C. annuum cv Early Jalapeno bin map.

NM06 Table 2. Consensus haplotype for each mapped bin. 

NM06 Table 3. Capsicum annuum Criollo de Morelos 334 (CM334) X C. annuum cv Early Jalapeno map including all mapped markers.

NM06 Table 4. Consensus haplotype for each mapped marker.

NM06 Table 5. All polymorphic positions (SPPs) file.

Table 6. NM06 Table of conversion of four letter IDs to original contig names.Four letter codes were used for mapping to shorten
IDs and allow for easy alignment on graphical map and genotype images.

NM06 Table 7. Cross reference of column numbers to RIL IDs in mapping files.

NM06 Table 8. Summary table of Bins and Markers by linkage group.

NM06 Table 9. Contigs with multiple haplotypes/markers where 2 markers were mapped.

Definitions 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 = contigID for contig selected to repersent a mapped bin in map iteration 1.
ContigName = Original contig designation created during EST assembly in Ashrafi et al. 2012 
ContigID = Four letter code assigned to contigs.
Marker = Designation for consensus contig haplotypes used to generate the map. This designation consists of: ContigID_Haplotype#. If there is no haplotype# there was a single haplotype mapped for that contig.
#Markers = The number of contigs found within a given bin.



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
