The High-Density Genetic Map for Pepper Genome Assembly By Whole Genome Shotgun Sequencing

The de novo genome assembly of plants, especially highly repetitive and large genome, has been challenging to complete. To make pseudomolecule of pepper genome, high density genetic map was developed for the reference pepper genome using whole genome sequencing (WGS) of 120 recombinant inbred lines (RILs), derived from a cross between the C. annuum cv. Perennial and C. annuum cv. Dempsey. Among 1,798,058 polymorphic single nucleotide polymorphism (SNP) between Perennial and Dempsey, we picked out 771,587 SNP presented in the contigs of more than 10 kb, and made a SNP genotyping matrix of 120 RILs. We also defined chromosome bin map, and selected the 22,867 representing markers for bins. These markers were used for the construction of genetic map consisting of twelve linkage groups, and the formation of pepper pseudomolecule with anchoring scaffolds. The genetic order of SNP marker was validated via the comparison with pepper conserved ortholog set (COS) marker. To improve the quality of pepper genome, re-construction of high resolution genetic map is currently underway.