Development and exploitation of a Pepper (Capsicum spp.) ~6.55 Million Feature Affymetrix GeneChip for Massively Parallel Genotyping


Pepper chip design is under the direction of Drs. Allen Van Deynze, Jim Prince and Alexander Kozik based on their proposal "A Whole Genome Approach to Characterize Genes in Pepper". It is supported by seven companies and the UC Discovery grant. The ESTs that were used for chip design were kindly provided by Dr. Doil Choi from Seoul National University (S. Korea).

This design is based on the public pepper ESTs and genetic information from GeneBank and the EST information of 21 libraries from Seoul National University (S. Korea). The public and private pepper ESTs account for 6.08% and 93.92% of the total ESTs, respectively. The detailed information about the chip and experiments can be found at intranet section of the web site. Briefly, the pepper chip is a 5 mm format Affymetrix GeneChip, holding probes to its maximum capacity of 6,540,321 cells, including:

  1. 6,473,556 features of genomic probes in a 2 base pair overlap tiling pattern
  2. 16,900 technical replicates probes (10 genes) in a 13X13 control block orientation
  3. 33,886 Affymetrix designed antigenomic probes
  4. 2,482 Affymetrix bacterial probes
  5. 13,497 Quality control probes including 3,200 gridding probes, 9,912 border probes and 385 probes used for the text on the array.

Latest Updates

The last release of the Pepper genetic map of Capsicum frutescens accession BG2814-6 x C. annuum cv. NuMexRNaky RIL population (119 RILs) is available in Data. Linkage groups were assigned to the Wu et al. (2009) linkage groups, and 65 markers were added to the map.

The Second Release of the Pepper genetic map of Capsicum frutescens accession BG2814-6 x C. annuum cv. NuMexRNaky RIL population (119 RILs) was presented at the Solanaceae workshop at Plant and Animal Genome in San Diego on Tuesday Jan 18th, 2011.

The Pepper Chip is publicly available from Affymetrix with part #520549.

The results of the Diversity Panel Analysis and preliminary pepper genetic map of a RIL population of 123 individuals from a cross between Capsicum. annuum cv. NuMexRNaky x C. frutescence accession number 2814-6 now available in Data.

The Manual on how to set up the database and to perform SPP scan analysis is added to the website. Scripts of SPP scan analysis can be downloaded from the Manual section.

By downloading the pepper SPP scripts or mapping data you are accepting them on an "as is basis" under the following condition: UC Davis makes no warranties for the scripts accuracy in calling SPPs or map data.


Contact us:

All questions about the project:
Allen E. Van Deynze

Questions about the chip design procedures:
Alexander Kozik

Question about laboratory procedures:
Theresa Hill

Questions about the analysis procedures and this website:
Hamid Ashrafi

This site was designed by Hamid Ashrafi.

Former Group Member(s):

Yao Jiqiang (Post doc scholar)

Sebastian Chin-Wo Reyes (Junior Specialist)

Marcelo Solano (Visiting Intern)


Funding Agencies

De Ruiter Seeds
Harris Moran
Rijk Zwaan      Enza Zaden
University of Wisconsin
Fresno State University
Cornell University
UCD Genome Center
UC Discovery Grant    Seed Biotechnology Center