Characterization of <em>Capsicum annuum</em> Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

<div><p>The widely cultivated pepper, <em>Capsicum spp</em>., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of <em>Capsicum</em> diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing <em>Capsicum</em> genetic diversity is limited. The development and application of high-throughput genome-wide markers in <em>Capsicum</em> will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in <em>Capsicum</em>. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse <em>C. annuum</em> lines, used in breeding and research programs, and a representative from three additional cultivated species (<em>C. frutescens, C. chinense</em> and <em>C. pubescens</em>) detected 33,401 SPP markers within 13,323 unigenes. Among the <em>C. annuum</em> lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these <em>C. annuum</em> lines. In addition, an 8.7 cM region without polymorphism was detected around <em>Pun1</em> in non-pungent <em>C. annuum</em>. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among <em>Capsicum annuum</em>.</p>