Abstract
The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum 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 Capsicum. 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 C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum 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 C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. 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 Capsicum annuum.
Highlights
Peppers, Capsicum spp., are grown worldwide for vegetable, spice, ornamental, medicinal and lachrymator uses and are a significant source of vitamins A and C [1]
Baccatum) are thought to have been domesticated through at least five independent events [6]. These domesticates are believed to be derived from three distinct genetic lineages, with C. pubescens and C. baccatum each representing independent lineages while the domesticated taxa C. annuum, C. frutescens and C. chinense are considered members of a species complex that were each independently derived from wild progenitors that may or may not be independent species [3,7]
A high correlation of allele calls was observed, with an exact match between the Single nucleotide polymorphisms (SNPs) and single position polymorphism (SPP) assays for 95% of all alleles called and 99.9% of all unambiguous calls made by both assays (Table S2)
Summary
Capsicum spp., are grown worldwide for vegetable, spice, ornamental, medicinal and lachrymator uses and are a significant source of vitamins A and C [1]. Baccatum) are thought to have been domesticated through at least five independent events [6] These domesticates are believed to be derived from three distinct genetic lineages, with C. pubescens and C. baccatum each representing independent lineages while the domesticated taxa C. annuum, C. frutescens and C. chinense are considered members of a species complex that were each independently derived from wild progenitors that may or may not be independent species [3,7]. This is supported by the ability to make interspecific hybrids between these three Capsicum species. C. annuum has subsequently become one of the most important spice commodities as well as an important vegetable crop globally [1,2]
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