Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.
Our ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper.
Seed Biotechnology Center, University of California, Davis, California 95616 Department of Plant Sciences, University of California, Davis, California 95616.
Theresa
T
Hill
Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695.
Hamid
H
Ashrafi
The Genome Center, University of California, Davis, California 95616.
Sebastian Reyes
SR
Chin-Wo
Seed Biotechnology Center, University of California, Davis, California 95616.
Kevin
K
Stoffel
The Genome Center, University of California, Davis, California 95616.
Maria-Jose
MJ
Truco
The Genome Center, University of California, Davis, California 95616.
Alexander
A
Kozik
Department of Plant Sciences, University of California, Davis, California 95616 The Genome Center, University of California, Davis, California 95616.
Richard
R
Michelmore
Seed Biotechnology Center, University of California, Davis, California 95616 Department of Plant Sciences, University of California, Davis, California 95616 avandeynze@ucdavis.edu.
Allen
A
Van Deynze
D002212:Capsicum / Q000145:classification / Q000235:genetics*; D056905:Chromosome Breakpoints; D008040:Genetic Linkage; D049810:Genetic Speciation; D018745:Genome, Plant; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D032322:Solanum / Q000145:classification / Q000235:genetics; D026801:Synteny; D059467:Transcriptome
GeneChip; Pseudolinkage; Solanum lycopersicum Solanaceae genomics; Solanum tuberosum