title: A wild origin of the loss-of-function lycopene beta cyclase (CYC-b) allele in cultivated, red-fleshed papaya (Carica papaya).
abstract: OBJECTIVE
  The red flesh of some papaya cultivars is caused by a recessive loss-of-function mutation in the coding region of the chromoplast-specific lycopene beta cyclase gene (CYC-b). We performed an evolutionary genetic analysis of the CYC-b locus in wild and cultivated papaya to uncover the origin of this loss-of-function allele in cultivated papaya.
  
  
  METHODS
  We analyzed the levels and patterns of genetic diversity at the CYC-b locus and six loci in a 100-kb region flanking CYC-b and compared these to genetic diversity levels at neutral autosomal loci. The evolutionary relationships of CYC-b haplotypes were assessed using haplotype network analysis of the CYC-b locus and the 100-kb CYC-b region.
  
  
  RESULTS
  Genetic diversity at the recessive CYC-b allele (y) was much lower relative to the dominant Y allele found in yellow-fleshed wild and cultivated papaya due to a strong selective sweep. Haplotype network analyses suggest the y allele most likely arose in the wild and was introduced into domesticated varieties after the first papaya domestication event. The shared haplotype structure between some wild, feral, and cultivated haplotypes around the y allele supports subsequent escape of this allele from red cultivars back into wild populations through feral intermediates.
  
  
  CONCLUSIONS
  Our study supports a protracted domestication process of papaya through the introgression of wild-derived traits and gene flow from cultivars to wild populations. Evidence of gene flow from cultivars to wild populations through feral intermediates has implications for the introduction of transgenic papaya into Central American countries.
authors.affiliation: Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA.
authors.forename: Meng
authors.initials: M
authors.lastname: Wu
authors.affiliation: Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104 USA.
authors.forename: Jamicia
authors.initials: J
authors.lastname: Lewis
authors.affiliation: Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA moorerc@miamiOH.edu.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Moore
mesh_terms: D000483:Alleles; D029441:Carica / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D002489:Central America; D019143:Evolution, Molecular; D051456:Gene Flow; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D019753:Intramolecular Lyases / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D009154:Mutation; D010641:Phenotype; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D018087:Plastids / Q000235:genetics
chemical_list: D010940:Plant Proteins; D019753:Intramolecular Lyases; C070925:lycopene cyclase-isomerase
keywords: Carica papaya; Caricaceae; domestication; fruit color; gene flow; selective sweep