Figure 4

Relationship of Pun1 alleles in Capsicum. (a) Pun1 alleles from C. annuum, C. chinense and C. frutescens differ by single-nucleotide polymorphisms (SNPs) scattered throughout the gene. The Pun1 allele recovered in C. chacoense PI260433-np contains an intron insertion and several SNPs in the intron that were used for genotyping. As observed in C. chacoense and C. chinense F₂ progeny, pungency requires both Pun1 and Pun2 alleles. A large five′ deletion produced pun1¹, a frameshift mutation in the second exon is found in pun1² and an indel truncates the second exon of pun1³. The pun1¹ and pun1³ mutations are not transcribed, while transcription but not translation has been observed for pun1². (b) Phylogeny of Pun1 alleles of selected Solanaceae (GenBank accession numbers: FJ871984, FJ871985, AY819026, AY819027, AY819029, FJ687524-FJ687531, FJ755160–FJ755176). Bayesian phylogenetic analysis of 21 Pun1 alleles from a diverse sampling of species and cultivars within Capsicum as well as from domesticated and representative genera in the Solanaceae shows that the pun1 series of null alleles are scattered and not clustered together into a single clade suggesting multiple origins of the loss of pungency alleles followed by lineage sorting. Pun1 from C. chacoense PI260433-np is most closely related to the sister line C. chacoense PI260433-P suggesting possible gene flow between the two populations for this allele.