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The yield of pepper plants ( Capsicum  spp.) is their most important trait and is affected by the flower number and flowering time.  Capsicum annuum  produces a single flower per node and has an early flowering habit. By contrast,  Capsicum chinense  yields multiple flowers per node and has a late flowering character. However, the genetic mechanism underlying the control of these floral traits remains largely unknown. In this study, 150 F 2  populations from an interspecific cross between the inbred lines 740 ( C .  chinense ) and CA1 ( C .  annuum ) and their parents were used to construct a molecular genetic linkage map using the specific length amplified fragment sequencing (SLAF-seq) technique. This linkage map, spanning 1,586.78 cM in length, contained 9,038 markers on 12 chromosomes, with a mean marker distance of 0.18 cM. Phenotypic data on the flowering time and flower number per node were collected over multiple years, and QTL analysis identified 6 QTLs for the flowering time and flower number per node by composite interval mapping (CIM) and genome-wide composite interval mapping (GCIM) methods at least in two environments. The candidate genes within the major QTL were predicted. In the major flowering time QTL, the candidate gene  Capana0 2 g000700 , which encodes the homeotic protein APETALA2, was identified. Quantitative reverse-transcription PCR (qRT-PCR) analysis indicated that its expression level in 740 was higher than that in CA1. Gene expression analysis indicated that the expression of  Capana02g000700  was significantly upregulated in flowers, and many floral development-related genes were found to be coexpressed with  Capana02g000700 , supporting the function of this gene in association with flowering time in  C .  chinense  and  C .  annuum  species.

Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits