BSA-seq and transcriptome analyses reveal candidate gene associated with petiole color in papaya (<i>Carica papaya</i> L.)

Papaya (<i>Carica papaya</i> L.) is an important tropical species popular for highly nutritious fruit as well as medicinal value. In addition, non-commercial cultivation of papaya trees has resulted in dual-purpose cultivars grown for both fruit and ornamental value in residential areas. Petiole color is a key ornamental trait in papaya that varies amongst cultivars depending on anthocyanin accumulation resulting in purple or green pigmentation. Although inherited as a simple trait, genetic characterization and genomic loci responsible for the purple petiole color in papaya is unknown. In this study, F₁ and F₂ populations generated from two breeding lines PR-2043 (green petiole) and T5-2562 (purple petiole) were used to evaluate the inheritance patterns of petiole color as well as determine genetic loci and genes involved in petiole pigmentation in papaya through bulk segregant analysis (BSA) and transcriptome sequencing. The segregation of purple petiole color followed a single dominant gene inheritance model (3:1). BSA-seq analysis indicated key genes influencing petiole color are mainly located in chromosome 1 (0.01 to 5.96 Mb) of the papaya genome. Four major genes, including <i>CHS</i>, <i>MYB20</i>, <i>MYB315</i>-like, and <i>MYB75</i>-like within this region exhibited significant differential expression in a comparison between purple and green petiole papaya plants. A relatively high abundance of <i>CHS</i> transcripts was observed in purple petioles and may signify a major involvement in regulating anthocyanins accumulation in papaya petioles. The findings of this study facilitate the future efforts of breeding papaya cultivars with higher economical value in residential landscapes.