Fine mapping and identification of regulatory genes for fruit neck length in bottle gourd (Lagenaria siceraria)

Fruit neck length (FNL) is one of the important commercial characteristics of bottle gourd (Lagenaria siceraria), which is usually desirable by consumers based on their preferences. At present, there has not been extensive research on the genetics of bottle gourd FNL. In this study, an F₂ segregating population was constructed using the long fruit neck material H16 and the short fruit neck material H06. Bulked segregant analysis and kompetitive allele-specific PCR techniques were used to identify candidate regions regulating FNL in bottle gourd. InDel markers were used to narrow the final candidate region interval to 0.16 Mb, which contained 8 genes. A combined analysis using a gene annotation library, real-time fluorescence quantitative expression, and sequence analysis of candidate genes in the region indicated that the HG_GLEAN_10011965 gene might be involved in the regulation of bottle gourd FNL and was named LsFNL1.1. Based on the most narrowed candidate gene interval, an InDel marker was developed for molecular marker assisted breeding of bottle gourd FNL. The phenotypic-genotype association rate of this InDel marker was 83%. This study provides a theoretical basis for further exploring the molecular mechanisms underlying bottle gourd fruit traits and can accelerate the breeding of varieties with desirable characteristics.