Identification of candidate genes associated with blade length in Pyropia haitanensis based on BSA-seq and RNA-seq analysis

Blade length, which is a quantitative trait controlled by multiple genes, is a key trait determining the yield in Pyropia haitanensis. However, there are few studies on the identification of candidate genes associated with it. In this study, the double haploid (DH) strains from the hybrid offspring of P. haitanensis were used to construct two DNA pools from extremely long-length and short-length strains, respectively. Using bulk segregant analysis sequencing (BSA-seq), three candidate regions associated with the blade length were identified on the genome, all of which were located on chromosome 1. These regions contain a total of 625 genes. One extremely long-length strain and one extremely short-length strain were selected respectively, and their 35-day blades were used for RNA sequencing (RNA-seq). It was found that the genes related to carbon fixation in photosynthetic organisms, glycolysis/gluconeogenesis and carbon metabolism were up-regulated in long blades, and 145 genes were differentially expressed in the candidate regions. Subsequently, eight candidate genes were screened using strict criteria (delta SNP-index ≥ 0.9), which encode WD40-repeat containing protein, major facilitator superfamily, LPXTG-anchored surface-anchored adhesin, RmlC-like cupin superfamily, EMP24_GP25L and three unknown functional proteins, respectively. Further SNP molecular marker verification showed that the success rate of selection of these 8 genes for blade length was greater than 90