Mining Candidate Genes for Seed Length and Width in Seed‐Used Pumpkin ( <scp> <i>Cucurbita pepo</i> </scp> L.) Based on BSA‐seq and Transcriptome Analysis

ABSTRACT Seed‐used pumpkin ( Cucurbita pepo L.) is an economically important crop in arid and semi‐arid regions worldwide. Seed‐related traits, including seed length, seed width and hundred‐seed weight, are core determinants of yield and quality. However, the genetic basis underlying these traits remains incompletely understood, and the quantitative trait loci (QTLs) controlling their variation, along with key candidate genes, still require further in‐depth exploration. In this study, we constructed six‐generation populations for two separate traits using lines ZHL‐2 and ZHL‐6 (for length) as well as ZHL‐2 and ZHL‐4 (for width) as parents. Extreme trait pools were constructed from the F 2 segregating population for Bulked Segregant Analysis Sequencing (BSA‐seq) to identify candidate genomic intervals associated with the two traits. Based on the variant information obtained from BSA‐seq, and after screening for parental polymorphism and validation in individual F 2 plants, we ultimately developed three Indel markers closely linked to the length trait and three polymorphic Indel markers closely linked to the width trait. Subsequently, genetic linkage maps for both traits were constructed. Furthermore, by integrating transcriptome data, we located three candidate genes potentially related to seed length and eleven candidate genes potentially related to seed width. These results not only provide some new insights into the molecular genetic mechanisms underlying seed size traits in seed‐used pumpkin ( C. pepo L.) but also offer polymorphic markers and linkage maps of practical value. This work may provide a relevant theoretical basis and technical support for breeding varieties with high seed yield.