Identification and transcriptome analysis of a major locus for eye depth in tetraploid potato Jinshu 16

Tuber eye depth is a key agronomic trait in potato, influencing both processing efficiency and market appearance. To investigate the genetic basis of deep-eye phenotype in the elite Chinese tetraploid cultivar Jinshu 16, we constructed an F1 segregating population by crossing Jinshu 16 (deep eye) with Atlantic (shallow eye). Phenotypic evaluation across two seasons revealed a 1:1 segregation ratio for eye depth (Eyd), indicative of control by a single dominant locus. By integrating whole-genome resequencing and bulk segregant analysis (BSA-seq) of extreme phenotypes, we fine-mapped the major locus to a 49.0–50.7 Mb interval on chromosome 10, co-localizing with the previously reported Eyd locus. Cytological examination showed increased cell density in the eye region of Jinshu 16 tubers. Transcriptome analysis identified specific upregulation of several lipid transfer protein and peroxidase genes within the mapped region in Jinshu 16 eye tissues, implicating lipid metabolism and cell wall modification in eye depth determination. Developed Insertion‑Deletion (InDel) markers from this region were significantly associated with the phenotype in the population. Our study defines the genetic locus responsible for the deep-eye trait in Jinshu 16, providing a foundation for gene functional studies and molecular marker-assisted breeding in this cultivar.