Work

Development and application of a 40K liquid chip enriched with structural variation markers for watermelon breeding

Year: 2026

Type: article

Abstract: Watermelon (Citrullus lanatus) has undergone severe loss of genetic diversity due to domestication, necessitating the exploitation of wild relatives for trait improvement. While structural variations (SVs) represent a major source of genetic diversity, high-throughput SV genotyping remains technically challenging, and existing single-nucleotide polymorphism (SNP) arrays fail to capture presence/absence variations (PAVs) that differentiate wild from cultivated germplasm. Here, we developed the ‘Watermelon 40K SNP-SV Chip,’ the first liquid-phase genotyping chip enriched with SV markers, leveraging a telomere-to-telomere super-pangenome of seven Citrullus species. The chip comprises 7087 SV markers (enriched for PAVs) and 11 383 SNP/InDel markers. Technical validation in 12 accessions and large-scale genotyping of 228 diverse accessions demonstrated high reproducibility (≥98.5% concordance) and robust call rates (>97%), though performance declined in deeply divergent wild species. Genome-wide association studies revealed SV-specific signals for flesh color and rind pattern that co-localized with known quantitative trait loci (QTL), including a strong candidate regulatory PAV upstream of LCYB. The predominance of rare variants (74.3% SVs with minor allele frequency < 0.05) limits statistical power for detecting QTL underlying polygenic domestication traits such as yield but confers exceptional utility for tracking wild introgressions in early-generation breeding populations. The 40K SNP-SV chip bridges the gap between fundamental SV research and practical breeding, enabling SV-assisted genomic selection for watermelon improvement.

Source: Horticulture Research

DOI: 10.1093/hr/uhag221