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Cucumber core collection fruit morphological traits raw data (2019-2022)

Lin, Ying-Chen1; Weng, Yiqun2; Fei, Zhangjun3; Grumet, Rebecca1

Published Apr 15, 2025 on Dryad. https://doi.org/10.5061/dryad.tb2rbp0b9

Data files

Apr 15, 2025 version files 710.46 KB

Abstract

Commercial value of cucumber is primarily driven by fruit quality.  However, breeding goals frequently focus on production constraints caused by biotic and abiotic stresses.  As sources of resistances are often present in unadapted germplasm, we sought to provide morphological and genetic information characterizing the diversity of fruit quality traits present in the CucCAP cucumber core collection. These 388 accessions representing >96% of the genetic diversity for cucumber present in the U.S. National Plant Germplasm System harbor important sources of resistances and extensive morphological diversity.  Data were collected for skin color, length/diameter ratio (L/D), tapering, curvature, and spine density for young fruits [5-7 days post-pollination (dpp)], and length, diameter, L/D, skin color, netting, seed cavity size, flesh thickness, hollowness, and flesh color for mature fruits (30-40 dpp).  The multi-year photographic data have been made available via the Cucurbit Genomics Database (GuGenDB, http://cucurbitgenomics.org/v2/).  Significant associations of SNPs with each trait were identified from genome-wide association studies (GWAS).  In several cases, QTL for highly correlated traits were closely clustered.  Principal component analysis, driven primarily by the highly correlated traits of fruit length, young and mature L/D ratios, and curvature showed a clear divergence of East Asian accessions.  The longest fruits possessed length-associated alleles for significant SNPs distributed across five of the seven chromosomes, indicating broad genomic effects of selection.  Many of the SNPs identified for the morphological traits were in close vicinity to previously identified fruit trait QTL and candidate genes while several novel genes potentially important for these traits were also identified.