Cucumber core collection fruit morphological traits raw data (2019-2022)
Data files
Apr 15, 2025 version files 710.46 KB
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carpel_num_raw.csv
18.19 KB
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cavity_raw.csv
38.33 KB
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curvature_raw.csv
29.78 KB
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flesh_thickness_raw.csv
38.29 KB
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hollowness_raw.csv
29.65 KB
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mature_diameter_raw.csv
38.46 KB
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mature_flesh_color_raw.xlsx
53.92 KB
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mature_LD_ratio_raw.csv
38.15 KB
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mature_length_raw.csv
40.90 KB
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mature_skin_color_raw.xlsx
157.30 KB
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netting_raw.csv
26.57 KB
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README.md
3.61 KB
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spine_density_raw.csv
23.98 KB
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young_diameter_raw.csv
23.05 KB
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young_ld_raw.csv
23.26 KB
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young_length_raw.csv
23.65 KB
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young_skin_color_raw.xlsx
80.39 KB
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young_tapering_raw.csv
22.96 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.
https://doi.org/10.5061/dryad.tb2rbp0b9
The Data
The data was collected from the USDA cucumber core collection from 2019-2022. Each file contain the measurements of the morphological trait as shown in the file name. Six representative fruits from each accession were selected for photograph when harvesting. The description and illustration of the measurement method can be found in the Material and Method in the publication.
Fruit shape traits
Fruit length, diameter, carpel number, seed cavity, flesh thickness, hollowness, spine density, netting, tapering
These traits had one measurement per fruit. The letters are the abbreviation for the trait, the numbers followed indicate the fruit order. The two digits number after the decimal indicate the year of data collected. For example:
mature_length_raw.csv
- len.1.19: fruit length measurement of the 1st fruit in 2019
- len.2.19: fruit length measurement of the 2nd fruit in 2019
mature_diameter_raw.csv
- d3.20: fruit diameter measurement of the 3rd fruit in 2020
- d4.20: fruit diameter measurement of the 4th fruit in 2020
cavity_raw.csv
- s5.21: seed cavity size measurement of the 5th fruit in 2021
- s6.21: seed cavity size measurement of the 6th fruit in 2021
Curvature
There may be 1-2 curves in each fruit. The first number indicates the fruit order, the number between the decimals indicates the first or the second curve, the two digits number after the decimals indicates the year of data collected. For example:
- c1.1.21: the first curvature measurement of the 1st fruit in 2021
- c1.2.21: the second second curvature measurement of 1st fruit in 2021
- c2.1.21: the first curvature measurement of the 2nd fruit in 2021
- c2.2.21: the second second curvature measurement of 2nd fruit in 2021
LD ratio for young and mature fruits
LD (length/diameter) ratios are calculated based on the length and diameter of each fruit measured. For example:
young_ld_raw.csv
- ld.1.19: LD ratio of the 1st fruit in 2019
- ld.2.19: LD ratio of the 2nd fruit in 2019
Color Traits
The color traits were recorded in RGB format. For each measurement, the values for R, G, and B values were recorded.
Fruit skin color (young and mature)
For mature fruits, three measurements were taken for each fruit (top, middle and bottom sections), while two measurements (the first and third quarters sections) for young fruits. For example:
- R1.1.19: the R value of the first measurement of the 1st fruit in 2019
- G1.1.19: the G value of the first measurement of the 1st fruit in 2019
- B1.1.19: the B value of the first measurement of the 1st fruit in 2019
- R1.2.19: the R value of the second measurement of the 1st fruit in 2019
- G1.2.19: the G value of the second measurement of the 1st fruit in 2019
- B1.2.19: the B value of the second measurement of the 1st fruit in 2019
- R1.3.19: the R value of the third measurement of the 1st fruit in 2019
- G1.3.19: the G value of the third measurement of the 1st fruit in 2019
- B1.3.19: the B value of the third measurement of the 1st fruit in 2019
Mature fruit flesh color
A single measurement for the mid-section of each fruit.
- R1.19: the R value of the 1st fruit in 2019
- G1.19: the G value of the 1st fruit in 2019
- B1.19: the B value of the 1st fruit in 2019
- R2.19: the R value of the 2nd fruit in 2019
- G2.19: the G value of the 2nd fruit in 2019
- B2.19: the B value of the 2nd fruit in 2019