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Table 1 Descriptive statistics, genomic heritability (h2) and number of significant SNPs in the GWAS for sperm quality parameters (N = 300)

From: A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine

Trait Acronym Mean (SD) h2 (SE) Number of SNPs in autosomal chromosomes Number of SNPs in unplaced scaffolds
Concentration (sperm/mL) CON 141.3 (65.5) 0.13 (0.11) 0 0
Viability 5 min VIAB_5 90.1 (6.3) 1 × 10–6 (0.11) 0 0
Viability 90 min VIAB_90 77.4 (17.3) 0.14 (0.13) 0 0
Osmotic resistance test ORT 79.8 (12.5) 0.13 (0.12) 0 0
Head abnormalities HABN 2.1 (5.9) 0.16 (0.11) 41 0
Neck abnormalities NABN 3.0 (4.9) 1 × 10–6 (0.13) 18 0
Tail abnormalities TABN 2.7 (3.4) 0.09 (0.12) 0 0
Proximal droplets PDROP 3.5 (5.1) 0.12 (0.15) 1 0
Distal droplets DDROP 4.5 (4.5) 0.06 (0.11) 0 0
Motility 5 min MT_5 75.4 (18.1) 0.21 (0.15) 3 217
Motility 90 min MT_90 64.1 (22.0) 0.39 (0.14) 2 252
Average path velocity 5 min (µm/seg) VAP_5 34.0 (10.2) 0.17 (0.11) 0 0
Average path velocity 90 min (µm/seg) VAP_90 30.8 (9.5) 0.35 (0.13) 0 0
Curvilinear velocity 5 min (µm/seg) VCL_5 46.2 (12.5) 0.11 (0.10) 0 0
Curvilinear velocity 90 min (µm/seg) VCL_90 39.7 (10.2) 0.35 (0.13) 0 0
Straight line velocity 5 min (µm/seg) VSL_5 27.0 (8.3) 0.23 (0.13) 0 38
Straight line Velocity 90 min (µm/seg) VSL_90 25.9 (8.3) 0.34 (0.13) 0 0
Abnormal acrosomes 5 min ACRO_5 7.0 (5.6) 0.08 (0.11) 4 0
Abnormal acrosomes 90 min ACRO_90 16.4 (12.6) 0.06 (0.10) 0 0
Ratio motility R_MT 0.9 (0.2) 1 × 10–6 (0.11) 0 0
Ratio average path velocity R_VAP 0.9 (0.3) 1 × 10–6 (0.08) 0 0
Ratio Curvilinear velocity R_VCL 0.9 (0.3) 1 × 10–6 (0.09) 0 0
Ratio straight line velocity R_VSL 1.0 (0.3) 0.06 (0.10) 0 0
Ratio viability R_VIAB 0.9 (0.3) 0.08 (0.11) 0 0
Ratio acrosomes R_ACRO 3.4 (3.5) 0.08 (0.11) 1 0
  1. All traits except stated are presented as a percentage
  2. Number of SNPs = GWAS number of single nucleotide polymorphisms significantly associated (FDR) with the trait
  3. The values shown are raw excepting the ratios which were previously corrected and stabilized
  4. SD standard deviation, SE standard error