Supporting information Table S1. Percentage of reads mapping to different RNA biotypes. Average and Standard Deviation (SD) for the dataset of 34 ejaculates. The proportion of these biotypes were assessed based on the proportion of mapped reads without prior filtering of read length. Biotype Mean SD Mitochondrial transfer RNA (Mt tRNA) 46.9% 11.3% Piwi-interacting (piRNA) 15.6% 4.9% small nuclear RNA (snRNA) 8.1% 3.3% Mitochondrial ribosomal RNA (Mt rRNA) 8.1% 2.5% transfer RNA (tRNA) 9.4% 3.1% microRNA (miRNA) 8.6% 3.4% ribosomal RNA (rRNA) 3.1% 1.4% small nucleolar RNA (snoRNA) 0.1% 0.0% Table S3. Number of human, mouse and swine piRNAs from the piRBase database retrieved, mapped, present in the boar sperm and associated to semen quality. Retrived Mapped piRNAs present piRNAs significantly Species piRNAs piRNAs in sperm associated with sperm traits Bos taurus 3,891,092 104,664 1,348 234 (testis) Homo sapiens 35,866 1,470 24 5 (testis) Mus musculus 30,165 132 10 1 (testis) Sus scrofa (testis, sperm, 741,157 174,234 5,189 1,073 zygote) Multiple -- 2,882 158 42 species Total 4,698,280 283,382 6,729 1,355 Table S5. Distance between the phenotype-associated piRNAs and Repetitive Element (RE) classes and number of piRNAs in the vicinity of each RE class. SINE = Short interspersed nuclear element; LINE = Long interspersed nuclear element; DNA/hAT = hAT DNA transposon; LTR = Long terminal repeats. Nr of significant Average distance Median distance RE type Percentage piRNAs (bp) (bp) SINE 447 33.2% 496.0 322 Simple 341 25.3% 448.8 238 repeat LINE 283 21.0% 383.3 237 DNA/hAT 98 7.3% 442.7 223.5 LTR 93 6.9% 391.7 233 Low 78 5.8% 416.5 260 complexity tRNA 4 0.3% 389.5 392 rRNA 1 0.1% 2.0 2.0 Satellite 1 0.1% 315.0 315.0 Unkown 2 0.1% 1084.0 1084.0 Table S6. Correlation between total piRNA abundance and the 13 phenotypes. Acronym phenotypes can be found in Table S1. Phenotype Overall abundance correlation P TABN -0.32 0.07 HABN -0.31 0.07 PDROP -0.27 0.12 ACRO -0.12 0.48 DDROP -0.11 0.54 ORT -0.01 0.96 NABN 0.00 0.98 MT 0.11 0.53 VIAB 0.12 0.48 VCL 0.23 0.19 CONC 0.24 0.17 VSL 0.25 0.15 VAP 0.30 0.09 Figure S1. Relative nucleotide composition of the 6,729 piRNAs with CPM > 1 in more than 75% of the samples from position 1 to position 10. Figure S2. Number of significantly associated piRNAs for each of the 13 phenotypes. Figure S3. Violin plots of piRNA distribution within each Repetitive Element class. SINE = Short interspersed nuclear element; LINE = Long interspersed nuclear element; DNA/hAT = hAT DNA transposon; LTR = Long Terminal Repeat.