Additional file 2 of Deficiency in homozygous haplotypes reveals recessive lethal variants affecting fertility and viability in the Friesian horse

Additional file 2: Table S1. The filtered 40,809 SNPs that were included in the analysis. The table shows .bim file including the chromosome, SNP id, position, allele1 and allele 2. Table S2. Quality of gDNA for the six samples for PCR validation was checked on Denovix and Qubit. Quality of the gDNA of all six animal samples (F1 – F6) was sufficient. Table S3. Primer design for PCR validation of two candidate variants. Primer design for the 14-bp frameshift deletion on chromosome 4 and the 261-kb deletion on chromosome 23. Table S4. Haplotypes with homozygous deficiency including the haplotype sequences. The 10 haplotypes with homozygous deficiency based on EquCab_Friesian_WUR reference genome with Bonferroni adjusted P < 0.05. In total, 70K SNP Chip data of 8,263 horses were included in the analysis. The table shows the genomic location and the haplotype sequences. The SNP IDs and their location of each SNP in the haplotype sequence can be found in Table S1. Table S5. The number of matings, insemination success, still birth rate and juvenile mortality in risk1, risk2 and non-risk matings. The relative differences in % for insemination success, still births and juvenile mortality of risk matings compared to non-risk matings are represented. To illustrate, for FH1, non-risk matings had an average insemination success of 76.4%. Risk1 matings had 38.2% lower insemination success compared to non-risk matings, resulting in average insemination success of 47.2% (76.4% – (76.4%*0.382)). Risk1 matings were defined when both the sire and dam were carrier. Risk2 matings were defined when the sire was carrier and the maternal grandsire was carrier. Non-risk matings were defined when the sire was non-carrier and the dam was carrier or maternal grandsire was carrier. Table S6. The number of matings, insemination success, still birth rate and juvenile mortality in matings of carrier sires and non-carrier sires. The relative differences in % for insemination success, still births and juvenile mortality of carrier sires compared to non-carrier sires are represented. To illustrate, for FH1, matings of non-carrier sires had an average insemination success of 61.0%. Matings of carrier sires had 1.0% lower insemination success compared to non-risk matings, resulting in average insemination success of 60.4% (61.0% – (61.0%*0.01)). All matings of carrier sires and non-carrier sires were included, independent of the carrier status of the dam or maternal grandsire. Table S7. High impact variants per candidate lethal haplotype. All high impact variants found per candidate lethal haplotype. Table S8. nBLAST results of ncRNAs in the 261-kb deletion of FH10. Discontiguous megablast was performed to look for similar RNA sequences in Homo sapiens. All similar RNA sequences with an E value < 10-35 are reported. Table S9. FPKM (fragments per kilobase per million fragments mapped) and TPM (transcripts per kilobase million) values for immatures testes and mature testes of six Mongolian horses. Table S10. Semen quality parameters between non-carriers and carriers of FH10. Median and interquartile range (IQR) are calculated for both non-carriers and carriers of FH10. P-value using the Wilcoxon rank sum test was calculated to test difference in median for semen quality parameters between non-carriers and carriers of the 261-kb deletion. P_adj is the Bonferroni-adjusted P-value. Table S11. PCR results of two tested candidate variants in six horses. F1 – F4 animals are homozygous wildtype for the 14-bp frameshift deletion and heterozygous for the 261-kb deletion. F5 and F6 animals are heterozygous for the 14-bp frameshift deletion and homozygous wildtype for the 261-kb deletion.