Supplementary Table 1. Primers and PCR conditions used for the amplification of the goat SCD1 cdna (PCR1 to PCR6) and three SCD1 polymorphic regions (PCR7 to PCR9) PCR Primers Sequence Position 1 Thermal profile PCR composition PCR1 PCR2 SCD-Fw1 SCD-Rv1 SCD-Fw2 SCD-Rv2 5 -AAC TCC GCT CCG CAG TCT CAG-3 5 -GAG TGT GGG CAG GAT GAA GCA C-3 5 -CTG ATC CCC ACA ATT CCC GAC-3 5 -GCT CTA GAG AGA AAG GGA GCA TGC TGG-3 141 161 871 892 699 719 1931 1957 94 C-1 min, 65 C-1 min, 72 C-2 min, for 35 94 C-1 min, 57 C-1 min, 72 C-2 min, for 35 1.5 mm MgCl 2 100 μm dntp 0.5 μm primer 2 μl cdna PCR3 SCD-Fw3 SCD-Rv3 5 -CCC AAG CTT TTG CTA GAT G-3 5 -ACT CAG TAA CCT TCT GAA TCC CC-3 1750 1768 2591 2613 94 C-1 min, 56 C-1 min, 72 C-2 min, for 35 0.05 U/μL Taq DNA pol 2 PCR4 SCD-Fw4 SCD-Rv4 5 -ATG GAG AAG TTG AGG GGC AG-3 5 -GCA TCT CAC ATC CTA AGC CTC A-3 2511 2530 3454 3475 94 C-1 min, 60 C-1 min, 72 C-2 min, for 35 PCR5 SCD-Fw5 SCD-Rv5 5 -CCC TAC CAC ACT GAT GAC TCC A-3 5 -TCT GGG TCA TTA ACG CAT CAT T-3 3076 3097 4097 4118 94 C-1 min, 61 C-1 min, 72 C-2 min, for 35 PCR6 SCD-Fw6 5 -GGT CAT CAG ATG CAT GCT TTA CA-3 3896 3918 94 C-1 min, 64 C-1 min, 72 C-2 min, for 35 PCR7 PCR8 PCR9 SCD-Rv6 SNP1-Fw SNP1-Rv SNP2-Fw SNP2-Rv SNP3-Fw SNP3-Rv 5 -GGA AAA ATC CCA CCC AAT CAA-3 5 -TTC ATC CTG CCC ACA CTC G-3 5 -CGG GGG TTG ATG GTC TTG T-5 5 -TCA CTT GGC CTC CAG AGT CT-3 5 -CAG TAA GCA GGG GGC ATC C-3 5 -GTG ACC CTG GGC AAG TCA TTT A-5 5 -GTG GTT CAT GGT GGA CAC ACT T 5 1 Primer locations with regard to sequence AF325499. 2 Taq DNA polymerase from Ecogen SRL (Barcelona, Spain). 4992 5012 875 893 1026 1044 3037 3056 3259 3277 4650 4671 4826 4847 94 C-1 min, 62 C-1 min, 72 C-2 min, for 35 94 C-1 min, 62 C-1 min, 72 C-2 min, for 35 94 C-1 min, 66 C-1 min, 72 C-2 min, for 35 1.5 mm MgCl 2 100 μm dntp 0.5 μm primer 4 ng/μl genomic DNA 0.05 U/μL Taq DNA pol 2
Supplementary Table 2. Phenotypic means and standard errors (SE) of dairy traits (309 individuals, 1042 records) and milk fatty acid composition traits (n = 176 individuals, 525 records) in Murciano-Granadina goats TRAITS MEAN ± SE Dairy traits Milk, kg/day 1.76 ± 0.02 Protein, % 3.69 ± 0.01 Fat, % 5.84 ± 0.05 Lactose, % 4.85 ± 0.01 Dry matter, % 11.50 ± 0.09 Log SCC 1 2.72 ± 0.02 Milk FA composition (%) 2 C4:0 0.65 ± 0.03 C6:0 0.32 ± 0.01 C8:0 2.49 ± 0.04 C10:0 12.76 ± 0.15 C11:0 0.11 ± 0.004 C12:0 5.45 ± 0.07 C13:0 0.09 ± 0.002 C14:0 10.09 ± 0.06 C14:1 0.16 ± 0.002 C15:0 0.76 ± 0.01 C15:1 0.17 ± 0.003 C16:0 31.76 ± 0.14 C16:1 0.95 ± 0.01 C17:0 0.48 ± 0.003 C17:1 0.17 ± 0.002 C18:0 10.06 ± 0.11 C18:1n9t 2.43 ± 0.07 C18:1n11t 2.38 ± 0.06 C18:1n9c 14.26 ± 0.16 C18:2n6t 0.30 ± 0.02 C18:2n6c 2.44 ± 0.02 C18:3n3a 0.19 ± 0.004 C18:3n6g 0.06 ± 0.002 cis-9, trans-11 CLA 0.45 ± 0.01 trans-10, cis-12 CLA 0.14 ± 0.004 Other CLA 0.13 ± 0.003 C20:0 0.04 ± 0.01 C20:1 0.10 ± 0.002 C20:2 0.06 ± 0.003 C21:0 0.19 ± 0.01 SFA 75.30 ± 0.17 MUFA 20.64 ± 0.15 PUFA 4.06 ± 0.04 Total CLA 0.72 ± 0.01 Omega 3 0.30 ± 0.004 Omega 6 2.97 ± 0.03 De novo FA 3 33.05 ± 0.28 Performed FA 3 34.15 ± 0.25 1 Decimal logarithm of SCC value/1,000. 2 FA concentrations have been expressed as percentages of the total fatty methyl esters. 3 Calculated as indicated by Moate et al. (2007).
Supplementary Table 3. Associations between dairy traits and goat SCD1 genotypes (Lsmeans ± SE) c.732c > T c.*1902_1904deltgt c.*3504g > A Trait P- P- P- CC CT TT DelTGT/DelTGT DelTGT/TGT TGT/TGT AA AG GG value value value Milk, kg/day 1.59 ± 0.13 1.69 ± 0.11 1.73 ± 0.10 0.44 1.74 ± 0.10 1.72 ± 0.10 1.60 ± 0.15 0.56 1.64 ± 0.15 1.71 ± 0.10 1.73 ± 0.10 0.76 Protein, % 3.71 ± 0.07 3.59 ± 0.06 3.57 ± 0.06 0.07 3.59 ± 0.05 3.61 ± 0.06 3.62 ± 0.08 0.93 3.63 ± 0.08 3.60 ± 0.06 3.59 ± 0.06 0.87 Fat, % 5.69 ± 0.22 5.69 ± 0.18 5.65 ± 0.18 0.91 5.68 ± 0.18 5.62 ± 0.18 5.53 ± 0.25 0.70 5.52 ± 0.26 5.63 ± 0.18 5.68 ± 0.18 0.73 Lactose, % 4.96 ± 0.04 a 4.90 ± 0.04 b 4.96 ± 0.03 a 0.02 4.97 ± 0.03 a 4.91 ± 0.03 b 4.99 ± 0.05 a 0.009 4.99 ± 0.05 a 4.91 ± 0.03 b 4.97 ± 0.03 a 0.02 Dry matter, % 12.67 ± 0.21 12.43 ± 0.18 12.61 ± 0.17 0.22 12.59 ± 0.19 12.57 ± 0.20 12.51 ± 0.28 0.92 12.52 ± 0.29 12.57 ± 0.20 12.59 ± 0.20 0.96 LogSCC 1 2.68 ± 0.09 2.71 ± 0.07 2.73 ± 0.07 0.77 2.76 ± 0.07 2.69 ± 0.07 2.80 ± 0.21 0.23 2.80 ± 0.10 2.68 ± 0.07 2.75 ± 0.10 0.14 1 Decimal logarithm of SCC value/1,000. a,b Means within rows with different superscripts show either highly suggestive (0.0083 < P < 0.01) or suggestive (0.01 < P < 0.05) differences.
Supplementary Table 4. Association between dairy traits and SCD1 haplotypes in Murciano-Granadina goats (Lsmeans ± SE) Trait T/DelTGT/G vs C/TGT/A 1 P-value Milk, kg/day 0.017 ± 0.05 0.73 Protein, % 0.030 ± 0.07 0.66 Fat, % 0.141 ± 0.20 0.49 Lactose, % 0.016 ± 0.04 0.70 Dry matter, % 0.081 ± 0.23 0.82 LogSCC 2 0.060 ± 0.08 0.57 1 Effect of replacing haplotype T/DelTGT/G by haplotype C/TGT/A (only the two most frequent haplotypes have been compared). 2 Decimal logarithm of SCC value/1,000.
Supplementary Table 5. Associations between milk fatty acid composition traits and c.732c > T SCD1 genotypes in Murciano-Granadina goats (Lsmeans ± SE) Trait CC CT TT P-value C4:0 0.81 ± 0.09 0.73 ± 0.05 0.75 ± 0.05 0.70 C6:0 0.28 ± 0.03 0.28 ± 0.02 0.29 ± 0.02 0.85 C8:0 2.28 ± 0.12 2.38 ± 0.08 2.31 ± 0.08 0.57 C10:0 12.93 ± 0.26 12.73 ± 0.25 12.98 ± 0.44 0.82 C11:0 0.12 ± 0.02 0.11 ± 0.01 0.10 ± 0.01 0.48 C12:0 5.64 ± 0.22 5.39 ± 0.13 5.52 ± 0.13 0.47 C13:0 0.09 ± 0.008 0.09 ± 0.005 0.09 ± 0.005 0.98 C14:0 10.04 ± 0.22 10.08 ± 0.13 10.16 ± 0.14 0.81 C14:1 0.15 ± 0.01 0.14 ± 0.006 0.14 ± 0.006 0.81 C15:0 0.74 ± 0.02 0.73 ± 0.01 0.72 ± 0.01 0.87 C15:1 0.17 ± 0.01 0.17 ± 0.006 0.17 ± 0.006 0.97 C16:0 31.69 ± 0.42 31.51 ± 0.26 31.52 ± 0.26 0.92 C16:1 0.94 ± 0.03 0.94 ± 0.02 0.93 ± 0.02 0.81 C17:0 0.49 ± 0.01 0.50 ± 0.006 0.49 ± 0.006 0.82 C17:1 0.16 ± 0.009 0.17 ± 0.005 0.17 ± 0.005 0.72 C18:0 10.6 ± 0.35 10.81 ± 0.22 10.53 ± 0.22 0.45 C18:1n9t 2.26 ± 0.23 2.11 ± 0.14 2.20 ± 0.14 0.77 C18:1n11t 2.14 ± 0.21 2.27 ± 0.13 2.27 ± 0.13 0.81 C18:1n9c 14.06 ± 0.47 14.48 ± 0.29 14.47 ± 0.29 0.65 C18:2n6t 0.25 ± 0.08 0.31 ± 0.05 0.27 ± 0.05 0.64 C18:2n6c 2.39 ± 0.27 2.37 ± 0.05 2.46 ± 0.05 0.27 C18:3n3a 0.21 ± 0.01 0.20 ± 0.006 0.20 ± 0.006 0.76 C18:3n6g 0.06 ± 0.009 0.05 ± 0.005 0.06 ± 0.005 0.58 cis-9, trans-11 CLA 0.37 ± 0.04 0.39 ± 0.02 0.41 ± 0.02 0.43 trans-10, cis-12 CLA 0.12 ± 0.005 0.13 ± 0.009 0.14 ± 0.009 0.29 Other CLA 0.13 ± 0.009 0.13 ± 0.005 0.13 ± 0.005 0.41 C20:0 0.06 ± 0.01 0.04 ± 0.01 0.03 ± 0.01 0.32 C20:1 0.11 ± 0.008 0.11 ± 0.005 0.11 ± 0.005 0.64 C20:2 0.06 ± 0.09 0.06 ± 0.006 0.06 ± 0.006 0.99 C21:0 0.22 ± 0.02 0.21 ± 0.005 0.21 ± 0.01 0.92 SFA 76.11 ± 0.55 75.62 ± 0.34 75.48 ± 0.34 0.54 MUFA 20.02 ± 0.50 20.43 ± 0.31 20.51 ± 0.31 0.65 PUFA 3.92 ± 0.12 3.96 ± 0.07 4.07 ± 0.07 0.35 Total CLA 0.63 ± 0.05 0.65 ± 0.03 0.70 ± 0.03 0.25 Omega 3 0.32 ± 0.012 0.31 ± 0.007 0.31 ± 0.007 0.91 Omega 6 2.80 ± 0.10 2.91 ± 0.06 2.97 ± 0.06 0.62 De novo FA 1 33.35 ± 0.81 32.84 ± 0.5 32.99 ± 0.5 0.82 Performed FA 1 33.91 ± 0.78 34.61 ± 0.48 34.47 ± 0.48 0.67 1 Calculated as indicated by Moate et al. (2007).
Supplementary Table 6. Association analysis between c.*1902_1904deltgt SCD1 genotype and milk fatty acid composition in Murciano-Granadina goats (Lsmeans ± SE) Trait DelTGT/DelTGT DelTGT/TGT TGT/TGT P-Value C4:0 0.76 ± 0.05 0.77 ± 0.05 0.71 ± 0.11 0.88 C6:0 0.29 ± 0.02 0.29 ± 0.02 0.30 ± 0.04 0.96 C8:0 2.29 ± 0.07 2.40 ± 0.07 2.22 ± 0.15 0.28 C10:0 12.67 ± 0.24 12.91 ± 0.25 11.89 ± 0.50 0.13 C11:0 0.11 ± 0.01 0.10 ± 0.01 0.10 ± 0.02 0.68 C12:0 5.50 ± 0.13 5.46 ± 0.13 5.18 ± 0.28 0.52 C13:0 0.09 ± 0.005 0.09 ± 0.005 0.08 ± 0.01 0.38 C14:0 10.14 ± 0.13 10.12 ± 0.13 9.66 ± 0.28 0.23 C14:1 0.14 ± 0.005 0.14 ± 0.006 0.14 ± 0.01 0.95 C15:0 0.72 ± 0.013 0.73 ± 0.01 0.74 ± 0.028 0.87 C15:1 0.17 ± 0.006 0.17 ± 0.006 0.15 ± 0.01 0.28 C16:0 31.56 ± 0.24 31.53 ± 0.26 32.06 ± 0.53 0.60 C16:1 0.94 ± 0.02 0.93 ± 0.02 0.94 ± 0.04 0.97 C17:0 0.49 ± 0.49 0.49 ± 0.006 0.50 ± 0.01 0.88 C17:1 0.17 ± 0.005 0.17 ± 0.005 0.17 ± 0.01 0.56 C18:0 10.55 ± 0.21 10.72 ± 0.22 11.55 ± 0.44 0.08 C18:1n9t 2.23 ± 0.13 2.10 ± 0.14 2.18 ± 0.29 0.68 C18:1n11t 2.35 ± 0.12 2.26 ± 0.13 2.10 ± 0.26 0.67 C18:1n9c 14.40 ± 0.27 14.27 ± 0.28 15.18 ± 0.58 0.30 C18:2n6t 0.27 ± 0.04 0.31 ± 0.04 0.25 ± 0.09 0.63 C18:2n6c 2.46 ± 0.04 a 2.37 ± 0.05 a 2.24 ± 0.10 b 0.05 C18:3n3a 0.20 ± 0.006 0.20 ± 0.006 0.17 ± 0.01 0.06 C18:3n6g 0.06 ± 0.005 0.05 ± 0.005 0.05 ± 0.01 0.88 cis-9, trans-11 CLA 0.42 ± 0.02 0.37 ± 0.02 0.36 ± 0.05 0.14 trans-10, cis-12 CLA 0.15 ± 0.008 a 0.13 ± 0.009 a 0.10 ± 0.01 b 0.0024 Other CLA 2 0.14 ± 0.005 0.13 ± 0.005 0.12 ± 0.01 0.14 C20:0 0.03 ± 0.01 0.05 ± 0.01 0.03 ± 0.022 0.22 C20:1 0.11 ± 0.005 0.10 ± 0.006 0.12 ± 0.010 0.38 C20:2 0.06 ± 0.005 0.06 ± 0.006 0.05 ± 0.01 0.46 C21:0 0.21 ± 0.01 0.21 ± 0.01 0.22 ± 0.22 0.90 SFA 75.45 ± 0.32 75.90 ± 0.33 75.32 ± 0.32 0.39 MUFA 20.51 ± 0.29 20.18 ± 0.30 21.01 ± 0.62 0.33 PUFA 4.08 ± 0.07 a 3.95 ± 0.07 b 3.71 ± 0.15 b 0.03 Total CLA 0.71 ± 0.02 a 0.64 ± 0.03 b 0.58 ± 0.06 b 0.01 Omega 3 0.31 ± 0.007 0.32 ± 0.007 0.31 ± 0.01 0.87 Omega 6 2.97 ± 0.06 2.91 ± 0.06 2.74 ± 0.13 0.21 De novo FA 1 32.90 ± 0.47 33.17 ± 0.49 31.22 ± 1.01 0.16 Performed FA 1 34.51 ± 0.46 34.27 ± 0.48 35.63 ± 0.97 0.38 a,b Means within rows with different superscripts show either highly suggestive (0.0013 < P < 0.01) or suggestive (0.01 < P < 0.05) differences. 1 Calculated as indicated by Moate et al. (2007). 2 Geometric and position isomers of cis-9, trans-11 and trans-10, cis-12 CLA.
Supplementary Table 7. Association between c.*3504g > A SCD1 genotypes and milk fatty acid composition in Murciano-Granadina goats (Lsmeans ± SE) Trait AA AG GG P-value C4:0 0.73 ± 0.12 0.75 ± 0.05 0.75 ± 0.05 0.98 C6:0 0.30 ± 0.05 0.29 ± 0.02 0.29 ± 0.02 0.99 C8:0 2.25 ± 0.17 2.40 ± 0.08 2.29 ± 0.07 0.34 C10:0 11.97 ± 0.56 12.95 ± 0.25 12.65 ± 0.24 0.17 C11:0 0.10 ± 0.02 0.10 ± 0.1 0.11 ± 0.01 0.67 C12:0 5.20 ± 0.30 5.50 ± 0.13 5.49 ± 0.13 0.62 C13:0 0.08 ± 0.01 0.09 ± 0.005 0.09 ± 0.005 0.46 C14:0 9.76 ± 0.30 10.15 ± 0.14 10.11 ± 0.13 0.47 C14:1 0.15 ± 0.01 0.14 ± 0.006 0.14 ± 0.006 0.89 C15:0 0.75 ± 0.03 0.73 ± 0.01 0.72 ± 0.01 0.78 C15:1 0.16 ± 0.01 0.17 ± 0.006 0.17 ± 0.006 0.58 C16:0 32.05 ± 0.58 31.50 ± 0.26 31.52 ± 0.25 0.66 C16:1 0.94 ± 0.05 0.94 ± 0.02 0.94 ± 0.02 0.99 C17:0 0.51 ± 0.01 0.49 ± 0.006 0.49 ± 0.006 0.63 C17:1 0.17 ± 0.01 0.17 ± 0.005 0.17 ± 0.005 0.52 C18:0 11.51 ± 0.48 10.67 ± 0.22 10.57 ± 0.21 0.15 C18:1n9t 2.08 ± 0.32 2.09 ± 0.14 2.24 ± 0.14 0.60 C18:1n11t 2.07 ± 0.28 2.25 ± 0.13 2.29 ± 0.18 0.74 C18:1n9c 15.08 ± 0.64 14.28 ± 0.29 14.49 ± 0.28 0.43 C18:2n6t 0.24 ± 0.10 0.31 ± 0.05 0.27 ± 0.04 0.65 C18:2n6c 2.27 ± 0.11 b 2.36 ± 0.05 ab 2.47 ± 0.04 a 0.03 C18:3n3a 0.18 ± 0.01 0.20 ± 0.006 0.20 ± 0.006 0.47 C18:3n6g 0.05 ± 0.01 0.06 ± 0.005 0.06 ± 0.005 0.84 cis-9, trans-11 CLA 0.34 ± 0.04 0.37 ± 0.02 0.43 ± 0.02 0.06 trans-10, cis-12 CLA 0.09 ± 0.02 b 0.13 ± 0.009 a 0.15 ± 0.008 a 0.0051 Other CLA 2 0.12 ± 0.01 0.13 ± 0.005 0.14 ± 0.005 0.21 C20:0 0.03 ± 0.02 0.05 ± 0.01 0.03 ± 0.01 0.21 C20:1 0.12 ± 0.01 0.10 ± 0.005 0.11 ± 0.005 0.19 C20:2 0.05 ± 0.01 0.06 ± 0.006 0.06 ± 0.006 0.59 C21:0 0.20 ± 0.03 0.21 ± 0.01 0.21 ± 0.01 0.91 SFA 75.52 ± 0.75 75.92 ± 0.34 75.03 ± 0.33 0.291 MUFA 20.80 ± 0.68 20.18 ± 0.31 20.58 ± 0.30 0.381 PUFA 3.73 ± 0.17 b 3.93 ± 0.07 b 4.10 ± 0.07 a 0.02 Total CLA 0.55 ± 0.06 b 0.63 ± 0.03 b 0.71 ± 0.03 a 0.0071 Omega 3 0.32 ± 0.01 0.31 ± 0.007 0.31 ± 0.007 0.90 Omega 6 2.77 ± 0.14 2.90 ± 0.06 2.98 ± 0.06 0.24 De novo FA 1 31.50 ± 1.11 33.27 ± 0.50 32.83 ± 0.43 0.26 Performed FA 1 35.37 ± 1.06 34.19 ± 0.48 34.62 ± 0.46 0.46 a,b Means within rows with different superscripts show either highly suggestive (0.0013 < P < 0.01) or suggestive (0.01 < P < 0.05) differences.
1 Calculated as indicated by Moate et al. (2007). 2 Geometric and position isomers of cis-9, trans-11 and trans-10, cis-12 CLA.
Supplementary Table 8. Association between goat SCD1 genotypes and desaturase indices (Lsmeans ± SE) Index c.732c > T c.*1902_1904deltgt c.*3504g > A CC CT TT P-value DelTGT/ DelTGT/TGT TGT/TGT P- AA AG GG P-value DelTGT value C14 index 0.015 ± 0.003 0.014 ± 0.0008 0.014 ± 0.008 0.78 0.014 ± 0.0007 0.014 ± 0.0008 0.015 ± 0.001 0.86 0.01 ± 0.01 0.01 ± 0.008 0.014 ± 0.008 0.87 C16 index 0.03 ± 0.001 0.03 ± 0.0007 0.029 ± 0.0007 0.80 0.03 ± 0.0007 0.029 ± 0.007 0.029 ± 0.001 0.95 0.02 ± 0.001 0.03 ± 0.0007 0.03 ± 0.0007 0.97 C18 index 1.35 ± 0.04 1.37 ± 0.02 1.4 ± 0.02 0.47 1.39 ± 0.02 1.36 ± 0.02 1.33 ± 0.05 0.44 1.33 ± 0.06 1.39 ± 0.02 1.39 ± 0.02 0.41 CLA index 0.21 ± 0.02 0.21 ± 0.01 0.23 ± 0.01 0.59 0.22 ± 0.01 0.21 ± 0.01 0.23 ± 0.02 0.48 0.22 ± 0.03 0.21 ± 0.01 0.23 ± 0.01 0.42