Identification of SNPs
A total of 17 SNPs of the AGPAT3 gene was detected in this study (Table 1), which consisted of four (g.146702957G>A, g.146704373A>G, g.146704618A>G and g.146704699G>A) in 5' flanking region, one (g.146705692G>A) in 5' untranslated region (UTR), three (g.146725085T>C, g.146726096A>G and g.146729107A>C) in introns, one (g.146735090G>T) in 3' UTR, and eight (g.146737188C>T, g.146737545G>A, g.146737748T>C, g.146737849C>T, g.146737879T>G, g.146737916T>C, g.146737946C>T and g.146738055G>A) in 3' flanking region. The genotype and allele frequencies of the identified SNPs were presented in Table 1.
Estimation of LD among the identified SNPs of AGPAT3
We used the haploview 4.1 to estimate the LD among these 17 SNPs, and observed two haplotype blocks (Fig. 2) that was formed by four and 12 SNPs, respectively. The haplotype block 1 included four haplotype combinations, namely, H1: GAAG (38%), H2: GAAA (32.2%), H3: AGGG (26.6%), and H4: GAGG (3%), and the haplotype block 2 had six haplotype combinations: H1 = GTAAGCGTCTTC, H2 = GCACGTACTGCT, H3 = GCAATCGTCTTC, H4 = ACACGCGTCTTC, H5 = GTGATCGTCTTC, and H6 = GCAAGCGTCTTC with their frequencies of 20%, 39.8%, 13.4%, 13.4%, 7.9% and 4.1%.
Associations between AGPAT3 and milk FAs
The associations of the 17 SNPs with 24 milk FAs were summarized in Table 2. Among these SNPs, 17 were strongly associated with C6:0 (P < 0.0001 ~ 0.0004) and C8:0 (P < 0.0001 ~ 0.0384); 14 were significantly associated with total index (P < 0.0001 ~ 0.0318); ten were significantly associated with C10:0 (P = 0.0016 ~ 0.0151); nine were strongly associated with C17:1 (P < 0.0001 ~ 0.0149); seven were significantly associated with C20:0 (P < 0.0001 ~ 0.0072); five had significant associations with C14:0 (P < 0.0001 ~ 0.0477); five were strongly associated with C17index (P = 0.0006 ~ 0.0389); five had strong associations with C18:1cis-9 (P < 0.0001 ~ 0.0258); three had significant associations with C18:0 (P = 0.0020 ~ 0.0246); three had strong associations with SFA (P < 0.0001 ~ 0.0434); two were significantly associated with C17:0 (P = 0.0212 ~ 0.0413); two were significantly associated with UFA (P < 0.0001 and P = 0.0386); one was strongly associated with C18index (P = 0.0249); and one had significant association with SFA/UFA (P = 0.0005). However, no significant association was found with C11:0, C12:0, C13:0, C14:1, C15:0, C16:0, C16:1, C14index and C16index (P > 0.05).
Further, the additive (a), dominant (d), and allele substitution effects (α) of the 17 SNPs on each kind of fatty acid were calculated. Results showed that the 17 SNPs exhibited significant additive, dominant, and allele substitution effects on C6:0, C8:0, C10:0, C14:0, C16:0, C16:1, C17:0, C18:0, C18:1cis-9, C18index, C20:0, C14index, C16index, C17index, SFA, UFA, and total index (Table S2; P < 0.05). For C11:0, C12:0, C13:0, C14:1 and C15:0, none of significant additive, dominant, and allele substitution effects was found (P > 0.05).
Also, association analysis on two haplotype blocks with 24 milk FAs was performed (Table 3). The haplotype blcok1 was significantly associated with C6:0, C8:0, C10:0, C14:0, C18:0, C20:0, C17index and total index (P < 0.0001 ~ 0.0245), and the block 2 was strongly associated with C6:0, C8:0, C10:0, C14:0, C18:0, C17:1, C18:1cis-9, C18index, C20:0, C16index, C17index, SFA, UFA and total index (P < 0.0001 ~ 0.0498; Table 3). While, no significant association was found for C11:0, C12:0, C13:0, C14:1, C15:0, C16:0, C16:1, C14index and SFA/UFA (P > 0.05).
Prediction of TFBSs changing caused by the SNPs in 5' regulatory region
By performing Genomatix software suite v3.9, it was predicted that that four SNPs in the 5’ regulatory region of AGPAT3 gene, g.146702957G>A, g.146704373A>G, g.146704618A>G and g.146704699G>A altered the binding sites of some transcription factors (Table 4). The allele A of g.146702957G>A created a TFBS for SMARCA3 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3) and REX1 (REX1 transcription factor; zinc finger protein 42), respectively, and the allele G created a TFBS for VMYB (v-Myb, variant of AMV v-myb). The alleles A and G of g.146704373A>G created a TFBS for BRACH (Brachyury) and NKX26 (NK2 homeobox 6, Csx2), respectively. The allele G of g.146704618A>G created two TFBSs for ZBED4 (Zinc finger, BED-type containing 4; GC-box binding sites) and SP1 (Stimulating protein 1, ubiquitous zinc finger transcription factor). The allele G of g.146704699G>A created two TFBSs for USF1 (Upstream stimulating factor 1) and ARNT (AhR nuclear translocator homodimers), and the allele A created a TFBS for FOXA1 (Forkhead box protein A1, hepatocyte nuclear factor 3-alpha (HNF-3-alpha)).
Exploring for luciferase activity altered by the SNPs in 5' regulatory region
To validate the TFBS prediction results, the luciferase assay was further performed for the four SNPs (g.146702957G>A, g.146704373A>G, g.146704618A>G and g.146704699G>A) (Fig. 1b). We observed that the luciferase activities of six constructs containing g.146704373A>G, g.146704618A>G, and g.146704699G>A, were significantly higher than that of the pGL4.14 empty vector (P < 0.0007) and blank control (P < 0.0008), while g.146702957G>A did not (P > 0.05). Further, the luciferase activity of alleles A of g.146704373A>G and g.146704618A>G were significantly higher than that of their alleles G (P = 0.0004; Fig. 1b). The luciferase activity of allele G of g.146704699G>A was higher than that of allele A, while not significant (P > 0.05). These results indicated that the transcriptional activity of the AGPAT3 gene significantly altered by g.146704373A>G and g.146704618A>G might be the reasons strongly impacted on FAs.