A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

doi:10.21203/rs.3.rs-38950/v3

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A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

https://doi.org/10.21203/rs.3.rs-38950/v3

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published 01 Feb, 2021

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Background: People are paying more attention to the healthy and balanced diet with the improvement of their living standards. Milk fatty acids (FAs) have been reported that they were related to some atherosclerosis and coronary heart diseases in human. In our previous genome-wide association study (GWAS) on milk FAs in dairy cattle, 83 genome-wide significant single nucleotide polymorphisms (SNPs) were detected. Among them, two SNPs, ARS-BFGL-NGS-109493 and BTA-56389-no-rs associated with C18index (P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3 (AGPAT3) gene. AGPAT3 is involved in glycerol-lipid, glycerol-phospholipid metabolism and phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for milk FAs. The aim of this study was to further confirm the genetic effects of the AGPAT3 gene on milk FA traits in dairy cattle.

Results: Through re-sequencing the complete coding region, and 3,000bp of 5' and 3' regulatory regions of the AGPAT3 gene, a total of 17 SNPs were identified, including four in 5' regulatory region, one in 5' untranslated region (UTR), three in introns, one in 3' UTR, and eight in 3' regulatory region. By the linkage disequilibrium (LD) analysis with Haploview4.1 software, two haplotype blocks were observed that were formed by four and 12 identified SNPs, respectively. Using SAS9.2, we performed single locus-based and haplotype-based association analysis on 24 milk FAs in 1,065 Chinese Holstein cows, and discovered that all the SNPs and the haplotype blocks were significantly associated with C6:0, C8:0 and C10:0 (P < 0.0001~ 0.0384). Further, with Genomatix, we predicted that four SNPs in 5' regulatory region (g.146702957G>A, g.146704373A>G g.146704618A>G and g.146704699G>A) changed the transcription factor binding sites (TFBSs) for transcription factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT and FOXA1. Out of them, two SNPs were validated to impact transcriptional activity by performing luciferase assay that the alleles A of both SNPs, g.146704373A>G and g.146704618A>G, increased the transcriptional activities of AGPAT3 promoter compared with alleles G (P = 0.0004).

Conclusions: In conclusion, our findings first demonstrated the significant genetic associations of the AGPAT3 gene with milk FAs in dairy cattle, and two potential causal mutations were detected.

Animal Science

Medical Genetics

AGPAT3

Chinese Holstein

Genetic effects

Milk fatty acids

Potential causal mutation

Milk fat is one of critical breeding objectives in dairy cattle. It is comprised of triglyceride (>95%), diglyceride (2%), phospholipids (1%), cholesterol (0.05%) and small amount of free fatty acids (FAs) (~0.1%) [1]. The main components of triglyceride are glycerin and FAs, in which, the FAs act as precursors for the formation of other aroma components, such as esters and alcohols [2]. For the various milk fatty acid traits in Holstein cows, the estimated heritability values have been reported to be 0.14-0.33 for saturated fatty acids (SFAs) and 0.08-0.29 for unsaturated fatty acids (UFAs) [3-7].

Genome-wide association study (GWAS) is a commonly used strategy to identify potential genetic variants underlying important complex traits in human and domestic animals. So far, some candidate genes and QTL regions for milk production traits have been detected with GWA studies in dairy cattle, such as DLGAP1, AP2B1, SCD, BTA11 (1.59 ~ 3.37 Mbp), and BTA3 (70.34 ~ 73.69 Mbp) [8-13]. In our previous GWAS for milk FAs in Chinese Holstein cows, 83 genome-wide significant single nucleotide polymorphisms (SNPs) were detected in total [12], in which, two SNPs (ARS-BFGL-NGS-109493 and BTA-56389-no-rs) associated with C18index (P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3 (AGPAT3) gene. In addition, we performed a joint GWAS for milk FAs in combined Chinese and Danish Holstein populations and found that a chromosome-wide significant QTL region of 146.29 ~ 146.31 Mbp on BTA1 was associated with C18:0 [13]. The AGPAT3 gene was nearby this region with approximately 400 kb. 1-acylglycerol-sn-glycero 3-phosphate acyltransferase (AGPAT), encoded by the AGPAT3 gene, is one of the isoforms of AGPATs [14] and is involved in the glycerolipid (ko00561) and glycerophospholipid metabolisms (ko00564), and phospholipase D signaling pathway (ko04072). Mammalian AGPAT catalyzed the acylation of lysophosphatidic acid to form the phosphatidic acid that was the precursor of all glycerplipids [14]. Therefore, it was implied that the AGPAT3 gene was a promising candidate gene for milk FA traits in dairy cattle. The purpose of the present study was to further detect whether the AGPAT3 gene had significant genetic effects on milk FAs in a Chinese Holstein cow population.

Animals and phenotypic data

SNP identification and genotyping

Based on the genomic sequence of bovine AGPAT3 gene (Gene ID: 506607), 14 pairs of primers (Table S1) were designed by the Primer 3 version 4.0 (http://bioinfo.ut.ee/primer3-0.4.0/) and were synthesized in the Beijing Genomics Institute (Beijing, China) to amplify all the exons with partial adjacent intron region, and 3,000 bp of 5' and 3' regulatory regions. As previously descripted [15], two DNA pools were constructed and the polymerase chain reaction (PCR) amplifications were performed with each DNA pool as template. To identify potential polymorphisms, the PCR amplification products were bi-directionally sequenced with an ABI3730XL DNA analyzer (Applied Biosystems, Foster, CA, USA). Then, the identified SNPs were genotyped for the 1,065 cows by the matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF MS, Sequenom MassARRAY, Bioyong Technologies Inc, HK).

Linkage disequilibrium (LD) and association analyses

We estimated the LD among the identified SNPs of AGPAT3 gene with Haploview 4.1 (Broad Institute, Cambridge, MA, USA).

For association analysis, the 1,065 cows were traced back to three-generation pedigrees to construct the kinship matrix (A-matrix) by SAS 9.2 (SAS institute, Cary, NC, USA), so that 3,335 individuals were totally included. Single-locus and haplotype-based associations with 24 kind of milk FAs were performed by the following mixed animal model with SAS 9.2:

Prediction of changes of transcription factor binding sites (TFBSs) caused by the SNPs in 5' regulatory region

We used the Genomatix software suite v3.9 (http://www.genomatix.de/cgi-bin/welcome/welcome.pl?s=d1b5c9a9015b02bb3b1a806f9c03293f) [18] to predict whether the four SNPs in 5' regulatory region of AGPAT3 (g. 146702957G>A, g.146704373A>G, g.146704618A>G, and g.146704699G>A) changed the TFBSs.

Recombinant plasmid construction and luciferase assay

To detect the allele-specific effects of the SNPs g.146702957G>A, g.146704373A>G, g.146704618A>G, and g.146704699G>A on the transcriptional activity of AGPAT3 gene, eight luciferase reporter gene fragments (G and A of g. 146702957G>A; A and G of g.146704373A>G; A and G of g.146704618A>G; and G and A of g.146704699G>A) corresponding to the eight alleles of the four SNPs (Fig. 1a) were designed and synthesized (Genewiz, Suzhou, China). The eight fragments with the KpnⅠ and Nhel restriction sites at the 5′ and 3′ termini, respectively, were cloned into the pGL4.14 luciferase assay vector (Promega, Madison, USA). In addition, all the plasmids were purified by the Endo-free Plasmid DNA Mini Kit Ⅱ (OMEGA, omega bio-tek, Norcross, Georgia, USA), and were sequenced to confirm the integrity of each construct’s insertion.

The human embryonic kidney (HEK) 293T cells were cultured with Dulbecco′s modified Eagle′s medium (Gibco, Life Technologies) and 10% fetal bovine serum (Gibco) at 37℃ in a humidified incubator containing 5% CO₂. Before transfection, about 2×10⁵ cells were seeded in each 24-well plate. For eight luciferase reporter gene fragments of g. 146702957G>A, g.146704373A>G g.146704618A>G and g.146704699G>A, 500 ng constructed plasmid was co-transfected along with 10 ng pRL-TK Renilla luciferase reporter vector (Promega) into each well. All the experiments were performed in three replicates for each construct. Approximate 48h after transfection, the cells were harvested and the activity of both firefly and Renilla luciferases were measured with a Dual-Luciferase Reporter Assay System (Promega) on a Modulus microplate multimode reader (Turner Biosystems, CA, USA). The average statistic of three replicates were calculated as the normalized luciferase data (Firefly/Renilla).

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.

This study was a follow-up investigation for our previous GWAS on milk FAs in Chinese Holstein [12]. AGPAT3 is involved in pathways related to lipid metabolism (ko00561, ko00564 and ko04072). In human, docosapentaenoic acid as the substrate of AGPAT3 protein transfers a fatty acid in sn-2 position of lysophosphatic acid, a step in the phospholipid biosynthesis pathway [19]. Here, we detected that the AGPAT3 gene mainly impacted the medium-chain milk FAs in dairy cattle.

Mammalian AGPAT catalyzed the acylation of lysophosphatidic acid to form the phosphatidic acid, which was the precursor of all glycerplipids [14]. For the AGPAT families, AGPAT1 had significant association with milk FA CLA [20], and AGPAT6 was strongly associated with C14:0, C16:0, C10:1, C12:1, C14:1 and C16:1 [21]. In our previous GWA studies [12,13], AGPAT3 gene was identified as a candidate for two milk FAs, C18index and C18:0. In this study, using an independent Chinese Holstein population that was different from the previous GWA studies, we also observed that AGPAT3 showed a significant genetic effect on C18index and C18:0. In addition, our results revealed that the AGPAT3 had strong associations with C6:0, C8:0 and C10:0. Overall, the previous GWASs and this study suggested that AGPAT3 gene had significantly genetic effects on milk FAs.

Sequences-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that affects gene expression and hence heritable phenotypic variation [22,23]. Eukaryotic regulatory sequences, including enhancers and promoters, are typically between a hundred and several thousand base pairs in length, and can harbor many TFBSs [24]. It is essential to understand the evolution dynamics of transcription factor binding for understanding the evolution of gene regulation [25]. In this study, by prediction, g.146704373A>G changed the bindings of transcription factors (TFs) BRACH and NKX26, and g.146704618A>G altered the bindings of TFs ZBED4 and SP1. Further, we used the luciferase assay to verify that the alleles A of g.146704373A>G and g.146704618A>G strongly increased the transcription activity of the AGPAT3 gene than the alleles G. Previous studies showed that BRACH as a regulatory factor directly activated downstream mesoderm-specific genes to exert its mesoderm-inducing effects [26], and NKX26 restrained the transcription activity of Cx40 through the F151L missense mutation to impact the heart development [27]. ZBED4 could act as a co-repressor of nuclear hormone receptors (NHRs) by its LXXLL motifys in cones [28]. Through interfering with the recruitment of SP1 to ZNF132 promoter region, methylation of SP1-binding site can inhibit ZNF132 transcriptional expression to impact the tumor in the development of esophageal squamous cell carcinoma [29]. These reports have indicated that the TFs BRACH, NKX26, ZBED4 and SP1 could activate or repress the expression of their target genes. Based on our association analysis, the cows with the AA genotypes of g.146704373A>G and g.146704618A>G of AGPAT3, yielded significantly lower contents of C6:0 and C8:0 than those with GG genotypes. According to above, we deduced that the BRACH as a TF might activate AGPAT3 gene transcription activity by binding to the allele A of g.146704373A>G thereby reducing the contents of C6:0 and C8:0, while, the transcription factors NKX26, ZBED4 and SP1 might have the contrary effects.

Nowadays, genomic selection is the main implication for dairy cattle breeding, where the genomic chips are used. Among the SNP markers in these chips, most of them were collected from the current SNP database and almost evenly distributed across the whole genome. Hence, g.146704373A>G and g.146704618A>G of AGPAT3 as the potentially causal mutations could be put into the SNP chip instead of used in marker selection to increase selection efficiency in some specific dairy cattle populations to improve the contents of milk FAs.

In conclusion, through a post-GWAS approach, our study firstly indicated there were significant genetic associations between the AGPAT3 gene and milk FAs in dairy cattle. Further, we found that two SNPs in 5’ regulatory region (g.146704373A>G and g.146704618A>G) changed the transcriptional activity of AGPAT3 implying their potential causal function. These findings provided important molecular information for dairy cattle breeding.

a: Additive; AGPAT: 1-acylglycerol-sn-glycero 3-phosphate acyltransferase; AGPAT3: 1-acylglycerol-3-phosphate O-acyltransferase 3; ARNT: AhR nuclear translocator homodimers; BRACH: Brachyury; d: dominant; FA: fatty acid; FOXA1: Forkhead box protein A1, hepatocyte nuclear factor 3-alpha (HNF-3-alpha); GWAS: genome-wide association study; HEK: Human Embryonic Kidney; LD: linkage disequilibrium; NKX26: NK2 homeobox 6, Csx2; PCR: polymerase chain reaction; REX1: REX1 transcription factor; zinc finger protein 42; SFA: saturated fatty acids; SMARCA3: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3; SNP: single nucleotide polymorphism; SP1: Stimulating protein 1, ubiquitous zinc finger transcription factor; TFBS: transcription factor binding site; UFA: unsaturated fatty acid; USF1: Upstream stimulating factor 1; UTR: untranslated region; VMYB: v-Myb, variant of AMV v-myb; ZBED4: Zinc finger, BED-type containing 4; GC-box binding sites; α: substitution.

Acknowledgements

We appreciate Beijing Dairy Cattle Center and Beijing Sanyuanlvhe Dairy Farming Center for providing the milk, blood, and semen samples of Chinese Holstein.

Author contributions

DS and YY conceived and designed the experiments, LL prepared the DNA samples for SNP identification and genotyping with the help of XW, ZM, XL, YL, and FZ, XL measured the phenotypes of milk fatty acids, LS and XW analyzed the data, and LS, BH and DS prepared the manuscript. All authors read and approved the final manuscript.

Funding

This work was financially supported by the Beijing Science and Technology Program (20200105, D171100002417001), National Science and Technology Programs of China (2013AA102504), National Natural Science Foundation of China (31872330, 31802041), earmarked fund for Modern Agro-industry Technology Research System (CARS-36), and the Program for Changjiang Scholar and Innovation Research Team in University (IRT_15R62).

Availability of data and materials

All relevant data are available within the article and its supplementary information.

Ethics Approval and consent to participate

All protocols for collection of the samples of experimental individuals and phenotypic observations were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) at China Agricultural University (Permit Number: DK996). Milk, blood and semen samples were collected specifically for this study following standard procedures with the full agreement of the Beijing Sanyuanlvhe Dairy Farming Center who owned the Holstein cows and bulls, respectively.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Table 1 Information of 17 SNPs of AGPAT3 gene with genotypic and allelic frequencies

SNP name	Location	Position (UMD 3.1.1)	Gen Bank no.	Origin	Genotypes	NO.	Frequency	Allele	Frequency
g. 146702957G>A	5' flanking region	Chr1: 146702957	rs210638665	NCBI	AA	78	0.0741	A	0.2692
					GG	564	0.5356	G	0.7308
					GA	411	0.3903
g. 146704373A>G	5' flanking region	Chr1: 146704373	rs209442459	NCBI	AA	560	0.5369	A	0.7311
					GG	78	0.0748	G	0.2689
					GA	405	0.3883
g. 146704618A>G	5' flanking region	Chr1: 146704618	rs110551271	NCBI	AA	520	0.4910	A	0.7030
					GG	90	0.0850	G	0.2970
					GA	449	0.4240
g. 146704699G>A	5' flanking region	Chr1: 146704699	rs110278717	NCBI	AA	113	0.1076	A	0.3219
					GG	487	0.4638	G	0.6781
					GA	450	0.4286
g. 146705692G>A	5' UTR	Chr1: 146705692	rs43281404	NCBI	AA	10	0.0095	A	0.1360
					GG	778	0.7374	G	0.8640
					AG	267	0.2531
g. 146725085T>C	Intron-5	Chr1: 146725085	rs110897007	NCBI	GG	634	0.6021	G	0.7835
					TT	37	0.0351	T	0.2165
					GT	382	0.3628
g. 146726096A>G	Intron-6	Chr1: 146726096	rs378285374	NCBI	CC	380	0.3647	C	0.6027
					TT	166	0.1593	T	0.3973
					CT	496	0.4760
g. 146729107A>C	Intron-7	Chr1: 146729107	rs43276015	NCBI	AA	166	0.1582	A	0.3990
					GG	378	0.3603	G	0.6010
					GA	505	0.4814
g. 146735090G>T	3' UTR	Chr1:146735090	rs379405887	NCBI	CC	169	0.1608	C	0.4015
					TT	376	0.3578	T	0.5985
					CT	506	0.4814
g. 146737188C>T	3' flanking region	Chr1: 146737188	rs383583298	NCBI	CC	376	0.3588	C	0.6007
					TT	165	0.1574	T	0.3993
					CT	507	0.4838
g. 146737545G>A	3' flanking region	Chr1: 146737545	rs43766238	NCBI	GG	166	0.1587	G	0.3991
					TT	377	0.3604	T	0.6009
					GT	503	0.4809
g. 146737748T>C	3' flanking region	Chr1: 146737748	rs43760756	NCBI	CC	169	0.1608	C	0.4015
					TT	376	0.3578	T	0.5985
					TC	506	0.4814
g. 146737849C>T	3' flanking region	Chr1: 146737849	rs43760757	NCBI	CC	371	0.3540	C	0.5973
					TT	167	0.1594	T	0.4027
					CT	510	0.4866
g. 146737879T>G	3' flanking region	Chr1: 146737879	rs43760758	NCBI	AA	12	0.0114	A	0.1360
					GG	780	0.7393	G	0.8640
					AG	263	0.2493
g. 146737916T>C	3' flanking region	Chr1: 146737916	rs43760759	NCBI	CC	536	0.5174	C	0.7210
					TT	78	0.0753	T	0.2790
					TC	422	0.4073
g. 146737946C>T	3' flanking region	Chr1: 146737946	rs43760760	NCBI	AA	894	0.8442	A	0.9193
					GG	6	0.0057	G	0.0807
					AG	159	0.1501
g. 146738055G>A	3' flanking region	Chr1: 146738055	rs382304348	NCBI	AA	208	0.2006	A	0.4619
					CC	287	0.2768	C	0.5380
					CA	542	0.5227

Note: NO.: Number of cows with corresponding genotypes. UTR: untranslated region.

Table 2 Association between 17 SNPs and milk fatty acid traits in Chinese Holstein cows (LSM±SE)

SNP

Genotype (No.)

C6:0 (%)

C8:0 (%)

C10:0 (%)

C11:0 (%)

C12:0 (%)

C13:0 (%)

C14:0 (%)

C14:1 (%)

C15:0 (%)

C16:0 (%)

C16:1 (%)

C17:0 (%)

g. 146702957G>A

AA（66-73）

0.5840±0.0204^A

0.9946±0.0175^A

2.8618±0.0492

0.0583±0.0048

3.0058±0.0652

0.0977±0.0055

10.1091±0.1114^a

0.6665±0.0323

0.9937±0.0219

34.7663±0.3048

1.3640±0.0417

0.5631±0.0055

GG（473-509）

0.4264±0.0119^B

0.9187±0.0106^B

2.8278±0.0319

0.0584±0.0034

3.0015±0.0410

0.1003±0.0029

10.2460±0.0695

0.6475±0.0178

0.9909±0.0120

34.8480±0.1750

1.3327±0.0247

0.5693±0.0031

GA（337-367）

0.5226±0.0125^C

0.9914±0.0111^A

2.8646±0.0330

0.0586±0.0035

3.0068±0.0425

0.0985±0.0030

10.3670±0.0713^b

0.6730±0.0189

0.9968±0.0128

34.8295±0.1822

1.3238±0.0255

0.5653±0.0032

<.0001^**

0.2626

0.9962

0.9854

0.7895

0.0095^**

0.2843

0.8721

0.9581

0.5783

0.2642

g. 146704373A>G

AA（470-505）

0.4101±0.0120^A

0.8829±0.0106^A

2.8096±0.0318

0.0579±0.0035

3.0240±0.0410

0.0997±0.0028

10.2422±0.0699

0.6411±0.0179

0.9906±0.0121

34.8165±0.1762

1.3326±0.0246

0.5696±0.0031

GG（66-73）

0.5641±0.0205^B

0.9368±0.0173^B

2.8117±0.0499

0.0571±0.0047

3.0067±0.0652

0.0967±0.0055

10.1221±0.1115

0.6567±0.0324

0.9887±0.0222

34.8297±0.2999

1.3626±0.0423

0.5643±0.0055

GA（332-361）

0.5002±0.0127^C

0.9533±0.0111

2.8525±0.0334

0.0574±0.0036

3.0271±0.0429

0.0975±0.0030

10.3515±0.0717

0.6651±0.0190

0.9959±0.0129

34.8408±0.1846

1.3192±0.0260

0.5641±0.0033

<.0001^**

0.1676

0.9561

0.9398

0.7032

0.0261^*

0.3318

0.8781

0.9871

0.5151

0.1370

g. 146704618A>G

AA（437-474）

0.4167±0.0121^A

0.9070±0.0107^A

2.8322±0.0323^A

0.0579±0.0035

3.0223±0.0414

0.0998±0.0029

10.2405±0.0701

0.6421±0.0181

0.9925±0.0122

34.7496±0.1778

1.3183±0.0250

0.5698±0.0031^a

GG（76-84）

0.5594±0.0193^Ba

0.9726±0.0164^B

2.8859±0.0473

0.0582±0.0045

3.0483±0.0612

0.0982±0.0052

10.2407±0.1056

0.6692±0.0300

0.9926±0.0207

34.6202±0.2865

1.3507±0.0398

0.5638±0.0052

GA（368-396）

0.5155±0.0123^Bb

1.0007±0.0109^B

2.9155±0.0324^B

0.0588±0.0035

3.0496±0.0421

0.0997±0.0030

10.3059±0.0708

0.6706±0.0185

0.9956±0.0125

34.8113±0.1797

1.3120±0.0251

0.5621±0.0032^b

<.0001^**

0.0016^**

0.8984

0.6596

0.9495

0.4364

0.1903

0.9604

0.7525

0.5678

0.0212^*

g. 146704699G>A

AA（97-102）

0.4391±0.0173^A

0.9396±0.0151^A

2.8484±0.0435

0.0590±0.0043

3.0193±0.0569

0.0979±0.0047

10.3492±0.0976

0.6572±0.0273

0.9839±0.0189

34.6861±0.2593

1.2832±0.0362

0.5629±0.0048

AG（366-402）

0.4614±0.0125^A

0.9274±0.0108^A

2.8053±0.0325^A

0.0574±0.0035

3.0216±0.0421

0.0972±0.0030

10.2789±0.0714

0.6434±0.0185

0.9898±0.0125

34.8492±0.1810

1.3158±0.0253

0.5682±0.0032

GG（412-443）

0.5119±0.0124^B

0.9886±0.0110^B

2.8843±0.0330^B

0.0591±0.0035

3.0363±0.0417

0.1006±0.0030

10.3046±0.0707

0.6607±0.0185

1.0021±0.0126

34.7333±0.1806

1.3390±0.0252

0.5647±0.0032

<.0001^**

0.0040^**

0.6878

0.8808

0.5248

0.6869

0.5672

0.4571

0.6735

0.2175

0.3310

g. 146705692G>A

AA（9）

0.2969±0.0462^A

0.8508±0.0393

2.7974±0.1115

0.0544±0.0099

3.0099±0.1491

0.1107±0.0136

9.8944±0.2514

0.6254±0.0768

0.9965±0.0536

35.1757±0.7126

1.2628±0.0991

0.5820±0.0133

GG（638-690）

0.4844±0.0114^B

0.9413±0.0103

2.7966±0.0307

0.0577±0.0034

3.0048±0.0393

0.0975±0.0026

10.1890±0.0666^A

0.6495±0.0168

0.9888±0.0113

34.8014±0.1658

1.3316±0.0233

0.5665±0.0029

GA（230-250）

0.4644±0.0140^B

0.9309±0.0120

2.8012±0.0361

0.0596±0.0037

3.0349±0.0459

0.1021±0.0035

10.4710±0.0777^B

0.6425±0.0211

1.0037±0.0144

34.8758±0.2043

1.3301±0.0284

0.5663±0.0036

<.0001^**

0.0384^*

0.9829

0.6338

0.6684

0.2420

<.0001^**

0.8836

0.4783

0.7941

0.7785

0.4920

g. 146725085T>C

CC（449-486）

0.4525±0.0121^A

0.9110±0.0108^A

2.8094±0.0324

0.0587±0.0035

2.9767±0.0417

0.0991±0.0029

10.2790±0.0705

0.6482±0.0180

0.9924±0.0123

34.9341±0.1775

1.3135±0.0250

0.5675±0.0031

CT（347-376）

0.5018±0.0126^B

0.9664±0.0111^B

2.8207±0.0336

0.0576±0.0036

2.9839±0.0430

0.0981±0.0030

10.1990±0.0720

0.6559±0.0189

0.9954±0.0129

34.7645±0.1858

1.3526±0.0260

0.5690±0.0033

TT（65-70）

0.4274±0.0202^A

0.9116±0.0170^A

2.8365±0.0487

0.0610±0.0047

3.0082±0.0641

0.1018±0.0054

10.2449±0.1100

0.6607±0.0313

1.0009±0.0216

34.7673±0.2953

1.2804±0.0416

0.5651±0.0054

<.0001^**

0.7754

0.6288

0.8546

0.7757

0.3190

0.8512

0.9063

0.5001

0.0673

0.7081

g. 146726096A>G

AA（740-804）

0.4677±0.0113^A

0.9597±0.0101^A

2.8758±0.0304

0.0578±0.0034

3.0394±0.0390

0.0996±0.0026

10.3084±0.0657^a

0.6553±0.0166

0.9947±0.0111

34.9294±0.1634

1.3251±0.0230

0.5646±0.0028

AG（136-144）

0.4266±0.0157^Bb

0.9216±0.0136^B

2.8526±0.0395

0.0557±0.0040

3.0084±0.0521

0.0974±0.0041

10.1355±0.0879^b

0.6513±0.0242

0.9798±0.0166

34.4974±0.2316

1.3088±0.0324

0.5732±0.0042

GG（4-5）

0.6162±0.0686^a

0.9142±0.0513

3.0515±0.1473

0.0701±0.0129

3.1630±0.1962

0.0981±0.0180

10.5609±0.3391

0.5784±0.1024

0.9762±0.0715

34.9285±0.9476

1.2342±0.1318

0.5561±0.0178

0.0004^**

0.0015^**

0.3415

0.4269

0.5976

0.8364

0.0314^*

0.7439

0.5894

0.0865

0.6686

0.0541

g. 146729107A>C

AA（166-183）

0.5256±0.0149^Aa

0.9758±0.0127^A

2.8547±0.0375^b

0.0565±0.0039

2.9831±0.0487

0.0988±0.0037

10.1650±0.0823

0.6707±0.0228

0.9933±0.0156

34.7045±0.2154

1.3271±0.0304

0.5650±0.0039

CC（240-260）

0.4039±0.0138^B

0.8846±0.0119^B

2.7656±0.0356^Aa

0.0564±0.0037

2.9740±0.0458

0.0988±0.0034

10.2943±0.0782

0.6559±0.0207

0.9904±0.0142

34.7739±0.2011

1.3319±0.0282

0.5718±0.0036^a

CA（461-492）

0.4901±0.0121^Ab

0.9650±0.0108^A

2.8525±0.0323^B

0.0587±0.0035

3.0187±0.0413

0.0984±0.0029

10.2937±0.0696

0.6552±0.0180

0.9991±0.0121

34.8408±0.1767

1.3357±0.0247

0.5640±0.0031^b

<.0001^**

0.0020^**

0.5029

0.3680

0.9905

0.1253

0.7282

0.7714

0.7516

0.9431

0.0413^*

g. 146735090G>T

GG（524-568）

0.4596±0.0118^A

0.9428±0.0105

2.8328±0.0315

0.0589±0.0034

3.0735±0.0404

0.1001±0.0027

10.3081±0.0686

0.6514±0.0176

0.9965±0.0118

34.8202±0.1713

1.3414±0.0240

0.5697±0.0030

GT（326-349）

0.4480±0.0127^A

0.9288±0.0113^A

2.8230±0.0334

0.0576±0.0036

3.0090±0.0430

0.0974±0.0031

10.1970±0.0723

0.6592±0.0190

0.9898±0.0129

34.7381±0.1858

1.3009±0.0260

0.5673±0.0033

TT（26-31）

0.7225±0.0295^B

0.9944±0.0233^B

2.9134±0.0675

0.0537±0.0061

3.0448±0.0882

0.0929±0.0078

10.0790±0.1526

0.6209±0.0446

0.9771±0.0317

34.5408±0.4264

1.3066±0.0590

0.5726±0.0078

<.0001^**

0.0069^**

0.3563

0.5402

0.1107

0.4694

0.0477^*

0.6492

0.7195

0.7122

0.1367

0.5951

g. 146737188C>T

CC（317-344）

0.5244±0.0129^A

0.9949±0.0113^A

2.8918±0.0339^Aa

0.0589±0.0036

3.0228±0.0438

0.0999±0.0031

10.1935±0.0741

0.6581±0.0194

0.9988±0.0132

34.7063±0.1890

1.3351±0.0264

0.5678±0.0034

CT（413-448）

0.4912±0.0123^B

0.9489±0.0106^B

2.8306±0.0323^b

0.0585±0.0035

3.0423±0.0413

0.0981±0.0029

10.2310±0.0697

0.6511±0.0179

0.9955±0.0122

34.8170±0.1770

1.3330±0.0248

0.5697±0.0031

TT（137-148）

0.4013±0.0157^C

0.9270±0.0135^B

2.7818±0.0397^B

0.0579±0.0040

2.9847±0.0514

0.0968±0.0040

10.0919±0.0876

0.6586±0.0242

0.9790±0.0166

34.6458±0.2300

1.3487±0.0321

0.5753±0.0042

<.0001^**

0.0020^**

0.9407

0.3982

0.7234

0.1655

0.8950

0.4650

0.6289

0.8567

0.1793

g. 146737545G>A

AA（137-148）

0.4117±0.0157^A

0.9200±0.0135^Aa

2.8094±0.0396^a

0.0565±0.0040

2.9638±0.0514

0.0975±0.0040

10.1601±0.0876

0.6582±0.0241

0.9801±0.0166

34.5818±0.2305

1.3322±0.0322

0.5706±0.0042

GG（316-343）

0.5261±0.0130^B

0.9867±0.0113^B

2.9008±0.0339^b

0.0584±0.0036

3.0218±0.0435

0.1007±0.0031

10.2857±0.0729

0.6558±0.0194

1.0007±0.0132

34.6776±0.1877

1.3318±0.0263

0.5654±0.0033

GA（419-455）

0.5097±0.0121^B

0.9491±0.0107^Ab

2.8496±0.0319

0.0576±0.0035

3.0188±0.0412

0.0982±0.0029

10.3073±0.0697

0.6492±0.0179

0.9951±0.0122

34.8114±0.1754

1.3239±0.0247

0.5665±0.0031

<.0001^**

0.0134^*

0.7932

0.3853

0.6416

0.1234

0.8841

0.4545

0.4569

0.9184

0.4321

g. 146737748T>C

CC（139-151）

0.3955±0.0156^A

0.9086±0.0134^Aa

2.8149±0.0393^A

0.0575±0.0040

2.9404±0.0514

0.0977±0.0040

10.1822±0.0867

0.6542±0.0240

0.9773±0.0165

34.6990±0.2295

1.3348±0.0317

0.5735±0.0041

CT（420-455）

0.4892±0.0121^Ba

0.9386±0.0107^Ab

2.8760±0.0323

0.0583±0.0035

3.0032±0.0410

0.0994±0.0028

10.3018±0.0699

0.6476±0.0179

0.9927±0.0122

34.8666±0.1762

1.3342±0.0246

0.5674±0.0031

TT（314-341）

0.5161±0.0130^Bb

0.9793±0.0113^B

2.9154±0.0336^B

0.0585±0.0036

2.9957±0.0439

0.1015±0.0031

10.2819±0.0737

0.6574±0.0194

0.9975±0.0131

34.7461±0.1888

1.3359±0.0267

0.5663±0.0034

<.0001^**

0.0106^*

0.9369

0.3252

0.6124

0.2573

0.8346

0.4587

0.6140

0.9969

0.1867

g. 146737849C>T

CC（313-340）

0.5257±0.0130^Aa

0.9965±0.0114^A

2.8975±0.0338^Aa

0.0593±0.0036

2.9970±0.0438

0.1005±0.0031

10.2313±0.0740

0.6588±0.0194

0.9977±0.0133

34.6572±0.1886

1.3386±0.0265

0.5673±0.0034

CT（421-457）

0.4959±0.0121^Ab

0.9498±0.0106^B

2.8322±0.0324^b

0.0586±0.0035

3.0009±0.0410

0.0980±0.0029

10.2479±0.06960

0.6471±0.0178

0.9947±0.0122

34.8335±0.1766

1.3318±0.0246

0.5693±0.0031

TT（136-147）

0.4106±0.0157^B

0.9285±0.0134^B

2.7934±0.0392^B

0.0579±0.0040

2.9274±0.0518

0.0968±0.0040

10.1267±0.0874

0.6600±0.0243

0.9804±0.0166

34.6245±0.2293

1.3495±0.0323

0.5746±0.0042

<.0001^**

0.0022^**

0.8856

0.2126

0.6079

0.2572

0.7288

0.5650

0.4155

0.8199

0.2053

g. 146737879T>G

GG（137-148）

0.4117±0.0158^A

0.9053±0.0135^Aa

2.7827±0.0399^A

0.0575±0.0040

2.9852±0.0514

0.0962±0.0040

10.1224±0.0876

0.6588±0.0239

0.9809±0.0167

34.7225±0.2283

1.3232±0.0319

0.5739±0.0042

GT（416-452）

0.5013±0.0121^B

0.9359±0.0107^Ab

2.8248±0.0323^a

0.0589±0.0035

3.0364±0.0412

0.0977±0.0029

10.2698±0.0696

0.6513±0.0178

0.9975±0.0122

34.8734±0.1770

1.3154±0.0246

0.5663±0.0031

TT（314-341）

0.5384±0.0130^C

0.9831±0.0113^B

2.8914±0.0337^Bb

0.0596±0.0036

3.0380±0.0437

0.0998±0.0031

10.2327±0.0735

0.6594±0.0194

1.0019±0.0132

34.7756±0.1892

1.3229±0.0266

0.5655±0.0034

<.0001^**

0.0017^**

0.7680

0.4448

0.6531

0.1295

0.8731

0.4325

0.6984

0.9269

0.0919

g. 146737916T>C

CC（139-151）

0.3909±0.0155^A

0.9080±0.0133^A

2.8087±0.0392^a

0.0572±0.0040

2.9481±0.0512

0.0969±0.0040

10.2239±0.0870

0.6547±0.0239

0.9769±0.0165

34.6490±0.2278

1.3256±0.0320

0.5741±0.0042

TT（315-342）

0.5185±0.0129^B

0.9891±0.0113^B

2.9066±0.0338^b

0.0582±0.0036

3.0094±0.0435

0.1009±0.0031

10.2947±0.0734

0.6549±0.0194

0.9981±0.0131

34.7363±0.1881

1.3300±0.0266

0.5672±0.0033

CT（419-454）

0.4963±0.0122^B

0.9291±0.0107^A

2.8552±0.0320

0.0580±0.0035

3.0156±0.0411

0.0983±0.0029

10.3252±0.0696

0.6464±0.0180

0.9921±0.0122

34.7903±0.1759

1.3212±0.0246

0.5683±0.0031

<.0001^**

0.0088^**

0.9406

0.2742

0.5637

0.3730

0.8589

0.4280

0.7790

0.9201

0.2206

g. 146737946C>T

CC（309-336）

0.5219±0.0130^A

1.0049±0.0113^A

2.8350±0.0341^a

0.0588±0.0036

2.9994±0.0439

0.1004±0.0032

10.2241±0.0738

0.6597±0.0193

1.0016±0.0134

34.7602±0.1890

1.3334±0.0264

0.5630±0.0034

TT（138-149）

0.4155±0.0156^B

0.9113±0.0135^B

2.7486±0.0392^b

0.0575±0.0040

2.9507±0.0512

0.0968±0.0040

10.1050±0.0876

0.6572±0.0242

0.9796±0.0165

34.6590±0.2300

1.3427±0.0324

0.5682±0.0042

CT（424-460）

0.4999±0.0122^A

0.9464±0.0106^C

2.7811±0.0319

0.0582±0.0035

3.0044±0.0411

0.0981±0.0029

10.2450±0.0689

0.6447±0.0179

0.9973±0.0121

34.8888±0.1760

1.3304±0.0247

0.5650±0.0031

<.0001^**

0.0151^*

0.8961

0.4414

0.6268

0.1510

0.6382

0.3945

0.4662

0.9099

0.4202

g. 146738055G>A

AA（10-12）

0.6010±0.0459^A

1.0161±0.0354

2.8684±0.1023

0.0479±0.0090

3.0416±0.1363

0.0976±0.0122

10.3654±0.2293

0.6569±0.0695

0.9913±0.0486

35.1841±0.6782

1.3472±0.0940

0.5674±0.0122

AG（218-237）

0.5257±0.0138^A

0.9751±0.0122^A

2.7914±0.0360

0.0584±0.0037

2.9691±0.0461

0.0968±0.0035

10.1430±0.0783

0.6599±0.0210

0.9892±0.0144

34.7921±0.2040

1.3007±0.0284

0.5638±0.0036

GG（650-700）

0.4368±0.0115^B

0.9454±0.0102^B

2.8074±0.0310

0.0592±0.0034

3.0454±0.0394

0.1003±0.0026

10.2445±0.0669

0.6563±0.0169

0.9931±0.0115

34.7389±0.1667

1.3298±0.0234

0.5711±0.0029

<.0001^**

0.0010^**

0.6593

0.3930

0.0792

0.5412

0.1855

0.9801

0.9508

0.7698

0.4293

0.0622

SNP

Genotype (No.)

C17:1 (%)

C18:0 (%)

C18:1cis-9 (%)

C18index (%)

C20:0 (%)

C14index (%)

C16index (%)

C17index (%)

SFA (%)

UFA (%)

SFA/UFA (%)

Total index (%)

g. 146702957G>A

AA（62-73）

0.1943±0.0042

13.8892±0.1615

19.1043±0.2147

57.6323±0.4830

0.1666±0.0031

6.4077±0.2370

3.7684±0.1055

25.6833±0.3643

67.7650±0.2901

30.4810±0.2651

2.2673±0.0383

27.6986±0.2400

GG（424-511）

0.1895±0.0024

14.1758±0.0849

19.1790±0.1155

57.3457±0.2687

0.1722±0.0017^A

6.1345±0.1378

3.6753±0.0635

24.9133±0.2143

67.8726±0.1595

30.4841±0.1442

2.2689±0.0209

27.6651±0.1408^a

GA（395-367）

0.1894±0.0026

14.0807±0.0916

18.9544±0.1220

56.9727±0.2812

0.1656±0.0018^B

6.3010±0.1449

3.6562±0.0658

24.9476±0.2258

68.0908±0.1672

30.1838±0.1525

2.2946±0.0221

27.3392±0.1492^b

0.4386

0.1580

0.1290

0.1783

0.0001^**

0.2470

0.5211

0.0648

0.2479

0.0767

0.3992

0.0137^*

g. 146704373A>G

AA（420-507）

0.1913±0.0024

14.1259±0.0853

19.2191±0.1150

57.5363±0.2686

0.1730±0.0017^A

6.0812±0.1397

3.6613±0.0633

24.8788±0.2148

67.8406±0.1588

30.4771±0.1448

2.2695±0.0210

27.5503±0.1427^A

GG（62-73）

0.1968±0.0042

13.8793±0.1644

19.1654±0.2165

57.9715±0.4858

0.1683±0.0030

6.3322±0.2387

3.7324±0.1072

25.6137±0.3613

67.7508±0.2936

30.5383±0.2663

2.2679±0.0387

27.5179±0.2397

GA（290-361）

0.1909±0.0026

13.9943±0.0926

18.9787±0.1240

57.1583±0.2841

0.1660±0.0018^B

6.2187±0.1449

3.6303±0.0667

24.8785±0.2281

68.1000±0.1698

30.1883±0.1544

2.2966±0.0224

27.1837±0.1520^B

0.3096

0.1494

0.0995

0.1186

<.0001^**

0.3517

0.5611

0.0732

0.1635

0.0790

0.3715

0.0065^**

g. 146704618A>G

AA（392-475）

0.1929±0.0025

14.1934±0.0867^a

19.3545±0.1167^a

57.3032±0.2720

0.1721±0.0017^A

6.1572±0.1406

3.6288±0.0640

24.6723±0.2156

67.9068±0.1614

30.5624±0.1480

2.2704±0.0212

27.6612±0.1445^a

GG（69-84）

0.1980±0.0039

13.8955±0.1515

19.2130±0.2015

57.7299±0.4541

0.1661±0.0029

6.3577±0.2214

3.6981±0.1002

25.3871±0.3399

67.7817±0.2744

30.6622±0.2488

2.2769±0.0362

27.7215±0.2257

GA（324-396）

0.1916±0.0025

13.9823±0.0885^b

19.0297±0.1199^b

57.2219±0.2775

0.1668±0.0018^B

6.3184±0.1421

3.6029±0.0647

24.6942±0.2223

68.1314±0.1646

30.2507±0.1491

2.3049±0.0217

27.3551±0.1486^b

0.2123

0.0182^*

0.0137^*

0.4975

0.0024^**

0.3292

0.5736

0.0623

0.2011

0.0386^*

0.2066

0.0173^*

g. 146704699G>A

AA（92-102）

0.1903±0.0036

13.8701±0.1379^b

19.3065±0.1844

57.8611±0.4127

0.1715±0.0025

6.2255±0.2057

3.5700±0.0924

24.3088±0.3144^A

67.8410±0.2477

30.3455±0.2268

2.2693±0.0330

27.7433±0.2080

AG（324-443）

0.1886±0.0025

14.2179±0.0895^Aa

19.1440±0.1202

57.1301±0.2779^a

0.1695±0.0017

6.1203±0.1428

3.6496±0.0646

24.5937±0.2213^A

68.0257±0.1649

30.3321±0.1507

2.2872±0.0217

27.3897±0.1458

GG（365-443）

0.1935±0.0025

13.9484±0.0895^B

19.2363±0.1189

57.7454±0.2775^b

0.1683±0.0017

6.2892±0.1427

3.7083±0.0653

25.1974±0.2243^B

67.8451±0.1655

30.4898±0.1492

2.2789±0.0219

27.6124±0.1479

0.0659

0.0020^**

0.5640

0.0249^*

0.4108

0.3721

0.2267

0.0006^**

0.4504

0.5095

0.8274

0.0692

g. 146705692G>A

AA（7-9）

0.1733±0.0099

14.3208±0.3965

19.6663±0.5313

57.2586±1.1637

0.1951±0.0077^A

6.0520±0.5535

3.4819±0.2506

23.4125±0.8489

68.1513±0.7081

30.5992±0.6477

2.2889±0.0942

27.5978±0.5625

GG（575-694）

0.1888±0.0023

14.1146±0.0794

19.2113±0.1066^A

57.3378±0.2523

0.1706±0.0016^B

6.3397±0.1305

3.6825±0.0560

25.0231±0.2052

67.9010±0.1488

30.4947±0.1354

2.2644±0.0197

27.5684±0.1365^A

GA（200-250）

0.1887±0.0028

14.0965±0.1040

18.8330±0.1399^B

56.9865±0.3164

0.1645±0.0020^C

6.1097±0.1620

3.6635±0.0723

25.0126±0.2497

68.2087±0.1901

30.1774±0.1714

2.2906±0.0251

27.1387±0.1658^B

0.2854

0.8464

0.0042^**

0.4179

<.0001^**

0.1835

0.6902

0.1576

0.159

0.0946

0.4718

0.0034^**

g. 146725085T>C

CC（397-486）

0.1909±0.0025

14.0468±0.0870

19.0157±0.1164

57.2455±0.2729

0.1677±0.0017^A

6.1641±0.1391

3.6277±0.0641

24.8455±0.2162

68.0279±0.1619

30.2848±0.1468

2.2931±0.0213

27.3956±0.1473^a

CT（311-378）

0.1942±0.0026

14.0184±0.0911

19.2591±0.1234

57.6639±0.2843

0.1712±0.0018

6.2935±0.1457

3.7375±0.0663

25.2682±0.2286

67.7874±0.1695

30.5957±0.1552

2.2615±0.0222

27.6832±0.1486^b

TT（58-70）

0.1995±0.0042

14.0374±0.1585

19.4598±0.2118

57.8594±0.4752

0.1768±0.0030^B

6.5092±0.2316

3.5625±0.1057

25.4392±0.3615

67.6933±0.2875

30.6268±0.2630

2.2696±0.0381

27.8078±0.2388

0.0502

0.9442

0.0227^*

0.1449

0.0026^**

0.2133

0.0520

0.0294^*

0.1896

0.0542

0.2723

0.0207^*

g. 146726096A>G

AA（672-805）

0.1894±0.0023^A

14.0391±0.0782^a

19.0281±0.1066^A

57.3355±0.2478

0.169±0.0015^A

6.1731±0.1295

3.6343±0.0594

24.7419±0.1997^A

68.0865±0.1467^A

30.2985±0.1327^Aa

2.2925±0.0193^A

27.4019±0.1349^A

AG（107-145）

0.2020±0.0032^B

14.3151±0.1199^b

19.6764±0.1610^B

57.6605±0.3664

0.1673±0.0024^A

6.3518±0.1821

3.6312±0.0822

25.5638±0.2780^B

67.3379±0.2192^Bb

31.0017±0.1996^B

2.2118±0.0288^Bb

28.0468±0.1811^Bb

GG（4-5）

0.1718±0.0133

14.6475±0.5272

18.4707±0.7012

55.4830±1.5514

0.1989±0.0100^B

5.1590±0.7400

3.3763±0.3321

23.7060±1.1232

70.1075±0.9410^a

28.1258±0.8622^Ab

2.5679±0.1243^a

25.9007±0.7434^a

<.0001^**

0.0246^*

<.0001^**

0.2737

0.0069^**

0.1794

0.7344

0.0011^**

<.0001^**

0.0005^**

<.0001^**

g. 146729107A>C

AA（157-183）

0.1904±0.0031

14.0091±0.1119

19.2419±0.1482

57.4468±0.3385

0.1745±0.0021^A

6.3828±0.1703

3.6593±0.0779

25.1709±0.2648

67.8911±0.2031

30.4868±0.185

2.2755±0.0266

27.7110±0.1753

CC（219-259）

0.1883±0.0028

14.1061±0.1012

19.1574±0.1368

57.4101±0.3144

0.1676±0.0020^C

6.0951±0.1568

3.6834±0.0720

24.7129±0.2420

67.7963±0.1872

30.5267±0.1705

2.2672±0.0248

27.5823±0.1642

CA（395-494）

0.1894±0.0025

13.9829±0.0864

19.1133±0.1161

57.5354±0.2712

0.1703±0.0017

6.0679±0.1391

3.6817±0.0634

24.9844±0.2181

67.9785±0.1603

30.3797±0.1454

2.2879±0.0213

27.5050±0.1431

0.7788

0.4157

0.6456

0.8887

0.0072^**

0.0883

0.9350

0.1738

0.5431

0.5871

0.6297

0.3631

g. 146735090G>T

GG（476-569）

0.1922±0.0024

14.0441±0.0833

19.0282±0.1124

57.3698±0.2622

0.1712±0.0016

6.0957±0.1366

3.6985±0.0616

24.8158±0.2105

68.0759±0.1559

30.3923±0.1411

2.2819±0.0204

27.5196±0.1422

GT（284-351）

0.1934±0.0026

14.1213±0.0926

19.0764±0.1241

57.0423±0.2871

0.1697±0.0018

6.2102±0.146

3.6004±0.0664

24.8500±0.2284

67.9829±0.1706

30.3837±0.1551

2.2809±0.0226

27.4330±0.1490

TT（20-31）

0.1984±0.0058

14.3172±0.2303

18.8872±0.3054

56.3973±0.6774

0.1786±0.0049

6.0045±0.3251

3.6534±0.1493

24.9340±0.5123

68.2537±0.4099

30.2155±0.3762

2.3215±0.0547

27.2316±0.3293

0.4841

0.3646

0.7827

0.1741

0.1494

0.5571

0.1695

0.9587

0.7056

0.8890

0.7477

0.5447

g. 146737188C>T

CC（284-344）

0.1937±0.0026^b

14.0802±0.0941

19.0166±0.1268

57.2315±0.2934

0.1716±0.0018

6.1741±0.1492

3.6909±0.0677

25.3794±0.2296

68.0396±0.1746

30.3617±0.1578

2.2880±0.0228

27.4624±0.1555

CT（361-448）

0.1877±0.0025^Aa

14.1547±0.0872

18.9851±0.1163

57.0650±0.2710

0.1689±0.0017

6.1248±0.1392

3.6688±0.0638

24.9450±0.2165

68.0867±0.1608

30.2470±0.1460

2.2958±0.0214

27.4299±0.1436^a

TT（127-148）

0.1961±0.0032^B

14.1171±0.1204

19.3227±0.1595

57.5732±0.3627

0.1687±0.0022

6.1684±0.1817

3.7299±0.0820

25.2577±0.2793

67.6431±0.2173

30.6818±0.1987

2.2482±0.0291

27.8433±0.1864^b

0.0017^**

0.6908

0.0814

0.3152

0.1887

0.9103

0.6926

0.0529

0.0888

0.0682

0.2209

0.0318^*

g. 146737545G>A

AA（128-148）

0.1945±0.0032^a

14.0514±0.1204

19.4701±0.1601

57.9106±0.3655

0.1696±0.0023

6.2266±0.1817

3.6997±0.0817

24.9182±0.2810

67.4893±0.2187^a

30.7602±0.1992

2.2208±0.0288

27.9350±0.1870^a

GG（283-343）

0.1931±0.0026^A

14.0176±0.0944

19.1472±0.1258

57.4943±0.2900

0.1711±0.0018

6.2523±0.1485

3.6694±0.0677

25.0728±0.2302

67.9662±0.1728

30.3993±0.1579

2.2747±0.0230

27.5125±0.1534^b

GA（368-455）

0.1866±0.0025^Bb

14.0964±0.0863

19.1421±0.1158

57.3574±0.268

0.1686±0.0017

6.1186±0.1391

3.6470±0.0635

24.6877±0.2175

68.0117±0.1589^b

30.3193±0.1449

2.2817±0.0210

27.5136±0.1426^b

0.0017^**

0.6564

0.0816

0.2603

0.3128

0.5090

0.7494

0.1064

0.0334^*

0.0622

0.0756

0.0232^*

g. 146737748T>C

CC（130-151）

0.1979±0.0032^a

14.0913±0.1188

19.3639±0.1597

57.7773±0.3626

0.1711±0.0022

6.2361±0.1823

3.6841±0.0805

24.9868±0.2789

67.5538±0.2170

30.6795±0.1968

2.2365±0.0285

27.8452±0.1856^a

CT（366-455）

0.1899±0.0025^b

14.0907±0.0871

19.0535±0.1157

57.2339±0.2677

0.1698±0.0017

6.1569±0.1387

3.6787±0.0634

24.8028±0.2166

68.0054±0.1596

30.2417±0.1456

2.2852±0.0211

27.4570±0.1426^b

TT（281-341）

0.1954±0.0026^a

14.0418±0.0941

19.0741±0.1267

57.2531±0.2940

0.1725±0.0018

6.2670±0.1472

3.6871±0.0681

25.1846±0.2305

68.0076±0.1746

30.3295±0.1583

2.2865±0.0230

27.4242±0.1548^b

0.0043^**

0.8370

0.1110

0.2416

0.2563

0.6416

0.9876

0.1187

0.0646

0.0634

0.1604

0.0294^*

g. 146737849C>T

CC（280-340）

0.1942±0.0026^b

14.0479±0.0944

19.0461±0.1275

57.2827±0.2941

0.1715±0.0018

6.2705±0.1497

3.6784±0.0679

25.2872±0.2299^a

68.0036±0.1752

30.2563±0.1585

2.2749±0.0231

27.3959±0.1549

CT（369-458）

0.1884±0.0025^Aa

14.1343±0.0867

19.0311±0.1157

57.1311±0.2686

0.1692±0.0017

6.1599±0.1381

3.6433±0.0634

24.8370±0.2170^b

68.1156±0.1595^a

30.1612±0.1454

2.2852±0.0211

27.3368±0.1429^a

TT（126-147）

0.1968±0.0032^B

14.1515±0.1209

19.3218±0.1608

57.6388±0.3647

0.1698±0.0023

6.2904±0.1813

3.7417±0.0821

25.1958±0.2806

67.599±0.2189^b

30.5937±0.1985

2.2359±0.0289

27.7909±0.1867^b

0.0022^**

0.5467

0.1496

0.3216

0.3580

0.5645

0.3874

0.0389^*

0.0434^*

0.0724

0.2010

0.0181^*

g. 146737879T>G

GG（127-148）

0.1950±0.0032^A

14.1331±0.1199

19.2864±0.1606

57.5884±0.3617

0.1668±0.0023

6.1986±0.1806

3.6782±0.0813

25.1214±0.2807

67.5294±0.2172

30.6096±0.1983

2.2448±0.0290

27.8407±0.1859^a

GT（363-452）

0.1860±0.0025^B

14.0937±0.0864

18.9996±0.1170

57.1175±0.2712

0.1662±0.0017

6.0816±0.1386

3.6252±0.0634

24.9443±0.2164

67.9798±0.1605

30.2380±0.1464

2.2917±0.0212

27.4284±0.1438^b

TT（281-341）

0.1926±0.0026^A

14.0683±0.0950

18.9898±0.1260

57.2233±0.2916

0.1694±0.0018

6.2251±0.1478

3.6573±0.0683

25.3307±0.2299

67.9566±0.1740

30.2822±0.1578

2.2935±0.0228

27.4250±0.1552^b

0.0007^**

0.8640

0.1380

0.3760

0.1390

0.4621

0.7092

0.1116

0.0763

0.1374

0.1878

0.0258^*

g. 146737916T>C

CC（130-151）

0.1958±0.0031^a

14.0216±0.1184

19.4421±0.1594

57.8855±0.3621

0.1702±0.0023

6.2201±0.1802

3.675±0.0810

25.1146±0.2768

67.5382±0.2176

30.7478±0.1974

2.2388±0.0284

27.8821±0.1855^a

TT（282-342）

0.1941±0.0026^A

13.9730±0.0943

19.1122±0.1261

57.3779±0.2917

0.1720±0.0018

6.2657±0.1487

3.6778±0.0683

25.3034±0.2313

67.9870±0.1741

30.3957±0.1581

2.2897±0.0229

27.4459±0.1536^b

CT（366-454）

0.1876±0.0025^Bb

14.0312±0.0863

19.1531±0.1157

57.3551±0.2685

0.1692±0.0017

6.1427±0.1386

3.6574±0.0634

24.9351±0.2172

67.9939±0.1593

30.3340±0.1453

2.2877±0.0211

27.4913±0.1430^b

0.0014^**

0.7903

0.1021

0.2644

0.2229

0.5851

0.9227

0.1358

0.0673

0.0831

0.1542

0.0260^*

g. 146737946C>T

CC（276-353）

0.1934±0.0026^a

14.0356±0.0944

19.0648±0.1269

57.3541±0.2931

0.1703±0.0018

6.2878±0.1493

3.6822±0.0677

25.2621±0.2307

67.9820±0.1743

30.4044±0.1588

2.2781±0.0231

27.4462±0.1556^b

TT（129-149）

0.1956±0.0032^A

14.0929±0.1198

19.3950±0.1605

57.7406±0.3642

0.1687±0.0022

6.2543±0.1810

3.7333±0.0830

24.8679±0.2786

67.5357±0.2182

30.7658±0.1999

2.2291±0.0290

27.9048±0.1867^Aa

CT（372-460）

0.1872±0.0025^Bb

14.1087±0.0864

19.0634±0.1159

57.2223±0.2683

0.1683±0.0017

6.1445±0.1379

3.6631±0.0633

24.8255±0.2163

68.0108±0.1592

30.3468±0.1450

2.2787±0.0210

27.4151±0.1428^B

0.0015^**

0.6954

0.0742

0.3013

0.4732

0.4699

0.6201

0.0533

0.0567

0.0783

0.1645

0.0073^**

g. 146738055G>A

AA（8-12）

0.2017±0.0090

13.9011±0.3614

18.0083±0.4790

55.7325±1.0632

0.1754±0.0077

5.8460±0.5058

3.6632±0.2374

24.8286±0.8041

69.0285±0.6442

29.7689±0.5866

2.3942±0.0853

26.4994±0.5087^a

AG（195-237）

0.1868±0.0029^a

14.1406±0.1041

18.9628±0.1381

56.8884±0.3155

0.1674±0.0020

6.2627±0.1586

3.5945±0.0726

24.4635±0.2501^a

68.2252±0.1883

30.2599±0.1723

2.2993±0.0251

27.2869±0.1638^b

GG（578-702）

0.1929±0.0023^b

14.1562±0.0803

19.1422±0.1083

57.3907±0.2534

0.1702±0.0016

6.1662±0.1317

3.6781±0.0602

24.9766±0.2047^b

68.0300±0.1500

30.5244±0.1358

2.2729±0.0197

27.5622±0.1357

0.0149^*

0.7729

0.0258^*

0.0632

0.2047

0.5865

0.3532

0.0353^*

0.1638

0.1078

0.1927

0.0146^*

Note: LSM means least square mean. SE means standard error. P indicates the significances of the association analysis between each SNP and milk fatty acid traits. P is the raw value. *: P < 0.05. **: P < 0.01. Different letter (small letters: P < 0.05; capital letters: P < 0.01) superscripts indicate significant differences among the genotypes. The number in the brackets represents the number of cows for the corresponding genotypes.

Table 3 Association between haplotype blocks in AGPAT3 and milk fatty acid traits in Chinese Holstein cows (LSM±SE)

Haplotype block

Haplotype combination (No.)

C6:0 (%)

C8:0 (%)

C10:0 (%)

C11:0 (%)

C12:0 (%)

C13:0 (%)

C14:0 (%)

C14:1 (%)

C15:0 (%)

C16:0 (%)

C16:1 (%)

C17:0 (%)

Block 1

H1H1（121-130）

0.3692±0.0166^A

0.8989±0.0140^ACa

2.7932±0.0413^a

0.0579±0.0041

2.9643±0.0538

0.1020±0.0043

10.1573±0.0917

0.6359±0.0253

0.9978±0.0175

34.9164±0.2400

1.3602±0.0336

0.5739±0.0044

H1H2（218-240）

0.4422±0.0142^B

0.8923±0.0122^Aa

2.7610±0.0367^A

0.0569±0.0038

2.9761±0.0470

0.0983±0.0035

10.2724±0.0804

0.6296±0.0213

0.9938±0.0149

34.8598±0.2082

1.3269±0.0292

0.5767±0.0037

H1H3（191-204）

0.5563±0.0146^C

1.0162±0.0128^Bb

2.9065±0.0373^Bb

0.0596±0.0039

3.0334±0.0487

0.1005±0.0037

10.3997±0.0839^a

0.6786±0.0225

1.0068±0.0153

34.7483±0.2175

1.3176±0.0303

0.5656±0.0039

H2H2（98-103）

0.4381±0.0175^B

0.9044±0.0152^ACDac

2.8120±0.0436

0.0594±0.0043

2.9978±0.0575

0.0987±0.0046

10.3001±0.0986

0.6575±0.0274

0.9853±0.0190

34.7264±0.2591

1.2820±0.0363

0.5686±0.0048

H2H3（136-150）

0.4610±0.0157^B

0.9441±0.0134^CDcd

2.7551±0.0400^A

0.0575±0.0040

2.9299±0.0521

0.0956±0.0041

10.1961±0.0869

0.6483±0.0243

0.9835±0.0166

35.0655±0.2324

1.3081±0.0326

0.5694±0.0042

H3H3（66-72）

0.5532±0.0206^C

0.9642±0.0177^BDd

2.8116±0.0513

0.0597±0.0048

3.0030±0.0657

0.0978±0.0056

10.0632±0.1132^b

0.6629±0.0329

0.9895±0.0227

34.8421±0.3116

1.3749±0.0428

0.5689±0.0056

<.0001**

0.0001**

0.9269

0.4138

0.8544

0.0105*

0.3696

0.8195

0.8036

0.3084

0.0962

Block 2

H1H2（126-139）

0.5694±0.0167^Aa

0.9932±0.0145^Aa

2.8297±0.0425^a

0.0580±0.0042

3.0485±0.0549

0.0962±0.0043

10.1137±0.0946

0.6361±0.0253

0.9918±0.0176

34.9810±0.2481

1.3447±0.0344

0.5703±0.0045

H1H3（56-62）

0.6103±0.0213^Da

1.0604±0.0180^B

2.8139±0.0519

0.0575±0.0050

2.9637±0.0688

0.0984±0.0057

9.9868±0.1182

0.6793±0.0335

0.9893±0.0231

34.7801±0.3163

1.3754±0.0439

0.5671±0.0058

H1H4（52-55）

0.4357±0.0224^Bbc

0.9280±0.0192^ACd

2.8422±0.0552

0.0631±0.0053

3.0676±0.0718

0.1029±0.0061

10.3528±0.1232

0.6664±0.0353

1.0077±0.0243

34.2739±0.3353

1.4103±0.0465

0.5652±0.0062

H2H2（138-149）

0.3787±0.0166^Cbe

0.8735±0.0140^Cde

2.7289±0.0417

0.0579±0.0042

2.9456±0.0546

0.0967±0.0042

10.0997±0.0927

0.6586±0.0250

0.9760±0.0171

34.7218±0.2397

1.3455±0.0335

0.5744±0.0043

H2H3（95-102）

0.5078±0.0181^Ac

0.8930±0.0155^Cbd

2.6966±0.0455

0.0611±0.0045

2.9215±0.0594

0.0950±0.0048

10.0970±0.1008

0.6550±0.0283

0.9821±0.0192

35.2877±0.2714

1.3358±0.0376

0.5593±0.0049

H2H4（96-107）

0.4629±0.0187^Fc

0.8165±0.0155^Dc

2.6801±0.0452^b

0.0580±0.0045

2.9780±0.0594

0.1005±0.0048

10.3642±0.1024

0.6403±0.0284

0.9990±0.0193

34.9866±0.2709

1.3292±0.0373

0.5769±0.0048

H2H5（63-68）

0.3384±0.0204^Ede

0.8526±0.0179^Cbce

2.7312±0.0510

0.0575±0.0049

2.9783±0.0671

0.0982±0.0056

10.0688±0.1129

0.6521±0.0319

0.9807±0.0223

34.6563±0.3081

1.4043±0.0426

0.5783±0.0056

<.0001**

0.0013**

0.8887

0.2555

0.9225

0.0127*

0.9124

0.8845

0.1205

0.4760

0.0193*

Haplotype block

Haplotype combination (No.)

C17:1 (%)

C18:0 (%)

C18:1cis-9 (%)

C18index (%)

C20:0 (%)

C14index (%)

C16index (%)

C17index (%)

SFA (%)

UFA (%)

SFA/UFA (%)

Total index (%)

Block 1

H1H1（105-130）

0.1992±0.0034

14.1901±0.1259

19.3463±0.1683

57.4699±0.3816

0.1791±0.0025^Aad

6.0996±0.1885

3.7792±0.0860

25.0181±0.2938

67.7674±0.2297

30.6829±0.2089

2.2565±0.0304

27.6878±0.1931^a

H1H2（193-241）

0.1904±0.0029

14.3563±0.1050^a

19.1954±0.1414

56.9474±0.3225

0.1710±0.0020^ABc

5.9684±0.1634

3.6878±0.0747

24.6437±0.2483

67.9734±0.1925

30.4159±0.1766

2.2675±0.0255

27.5081±0.1649

H1H3（167-204）

0.1926±0.0030

13.9560±0.1103^b

19.0385±0.1501

57.3701±0.3377

0.1635±0.0022^Bb

6.3161±0.1697

3.6750±0.0774

24.9275±0.2620

68.0604±0.2014

30.1895±0.1868

2.2838±0.0269

27.4224±0.1743

H2H2（93-103）

0.1912±0.0036

14.0036±0.1391

19.2225±0.1833

57.5431±0.4143

0.1731±0.0025^Aac

6.1465±0.2072

3.5740±0.0928

24.2275±0.3182^a

67.9786±0.2486

30.3912±0.2271

2.2608±0.0330

27.6407±0.2079

H2H3（119-150）

0.1922±0.0032

14.2354±0.1206

18.8881±0.1604

56.5368±0.3665

0.1697±0.0023^Abc

6.0705±0.1814

3.6158±0.0830

24.3598±0.2842^a

68.2035±0.2194

30.1933±0.1991

2.2977±0.0289

27.0443±0.1860^b

H3H3（61-72）

0.2002±0.0043

13.8767±0.1663

19.1521±0.2201

57.8332±0.4902

0.1669±0.0031^Bbc

6.3488±0.2396

3.8032±0.1081

25.6261±0.3649^b

67.7284±0.2962

30.6459±0.2693

2.2496±0.0391

27.5612±0.2436

0.0513

0.0051**

0.214

0.0649

<.0001**

0.3560

0.2434

0.0053**

0.5462

0.1757

0.7634

0.0245*

Block 2

H1H2（117-139）

0.1873±0.0034^A

14.1418±0.1267

19.0344±0.1692

57.4628±0.3893

0.1705±0.0024

6.1665±0.1940

3.6796±0.0878

24.8359±0.2983^a

67.9941±0.2332

30.3523±0.2134

2.2848±0.0307

27.5466±0.1948

H1H3（59-62）

0.1908±0.0043

14.0962±0.1695

19.0365±0.2254

57.1552±0.5004

0.1698±0.0030

6.6035±0.2487

3.7758±0.1121

25.4165±0.3779

67.9988±0.3013

30.2962±0.2735

2.2858±0.0404

27.5735±0.2497

H1H4（44-55）

0.1991±0.0046

13.7531±0.1790

19.3446±0.2403

58.2375±0.5405

0.1771±0.0035^A

6.2159±0.2621

3.9414±0.1180

25.5598±0.4005

67.3613±0.3257

30.8744±0.2977

2.2085±0.0432

27.8206±0.2639

H2H2（128-149）

0.1973±0.0034

14.1252±0.1253

19.4270±0.166^a

57.7791±0.3817

0.1679±0.0024

6.2908±0.1912

3.6936±0.0856

25.0985±0.2912

67.4990±0.2285

30.7484±0.2092^a

2.2254±0.0299

27.8762±0.1924^A

H2H3（80-102）

0.1877±0.0037^A

14.0980±0.1432

18.8617±0.1897

56.6882±0.4257

0.1714±0.0028

6.3426±0.2113

3.6030±0.0958

24.7605±0.3257^a

68.2658±0.2556

29.8952±0.2352^b

2.3174±0.0344

27.0508±0.2145^B

H2H4（88-107）

0.1877±0.0038^a

14.3357±0.1411

18.7635±0.1887^b

56.6694±0.4235

0.1622±0.0028^B

6.0775±0.2131

3.6211±0.0957

24.6392±0.3234^a

68.1996±0.2544

30.0572±0.2341

2.3011±0.0339

27.0983±0.2132^Ca

H2H5（50-69）

0.2051±0.0042^Bb

14.3662±0.1625

19.5612±0.2164^a

57.5823±0.4896

0.1644±0.0033

6.1397±0.2402

3.8763±0.1080

25.9925±0.368^b

67.4171±0.2947

30.8806±0.2665^a

2.2230±0.0391

28.0083±0.2341^ACb

<.0001**

0.0798

0.0036**

0.0345*

0.0020**

0.5789

0.0498*

0.0075**

0.0096**

0.0015**

0.0574

0.0001**

Note: LSM means least square mean. SE means standard error. P indicates the significances of the association analysis between the haplotype block and milk fatty acid traits. P is the raw value. ^*: P < 0.05. ^**: P < 0.01. Different letter (small letters: P < 0.05; capital letters: P < 0.01) superscripts indicate significant differences among the haplotype combinations. The number in the brackets represents the number of cows for the corresponding haplotype combination.

Table 4 Changes of transcription factor binding site (TFBS) caused by the SNP in the 5′untranslated (UTR) and flanking regions of AGPAT3

SNP	Sequence	Ttranscription factor	Name
g.146702957G>A	TCCCTGTGCCGTTTCCACTGA	VMYB	v-Myb, variant of AMV v-myb
	TCCCTGTGCCATTTCCACTGA	SMARCA3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3
	TCCCTGTGCCATTTCCACTGA	REX1	REX1 transcription factor; zinc finger protein 42
g.146704373A>G	CACGGGAAGTAGGTGTGCAGT	BRACH	Brachyury
g.146704373A>G	CACGGGAAGTGGGTGTGCAGT	NKX26	NK2 homeobox 6, Csx2
g.146704618A>G	CTCTTCCACCACCCTGGACAG
	CTCTTCCACCGCCCTGGACAG	ZBED4	Zinc finger, BED-type containing 4; GC-box binding sites
	CTCTTCCACCGCCCTGGACAG	SP1	Stimulating protein 1, ubiquitous zinc finger transcription factor
g.146704699G>A	AATGGGAAACGTGACAGGATT	USF1	Upstream stimulating factor 1
	AATGGGAAACGTGACAGGATT	ARNT	AhR nuclear translocator homodimers
	AATGGGAAACATGACAGGATT	FOXA1	Forkhead box protein A1, hepatocyte nuclear factor 3-alpha (HNF-3-alpha)

Note: The SNPs in sequences are highlighted in red.

TableS1.xlsx
Table S1 PCR primers information of AGPAT3 gene
TableS2.xlsx
Table S2 Additive (a), dominant (d) and allele substitution (α) effects of 17 SNPs on milk fatty acid traits of AGPAT3 gene in Chinese Holstein cows

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Journal Publication

published 01 Feb, 2021

Read the published version in Journal of Animal Science and Biotechnology →

Editorial decision: Accept
13 Dec, 2020
Editor assigned by journal
28 Oct, 2020
Submission checks completed at journal
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Editor invited by journal
28 Oct, 2020

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A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

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