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Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population

Contributed equally
BMC GeneticsBMC series – open, inclusive and trusted201718:47

https://doi.org/10.1186/s12863-017-0516-4

Received: 19 December 2016

Accepted: 11 May 2017

Published: 19 May 2017

Abstract

Background

Our previous RNA-sequencing study revealed that the ATF3 and CDKN1A genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population.

Results

By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5’promoter region, two in exons, seven in 3′ un-translated region (UTR), and six in 3’flanking region of ATF3 gene, and one SNP in exon 5, two in 3’UTR, and two in 3’flanking region of CDKN1A gene. Of these, only the SNP, c.271C > T (rs442346530), in exon 5 of CDKN1A gene was predicted to result in an amino acid replacement from arginine to tryptophan. Subsequent genotype-phenotype association analysis revealed that 19 SNPs in ATF3 and 5 SNPs in CDKN1A were evidently associated with 305-days milk yield, fat yield, protein yield, or protein percentage (P = < 0.0001 ~ 0.0494). Whilst, no significant SNPs in ATF3 gene were associated with fat percentage in both first and second lactations (P > 0.05), and only two SNPs of CDKN1A gene, c.271C > T (P = 0.0377) and c.*654C > T (P = 0.0144), were markedly associated with fat percentage in the first lactation. Further, linkage disequilibrium (LD) analyses were conducted among the identified SNPs in ATF3 and/or CDKN1A genes to further confirm the association results. We also observed that the four SNPs, g.72834301C > A, g.72834229C > A, g.72833969A > G, and g.72833562G > T altered the specific transcription factor (TF) binding sites in ATF3 promoter, and one SNP, c.271C > T, changed the CDKN1A protein secondary structure, suggesting they might be the promising potential functional mutations.

Conclusion

Our findings first profiled the genetic effects of ATF3 and CDKN1A genes for milk production traits in dairy cattle and will be available for marker-assisted breeding in dairy cattle.

Keywords

Genetic effects ATF3 CDKN1A Milk production traitsChinese Holstein

Background

Milk production traits are the most important economic traits in dairy development, including milk yield, fat yield, protein yield, fat percentage and protein percentage [1]. As we know, most economic traits of livestock are quantitative traits, caused by minor genes. In the past several decades, quantitative trait locus (QTL) mapping, candidate gene analysis, and genome-wide association study (GWAS) have been used to identify the causal genes or mutations for milk production in dairy cattle [24]. However, only the causative mutations in DGAT1, GHR, and ABCG2 gene, have been confirmed to date [57].

RNA sequencing (RNA-Seq) has become a comprehensive and accurate tool for analyzing the gene expression pattern [8]. Our previous RNA-Seq study has identified 31 differentially expressed genes between the mammary glands of lactating Chinese Holstein cows with the high and low milk protein percentage and fat percentage, of which, 17 genes are located within the known QTL regions for milk protein and fat traits and 21 contain or are near to the significant SNPs identified by previous GWAS, including ATF3 and CDKN1A [9]. The ATF3 gene (chr16: 72,820,025–72,832,974) were 1.9 Mb or 3.3 Mb close to the two SNPs, ARS-BFGL-NGS-70836 (chr16: 74,741,746) associated with milk protein percentage (P < 3.58E-07) and ARS-BFGL-NGS-85980 (chr16: 76,091,078) associated with fat percentage (P < 6.46E-07) and protein percentage (P < 8.33E-09) detected by a previous GWAS in dairy cattle [10]. ATF3 (activating transcription factor 3) is a transcription factor belonging to the mammalian activation transcription factor/cAMP responsive element-binding (CREB) protein family [11]. Our GO and Ingenuity Pathway Analysis (IPA) also found that ATF3 was involved in the lipid metabolism pathway, accumulation of glycoproteins, apoptosis, and regeneration of epithelial cells so that it is thought to be related to milk fat formation and development of mammary epithelial cells [9]. In addition, the CDKN1A gene (chr23: 10,560,498–10,568,780) is located within the known QTL regions (BTA23: 12.4 cM) that were confirmed to have large genetic effects on milk protein percentage [12]. CDKN1A (cyclin dependent kinase inhibitor 1A) encodes a 21-kD protein (p21) that is a cyclin-dependent kinase inhibitor, which is a rate-limiting regulator in the transition from G1 to S phase [13], and is also a key mediator of growth arrest that induced by the tumor suppressor protein p53 [14]. So far, there is no study revealing the associations of ATF3 and CDKN1A genes with milk production in dairy cattle.

Based on our previous RNA-Seq study [9], the purpose of this study was to identify whether ATF3 and CDKN1A genes have a genetic effect on milk production traits in dairy cows. Herein, we detected the SNPs in ATF3 and CDKN1A genes, and analyzed the association between these polymorphisms with five milk production traits in a Chinese Holstein population. In addition, bioinformatics analysis was performed to profile the promoter activity and protein structure variation of ATF3 and CDKN1A genes.

Methods

Animals and phenotypic data

A total of 1093 Chinese Holstein cows from 40 sire families were used in this study, and each sire had between 6 and 70 daughters with approximately 27 daughters on average per sire. These cows were from 22 dairy farms belonging to the Sanyuanlvhe Dairy Farming Center, where standard performance testing for dairy herd improvement (DHI) has been regularly conducted since 1999. Estimate breeding values (EBVs) for 305-days milk yield, fat yield, fat percentage, protein yield, and protein percentage during the first and second lactations were provided by the Beijing Dairy Cattle Center (http://www.bdcc.com.cn/). The descriptive statistics of phenotypic values for dairy production traits in two lactations were shown in Additional file 1. All protocols for sample collections of experimental individuals and phenotypic observations were approved by the Institutional Animal Care and Use Committee (IACUC) at China Agricultural University, and the permit number is DK996.

DNA extraction

The whole blood samples of 1093 Chinese Holstein cows were extracted by TIANamp Blood DNA Kit (Tiangen, Beijing, China) according to the manufacturer’s instructions. The genomic DNA from semen samples of the sires were extracted using the standard salt-out procedures. The quantity and quality of the extracted DNA were respectively measured using a NanoDrop 2000 Spectrophotometer (Thermo Scientific, DE, USA) and by the gel electrophoresis.

SNP identification and genotyping

We designed a total of 35 primers (Additional file 2) using Primer 3.0 (http://primer3.wi.mit.edu/) and Oligo 6.0 (Molecular Biology Insights, Inc., CO, USA) to amplify the entire coding region and 2000 bp of flanking sequences based on the genomic sequence of the bovine ATF3 (GenBank accession no.: AC_000173.1) and CDKN1A (GenBank accession no.: AC_000180.1) genes, and the primers were synthesized by the Beijing Genomics Institute (BGI, Beijing, China). We randomly divided the DNA samples of the 40 sires into two equal groups, and diluted all the DNA samples into the concentration of 50 ng/μL. Subsequently, we constructed two DNA pools (50 ng/mL) as the templates for the PCR amplification. The amplifications were performed using the PCR system or the touch-down PCR (Additional file 2). The purified PCR products were directly sequenced by ABI3730XL DNA analyzer (Applied Biosystems, Foster City, CA, USA), and the sequences were compared by DNAMAN 6.0 (Lynnon Biosoft, USA) and NCBI-BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to search potential SNPs. The identified SNPs were further individually genotyped for all the 1093 Chinese Holstein cows using the matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS, Sequenom MassARRAY, Bioyong Technologies Inc. HK).

Association analyses

Association analyses between SNP genotypes and/or haplotypes and the five milk traits were conducted by SAS 9.13 (SAS Institute Inc., Cary, NC, USA), based on the following animal model:
$$ \mathrm{Y}=\upmu +\mathrm{hys}+\mathrm{b}\times \mathrm{M}+\mathrm{G}+\mathrm{a}+\mathrm{e} $$

where, Y was the phenotypic values of each trait for the cows; μ was the overall mean; hys was the fixed effect of farm, year, and season; b was the regression coefficient of covariant M; M was the fixed effect of calving month; G was the SNP genotype or haplotype effect; a was the individual random additive genetic effect, distributed as \( \mathrm{N}\left(0,\mathrm{A}{\updelta}_a^2\right) \) \( \mathrm{N}\;\left({0,\mathrm{A}\updelta}_{\mathrm{a}}^2\right) \), with the additive genetic variance \( {\updelta}_{\mathrm{a}}^2 \); and e was the random residual, distributed as \( \mathrm{N}\;\left({0,\mathrm{I}\updelta}_{\mathrm{e}}^2\right) \), with identity matrix I and residual error variance \( {\updelta}_{\mathrm{e}}^2 \). Bonferroni correction was performed for multiple testing, and the significant level of the multiple tests was equal to the raw P value divided by number of tests. Currently, we considered the statistically significant association from being null effect if a raw P value is less than 0.05/N, where N represents the number of SNP loci.

We calculated the additive effect (a), dominant effect (d), and substitution effect (α) using SAS 9.13, and the computational formula was as follows: \( \mathrm{a}=\frac{\mathrm{AA}\hbox{-} \mathrm{BB}}{2};\mathrm{d}=\mathrm{AB}\hbox{-} \frac{\mathrm{AA}+\mathrm{BB}}{2};\upalpha =\mathrm{a}+\mathrm{d}\;\left(\mathrm{q}\hbox{-} \mathrm{p}\right) \). Where, AA, BB, and AB were the least squares mean of the milk production traits in the corresponding genotype.

Haplotype analysis

The linkage disequilibrium (LD) extent between all SNPs and haplotype blocks were estimated using Haploview 4.2 (Broad Institute of MIT and Harvard, Cambridge, MA, USA).

Bioinformatics analysis

To analysis the biological functions of the SNPs, we used the JASPAR database (http://jaspar.binf.ku.dk/cgi-bin/jaspar_db.pl?rm=browse&db=core&tax_group=vertebrates) to profile the genetic variants of the transcription factor binding sites (TFBSs) of the SNPs associated with milk production traits in the 5′ promoter region (relative score > 0.85). In addition, we utilized NPSA SOPMA SERVER (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html) to predict the variations of protein secondary structure caused by missense mutation in the coding regions, and the parameters were window width (17), similarity threshold (8), and number of states (4).

Results

SNPs identification

After sequencing the entire coding and up/downstream regions, we totally identified 19 and five SNPs for ATF3 and CDKN1A genes, respectively, and all the identified SNPs have been reported in the NCBI database (Table 1). There were four SNPs in the 5’promoter region, two in exons, seven in the 3’UTR, and six in the 3’flanking region of ATF3 gene. For CDKN1A gene, one SNP, c.271C > T, was located in the exon 5, c.*9C > G and c.*654C > T in the 3’UTR, and g.10569766 T > C and g.10569779 T > C in the 3’flanking region. Of these, only the SNP in exon 5 of CDKN1A gene (c.271C > T) was predicted to result in an amino acid replacement from arginine (CGG) to tryptophan (UGG), and the two SNPs of ATF3 gene in the coding region (c.291G > A and c.489G > A) were synonymous mutations.
Table 1

Information about identified SNPs of ATF3 and CDKN1A genes

Gene

Gene region

SNPs

Position (UMD 3.1)

Allele

Amino acid missence

GenBank no.

Origin

ATF3

5′ promoter region

g.72834301C > A

chr16:72,834,301

C/A

 

rs41634778

NCBI

g.72834229C > A

chr16:72,834,229

C/A

 

rs41634777

NCBI

g.72833969A > G

chr16:72,833,969

A/G

 

rs41823579

NCBI

g.72833562G > T

chr16:72,833,562

G/T

 

rs41823578

NCBI

exon 4

c.291G > A

chr16:72,822,913

G/A

 

rs209694892

NCBI

exon 5

c.489G > A

chr16:72,821,334

G/A

 

rs207598277

NCBI

3’UTR

c.*190A > G

chr16:72,821,087

A/G

 

rs136869959

NCBI

c.*321G > C

chr16:72,820,956

G/C

 

rs135704995

NCBI

c.*326A > G

chr16:72,820,951

A/G

 

rs137084971

NCBI

c.*640G > A

chr16:72,820,637

G/A

 

rs210941907

NCBI

c.*685G > C

chr16:72,820,592

G/C

 

rs209048412

NCBI

c.*735 T > C

chr16:72,820,542

T/C

 

rs210174407

NCBI

c.*1064G > A

chr16:72,820,213

G/A

 

rs211390316

NCBI

3′ flanking region

g.72819977 T > C

chr16:72,819,977

T/C

 

rs208866610

NCBI

g.72819850A > G

chr16:72,819,850

A/G

 

rs211185269

NCBI

g.72818819A > G

chr16:72,818,819

A/G

 

rs41823568

NCBI

g.72818818C > T

chr16:72,818,818

C/T

 

rs41823569

NCBI

g.72818292 T > C

chr16:72,818,292

T/C

 

rs209896483

NCBI

g.72818161 T > C

chr16:72,818,161

T/C

 

rs210138925

NCBI

CDKN1A

exon 5

c.271C > T

chr23:10,565,335

C/T

p.Arg91Trp

rs442346530

NCBI

3’UTR

c.*9C > G

chr23:10,567,031

C/G

 

rs210197882

NCBI

c.*654C > T

chr23:10,567,676

C/T

 

rs110284249

NCBI

3’flanking region

g.10569766 T > C

chr23:10,569,766

T/C

 

rs133659402

NCBI

g.10569779 T > C

chr23:10,569,779

T/C

 

rs110283961

NCBI

In addition, in this study, we performed the pooled sequencing method to identify the allelic variants across the entire coding and regulatory regions of ATF3 and CDKN1A genes, and detected a total of 24 SNPs. However, this method has disadvantage that it may miss rare allelic variants due to sequencing cannot catch the very low fluorescent signal of the alleles with very low frequencies. Further, the allelic frequencies cannot be obtained merely by pooled sequencing, hence, we further genotyped 1093 cows and performed association analysis.

Associates between SNPs and five milk traits

Associations between the total 24 SNPs of ATF3 and CDKN1A genes and five milk production traits were presented in Tables 2 and 3. Using single-SNP association analysis, we found that 14, 16, 16 and 3 SNPs of ATF3 gene were significantly associated with milk yield (P = < 0.0001 ~ 0.031), fat yield (P = 0.0002 ~ 0.0197), protein yield (P = < 0.0001 ~ 0.0331), and protein percentage (P = 0.0108 ~ 0.0494) in the first lactation, respectively. For example, the cows with allele C in g.72834301C > A showed higher milk yield, milk protein yield and fat yield than that with allele A (Table 2 ). Similarly, 13, 14, 11 and 8 SNPs were associated with milk yield (P = < 0.0001 ~ 0.0078), fat yield (P = < 0.0001 ~ 0.0395), protein yield (P = < 0.0001 ~ 0.0461), and protein percentage (P = 0.0003 ~ 0.0371) in the second lactation, respectively (Table 2). Of these, 13 SNPs of ATF3 gene (g.72834301C > A, g.72834229C > A, g.72833969A > G, g.72833562G > T, c.291G > A, c.489G > A, c.*685G > C, c.*1064G > A, g.72819850A > G, g.72818819A > G, g.72818818C > T, g.72818292 T > C, and g.72818161 T > C) were identified significantly associated with at least one milk trait in both the first and second lactations. Four SNP, c.*190A > G, c.*326A > G, c.*640G > A, and g.72819977 T > C, were only found evidently associated with the milk traits in the first lactation, and the other two SNPs, c.*321G > C and c.*735 T > C, were markedly associated with at least one milk trait in the second lactation (Table 2), however, the allelic effects of these six SNPs showed almostly same directions between the first and second lactations although some associations did not reach statistical significance of 0.05 (Table 2). Interestingly, no significant SNPs were associated with fat percentage in both first and second lactations.
Table 2

Associations of 19 SNPs of ATF3 gene with milk production traits in Chinese Holstein cattle during two lactations (LSM ± SE)

SNPs

Lactation

Genotype (No.)

Milk yield (kg)

Fat yield (kg)

Fat percentage (%)

Protein yield (kg)

Protein percentage (%)

g.72834301C > A

1

CC(222)

10,305 ± 73.52a

346.63 ± 3.19Aa

3.37 ± 0.03

306.89 ± 2.32Aa

2.98 ± 0.01

CA(553)

10,339 ± 62Aa

343.59 ± 2.77Aa

3.34 ± 0.026

305.6 ± 2.01Aa

2.96 ± 0.008

AA(299)

10,146 ± 68.79Bb

336.42 ± 3.01B

3.33 ± 0.028

300.12 ± 2.19B

2.96 ± 0.009

P

0.001**

0.0002**

0.2065

0.0003**

0.0737

2

CC(170)

10,707 ± 78.61ab

385.28 ± 3.39ab

3.61 ± 0.032

315.96 ± 2.47Aa

2.96 ± 0.011Aa

CA(371)

10,785 ± 64.99Aa

390.15 ± 2.89Aa

3.63 ± 0.027

322.03 ± 2.1B

2.99 ± 0.009B

AA(212)

10,567 ± 73.79Bb

379.59 ± 3.21Bb

3.59 ± 0.03

312.96 ± 2.34Aa

2.96 ± 0.01Aa

P

0.0051**

0.0004**

0.2901

<.0001**

0.0005**

g.72834229C > A

1

CC(221)

10,318 ± 73

346.25 ± 3.17Aa

3.36 ± 0.03

306.34 ± 2.31Aa

2.97 ± 0.01a

CA(553)

10,315 ± 61.81

341.19 ± 2.75b

3.32 ± 0.026

303.89 ± 2.01ab

2.95 ± 0.008b

AA(299)

10,194 ± 68.95

337.13 ± 3.02Bb

3.31 ± 0.028

301.01 ± 2.2Bb

2.96 ± 0.009ab

P

0.0523

0.003**

0.1234

0.0212*

0.0494*

2

CC(169)

10,691 ± 78.17a

383.01 ± 3.37a

3.6 ± 0.032

314.66 ± 2.45Aa

2.95 ± 0.011Aa

CA(369)

10,802 ± 64.49Aa

388.4 ± 2.86Aa

3.61 ± 0.027

321.87 ± 2.08B

2.99 ± 0.009B

AA(211)

10,493 ± 73.62Bb

374.92 ± 3.19Bb

3.58 ± 0.03

309.72 ± 2.32Ab

2.96 ± 0.01Aa

P

<.0001**

<.0001**

0.5118

<.0001**

0.001**

g.72833969A > G

1

GG(300)

10,147 ± 68.91Aa

333.48 ± 3.02Aa

3.3 ± 0.028

299.66 ± 2.2A

2.96 ± 0.009

GA(551)

10,318 ± 61.59Bb

338.88 ± 2.74b

3.31 ± 0.025

304.12 ± 2Ba

2.95 ± 0.008

AA(222)

10,273 ± 72.9ab

342.05 ± 3.16Bb

3.35 ± 0.03

304.89 ± 2.3Ba

2.97 ± 0.010

P

0.0049**

0.0033**

0.1466

0.0057**

0.053

2

GG(211)

10,466 ± 75.09A

372.1 ± 3.27A

3.56 ± 0.031

309.3 ± 2.38Aa

2.96 ± 0.010Aa

GA(369)

10,793 ± 65.5Ba

388.2 ± 2.91Ba

3.61 ± 0.027

321.77 ± 2.12B

2.99 ± 0.009B

AA(169)

10,700 ± 78.46Ba

382.28 ± 3.38Bb

3.59 ± 0.032

315.32 ± 2.46Ab

2.95 ± 0.011Aa

P

<.0001**

<.0001**

0.1837

<.0001**

0.0015**

g.72833562G > T

1

TT(221)

10,340 ± 73.11

347.61 ± 3.17Aa

3.37 ± 0.03

306.84 ± 2.31a

2.97 ± 0.01

TG(552)

10,360 ± 62.09

343.16 ± 2.77a

3.33 ± 0.026

305.18 ± 2.02a

2.95 ± 0.008

GG(299)

10,234 ± 68.85

338.54 ± 3.02Bb

3.32 ± 0.028

301.92 ± 2.2b

2.95 ± 0.009

P

0.0512

0.0029**

0.097

0.0275*

0.0779

2

TT(169)

10,769 ± 78.92Aa

386.76 ± 3.41Aa

3.6 ± 0.032

316.78 ± 2.48Aa

2.95 ± 0.011Aa

TG(370)

10,824 ± 64.37Aa

391.65 ± 2.85Aa

3.63 ± 0.027

322.38 ± 2.07B

2.98 ± 0.009B

GG(210)

10,528 ± 74.13B

377.34 ± 3.22B

3.59 ± 0.03

310.91 ± 2.34Ab

2.96 ± 0.01Aa

P

<.0001**

<.0001**

0.2651

<.0001**

0.0014**

c.291G > A

1

AA(31)

9757.9 ± 144.69A

326.63 ± 5.95Aa

3.37 ± 0.058

288.83 ± 4.34A

2.98 ± 0.021

AG(345)

10,202 ± 66.08Ba

339.19 ± 2.91b

3.34 ± 0.027

301.61 ± 2.12Ba

2.96 ± 0.009

GG(697)

10,268 ± 60.55Ba

343.04 ± 2.71Bc

3.35 ± 0.025

303.66 ± 1.98Ba

2.96 ± 0.008

P

0.0007**

0.0034**

0.6488

0.0008**

0.752

2

AA(25)

10,866 ± 165.07

400.94 ± 6.75Aa

3.68 ± 0.066

319.04 ± 4.93

2.94 ± 0.024

AG(226)

10,557 ± 73.54

382.33 ± 3.2Bb

3.62 ± 0.03

313.83 ± 2.33

2.98 ± 0.01

GG(503)

10,683 ± 61.69

385.82 ± 2.77b

3.62 ± 0.026

317.26 ± 2.01

2.98 ± 0.008

P

0.0504

0.0172*

0.6436

0.147

0.3771

c.489G > A

1

AA(31)

9774.7 ± 144.35A

326.99 ± 5.93Aa

3.36 ± 0.058

289.58 ± 4.32A

2.98 ± 0.021

AG(344)

10,239 ± 65.93Ba

338.76 ± 2.9c

3.32 ± 0.027

302.48 ± 2.11Ba

2.96 ± 0.009

GG(709)

10,294 ± 60.82Ba

342.86 ± 2.72Bb

3.34 ± 0.025

304.28 ± 1.98Ba

2.96 ± 0.008

P

0.0006**

0.0033**

0.4033

0.0009**

0.5871

2

AA(25)

10,971 ± 164.92ab

399.91 ± 6.75a

3.63 ± 0.066

322.88 ± 4.92ab

2.94 ± 0.024

AG(225)

10,657 ± 73.09Aa

386.05 ± 3.17b

3.61 ± 0.03

318.62 ± 2.31a

2.98 ± 0.01

GG(510)

10,847 ± 60.46Bb

390.87 ± 2.71ab

3.6 ± 0.025

323.16 ± 1.97b

2.97 ± 0.008

P

0.005**

0.0395*

0.8064

0.0461*

0.1971

c.*190A > G

1

AA(584)

10,178 ± 62.42a

338.65 ± 2.78Aa

3.35 ± 0.026

300.85 ± 2.02

2.96 ± 0.008

AG(444)

10,217 ± 63.84Aa

338.37 ± 2.83Aa

3.33 ± 0.026

301.91 ± 2.06

2.96 ± 0.009

GG(56)

9939.48 ± 113.17Bb

323.63 ± 4.7B

3.28 ± 0.046

294.8 ± 3.43

2.98 ± 0.016

P

0.031*

0.0014**

0.2273

0.0705

0.6105

2

AA(423)

10,792 ± 63.54

389.14 ± 2.82

3.61 ± 0.026

321.2 ± 2.05

2.98 ± 0.008

AG(295)

10,671 ± 67.97

387.7 ± 2.98

3.63 ± 0.028

318.92 ± 2.17

2.99 ± 0.009

GG(42)

10,736 ± 131.2

385.86 ± 5.42

3.58 ± 0.053

316.43 ± 3.95

2.94 ± 0.019

P

0.1326

0.7237

0.5687

0.249

0.0664

c.*321G > C

1

CC(53)

10,076 ± 114.66

329.19 ± 4.76

3.29 ± 0.046

298.66 ± 3.47

2.97 ± 0.016

CG(435)

10,277 ± 63.65

339.07 ± 2.82

3.32 ± 0.026

303.06 ± 2.05

2.96 ± 0.009

GG(587)

10,217 ± 62.36

338.28 ± 2.78

3.33 ± 0.026

301.31 ± 2.02

2.96 ± 0.008

P

0.1191

0.0698

0.5569

0.2362

0.583

2

CC(41)

10,584 ± 131.99

380.38 ± 5.45

3.6 ± 0.053

311.06 ± 3.97

2.94 ± 0.019a

CG(290)

10,690 ± 69.23

388.18 ± 3.04

3.64 ± 0.028

319.27 ± 2.21

2.99 ± 0.009b

GG(424)

10,706 ± 64.21

385.69 ± 2.86

3.62 ± 0.026

317.31 ± 2.08

2.97 ± 0.009ab

P

0.6383

0.2827

0.6702

0.0947

0.0371*

c.*326A > G

1

AA(587)

10,223 ± 62.03Aa

337.47 ± 2.77Aa

3.32 ± 0.026

301.41 ± 2.01Aa

2.96 ± 0.008

AG(431)

10,295 ± 63.85Aa

338.53 ± 2.83Aa

3.31 ± 0.026

303.33 ± 2.06Aa

2.95 ± 0.009

GG(57)

9904.58 ± 111.55B

322.04 ± 4.64B

3.28 ± 0.045

292.88 ± 3.38B

2.97 ± 0.016

P

0.0008**

0.0004**

0.5042

0.0026**

0.4722

2

AA(425)

10,789 ± 64.31

389.29 ± 2.86

3.62 ± 0.027

319.31 ± 2.08

2.97 ± 0.009

AG(285)

10,706 ± 68.79

387.76 ± 3.02

3.63 ± 0.028

318.88 ± 2.2

2.98 ± 0.009

GG(43)

10,572 ± 129.83

382.68 ± 5.36

3.62 ± 0.052

310.75 ± 3.91

2.95 ± 0.019

P

0.1309

0.3978

0.9601

0.0689

0.0988

c.*640G > A

1

AA(31)

9805.53 ± 145.34A

328.47 ± 5.97Aa

3.36 ± 0.058

290.54 ± 4.36A

2.97 ± 0.021

AG(340)

10,228 ± 66.3Ba

341.02 ± 2.92c

3.34 ± 0.027

302.39 ± 2.13Ba

2.95 ± 0.009

GG(709)

10,299 ± 60.44Ba

345.29 ± 2.7Bb

3.36 ± 0.025

304.73 ± 1.97Ba

2.96 ± 0.008

P

0.0009**

0.0018**

0.5681

0.0009**

0.655

2

AA(25)

10,910 ± 164.71

396.49 ± 6.74

3.63 ± 0.066

2.93 ± 0.024

2.93 ± 0.024

AG(221)

10,653 ± 73.17

381.19 ± 3.18

3.58 ± 0.03

2.97 ± 0.01

2.97 ± 0.01

GG(510)

10,763 ± 61.24

384.41 ± 2.75

3.58 ± 0.025

2.97 ± 0.008

2.97 ± 0.008

P

0.107

0.0533

0.7617

0.2326

0.2326

c.*685G > C

1

CC(30)

9978.84 ± 146.26

328.2 ± 6

3.32 ± 0.059

294.37 ± 4.38a

2.96 ± 0.021

CG(337)

10,272 ± 66.72

336.86 ± 2.94

3.3 ± 0.027

303.87 ± 2.14b

2.96 ± 0.009

GG(713)

10,302 ± 60.16

339.63 ± 2.69

3.31 ± 0.025

304.85 ± 1.96b

2.96 ± 0.008

P

0.0617

0.0588

0.6272

0.0331*

0.9781

2

CC(25)

11,131 ± 164.65Aa

398.09 ± 6.74a

3.57 ± 0.066

323.53 ± 4.92ab

2.92 ± 0.024

CG(221)

10,600 ± 73.44B

383.03 ± 3.19b

3.61 ± 0.03

314.94 ± 2.33a

2.97 ± 0.01

GG(511)

10,774 ± 61.52Ab

388.76 ± 2.77a

3.61 ± 0.025

319.05 ± 2.01b

2.97 ± 0.008

P

0.0008**

0.0168*

0.8299

0.0384*

0.05

c.*735 T > C

1

CC(30)

10,031 ± 146.66

330.74 ± 6.02

3.32 ± 0.059

296.27 ± 4.39

2.96 ± 0.021

CT(338)

10,256 ± 66.98

337.13 ± 2.95

3.3 ± 0.028

303.04 ± 2.15

2.96 ± 0.009

TT(712)

10,306 ± 60.38

339.99 ± 2.7

3.32 ± 0.025

304.31 ± 1.97

2.96 ± 0.008

P

0.1031

0.1125

0.7774

0.1133

0.9598

2

CC(25)

11,178 ± 166.12Aa

397.7 ± 6.82a

3.56 ± 0.067

326.05 ± 4.97a

2.92 ± 0.024

CT(222)

10,608 ± 73.59B

383.22 ± 3.2b

3.61 ± 0.03

315.95 ± 2.33b

2.98 ± 0.01

TT(511)

10,791 ± 61.3Ab

388.01 ± 2.75ab

3.6 ± 0.025

320.43 ± 2a

2.97 ± 0.008

P

0.0003**

0.0358*

0.7454

0.0166*

0.0571

c.*1064G > A

1

AA(30)

9789.35 ± 145.71A

324.33 ± 5.97Aa

3.34 ± 0.058

290.87 ± 4.35A

2.98 ± 0.021

AG(346)

10,225 ± 66.48Ba

336.45 ± 2.93b

3.31 ± 0.027

302.73 ± 2.13Ba

2.96 ± 0.009

GG(699)

10,290 ± 60.6Ba

340.29 ± 2.71Bb

3.33 ± 0.025

304.73 ± 1.97Ba

2.96 ± 0.008

P

0.0011**

0.0046**

0.6409

0.0019**

0.5754

2

AA(24)

11,065 ± 169.52a

411.69 ± 6.93A

3.7 ± 0.068

324.69 ± 5.05

2.94 ± 0.024

AG(227)

10,639 ± 72.64b

386.11 ± 3.16Ba

3.62 ± 0.03

317.56 ± 2.3

2.98 ± 0.01

GG(501)

10,797 ± 61.59a

391.84 ± 2.76Bb

3.63 ± 0.025

321.28 ± 2.01

2.98 ± 0.008

P

0.0062**

0.0004**

0.5116

0.0823

0.1711

g.72819977 T > C

1

TT(709)

10,252 ± 60.58Aa

341.13 ± 2.71Aa

3.34 ± 0.025

303.11 ± 1.97Aa

2.96 ± 0.008

TC(345)

10,190 ± 66.68Aa

336.44 ± 2.94b

3.32 ± 0.027

301.02 ± 2.14a

2.96 ± 0.009

CC(31)

9810.39 ± 144.46B

326.61 ± 5.93Bb

3.35 ± 0.058

290.6 ± 4.33Bb

2.97 ± 0.021

P

0.0037**

0.0034**

0.391

0.0044**

0.6802

2

TT(510)

10,795 ± 60.71

388.17 ± 2.72

3.6 ± 0.025

321.11 ± 1.98

2.97 ± 0.008

TC(225)

10,673 ± 72.24

385.16 ± 3.13

3.6 ± 0.03

318.52 ± 2.28

2.98 ± 0.01

CC(25)

10,953 ± 165.5

399.73 ± 6.77

3.64 ± 0.066

321.39 ± 4.94

2.94 ± 0.024

P

0.0686

0.0736

0.777

0.3541

0.2628

g.72819850A > G

1

GG(31)

9737.41 ± 143.71A

322.7 ± 5.9Aa

3.34 ± 0.058

287.79 ± 4.3A

2.97 ± 0.021

GA(342)

10,221 ± 66.54Ba

336.58 ± 2.93b

3.3 ± 0.027

301.93 ± 2.13Ba

2.95 ± 0.009

AA(706)

10,282 ± 60.43Ba

340.2 ± 2.7Bb

3.32 ± 0.025

303.63 ± 1.97Ba

2.95 ± 0.008

P

0.0003**

0.0021**

0.6324

0.0003**

0.7239

2

GG(25)

10,948 ± 164.92b

404.59 ± 6.75Aa

3.69 ± 0.066

321.58 ± 4.92ab

2.94 ± 0.024

GA(224)

10,546 ± 73.43Aa

381.72 ± 3.19B

3.62 ± 0.03

313.96 ± 2.32Aa

2.98 ± 0.01

AA(508)

10,773 ± 61.24Bb

388.75 ± 2.75Ab

3.61 ± 0.025

320.15 ± 2Bb

2.98 ± 0.008

P

0.0005**

0.0004**

0.5079

0.003**

0.2881

g.72818819A > G

1

GG(305)

10,154 ± 68.15Aa

336.43 ± 2.98A

3.33 ± 0.028

299.24 ± 2.17A

2.95 ± 0.009a

GA(557)

10,314 ± 61.4Bb

341.97 ± 2.74Ba

3.33 ± 0.025

303.62 ± 1.99Ba

2.95 ± 0.008Aa

AA(218)

10,301 ± 73.25b

346.69 ± 3.17Bb

3.38 ± 0.03

305.87 ± 2.31Ba

2.97 ± 0.01Bb

P

0.0068**

0.0004**

0.1048

0.0012**

0.0108*

2

GG(216)

10,481 ± 73.65A

374.35 ± 3.2A

3.57 ± 0.03

309.56 ± 2.33A

2.96 ± 0.01Aa

GA(373)

10,845 ± 64.47Ba

391.01 ± 2.86Ba

3.61 ± 0.027

323.76 ± 2.08B

2.99 ± 0.009B

AA(167)

10,778 ± 79.59Ba

384.6 ± 3.44Bb

3.57 ± 0.033

317.22 ± 2.51C

2.95 ± 0.011Aa

P

<.0001**

<.0001**

0.1906

<.0001**

0.0003**

g.72818818C > T

1

TT(305)

10,224 ± 68.77Aa

337.97 ± 3.01A

3.31 ± 0.028

301.6 ± 2.19A

2.95 ± 0.009ab

TC(555)

10,382 ± 61.58Bb

344.22 ± 2.75Ba

3.33 ± 0.025

305.98 ± 2Ba

2.95 ± 0.008a

CC(221)

10,330 ± 72.84ab

346.52 ± 3.16Ba

3.36 ± 0.03

306.65 ± 2.3Ba

2.97 ± 0.01b

P

0.0106*

0.0019**

0.1484

0.0075**

0.0355*

2

TT(216)

10,466 ± 74A

374.26 ± 3.22A

3.58 ± 0.03

308.75 ± 2.34A

2.96 ± 0.01Aa

TC(372)

10,767 ± 64.62Ba

389.23 ± 2.87Ba

3.63 ± 0.027

320.3 ± 2.09Ba

2.99 ± 0.009B

CC(169)

10,737 ± 78.69Ba

385.23 ± 3.4Ba

3.6 ± 0.032

315.35 ± 2.48Bb

2.95 ± 0.011Aa

P

<.0001**

<.0001**

0.1591

<.0001**

0.0006**

g.72818292 T > C

1

TT(709)

10,300 ± 60.49Aa

341.5 ± 2.71a

3.33 ± 0.025

304.06 ± 1.97a

2.96 ± 0.008

TC(336)

10,249 ± 66.63a

337.35 ± 2.93b

3.31 ± 0.027

302.39 ± 2.13a

2.95 ± 0.009

CC(33)

9929.1 ± 140.09Bb

330.35 ± 5.74b

3.34 ± 0.056

294.03 ± 4.19b

2.97 ± 0.02

P

0.0156*

0.0197*

0.453

0.0253*

0.632

2

TT(509)

10,683 ± 61.62c

382.44 ± 2.77Aa

3.6 ± 0.026

316.43 ± 2.02a

2.97 ± 0.008

TC(219)

10,522 ± 72.71Aa

377.12 ± 3.15Ab

3.6 ± 0.03

312.89 ± 2.3Aa

2.98 ± 0.01

CC(27)

11,074 ± 159.67Bb

405.34 ± 6.54B

3.64 ± 0.064

326.97 ± 4.77Bb

2.95 ± 0.023

P

0.0006**

<.0001**

0.7811

0.0057**

0.4872

g.72818161 T > C

1

TT(711)

10,326 ± 60.82Aa

343.62 ± 2.72A

3.34 ± 0.025

305.45 ± 1.98Aa

2.96 ± 0.008

TC(322)

10,206 ± 67.05Ab

338.41 ± 2.95Ba

3.32 ± 0.028

302.22 ± 2.15Ab

2.96 ± 0.009

CC(30)

9725.31 ± 145.87B

325.45 ± 5.98Bb

3.36 ± 0.059

287.93 ± 4.36B

2.97 ± 0.021

P

<.0001**

0.0004**

0.7091

<.0001**

0.6543

2

TT(511)

10,714 ± 61.04Aa

383.57 ± 2.74a

3.59 ± 0.025

317.97 ± 1.99

2.97 ± 0.008ab

TC(208)

10,546 ± 73.84Bb

378.91 ± 3.19Aa

3.6 ± 0.03

315.19 ± 2.33

2.99 ± 0.01a

CC(24)

10,933 ± 168.72a

397.23 ± 6.9Bb

3.63 ± 0.068

319.26 ± 5.03

2.93 ± 0.024b

P

0.0078**

0.014*

0.7997

0.2957

0.0239*

* indicates P < 0.05; ** indicates P < 0.01; a, b, c within the same column with different superscripts means P < 0.05; A, B, C within the same column with different superscripts means P < 0.01.

Table 3

Associations of 5 SNPs of CDKN1A gene with milk production traits in Chinese Holstein cattle during two lactations (LSM ± SE)

SNPs

Lactation

Genotype (No.)

Milk yield (kg)

Fat yield (kg)

Fat percentage (%)

Protein yield (kg)

Protein percentage (%)

c.271C > T

1

CC(582)

10,249 ± 62.43a

339.12 ± 2.79

3.32 ± 0.026ab

302.37 ± 2.03

2.95 ± 0.008

CT(412)

10,212 ± 65.4Aa

341.67 ± 2.89

3.36 ± 0.027a

301.44 ± 2.11

2.96 ± 0.009

TT(76)

10,478 ± 99.65Bb

340.05 ± 4.18

3.27 ± 0.04b

308.04 ± 3.05

2.95 ± 0.014

P

0.0162*

0.414

0.0377*

0.0522

0.8062

2

CC(394)

10,564 ± 64.48Aa

378.99 ± 2.86Aa

3.6 ± 0.027

313.03 ± 2.08A

2.97 ± 0.009Aa

CT(302)

10,772 ± 67.72Bb

387.31 ± 2.98Bb

3.6 ± 0.028

319.25 ± 2.17Ba

2.97 ± 0.009Aa

TT(54)

10,819 ± 119.09b

388.01 ± 4.94ab

3.61 ± 0.048

327.12 ± 3.6Bb

3.03 ± 0.017B

P

0.0012**

0.0018**

0.9967

<.0001**

0.0012**

c.*9C > G

1

CC(593)

10,229 ± 61.78a

338.35 ± 2.76

3.33 ± 0.026

301.99 ± 2.01

2.96 ± 0.008

CG(415)

10,173 ± 64.52Aa

339.45 ± 2.85

3.35 ± 0.027

300.37 ± 2.08

2.96 ± 0.009

GG(76)

10,428 ± 99.99Bb

338.21 ± 4.19

3.28 ± 0.04

306.56 ± 3.06

2.95 ± 0.014

P

0.0193*

0.8322

0.0956

0.0613

0.8896

2

CC(401)

10,603 ± 64.7A

380.64 ± 2.87Aa

3.6 ± 0.027

314.09 ± 2.09A

2.97 ± 0.009Aa

CG(305)

10,811 ± 67.06Ba

389.97 ± 2.96Bb

3.61 ± 0.028

320.55 ± 2.15B

2.97 ± 0.009Aa

GG(54)

10,922 ± 117.94Ba

391.5 ± 4.89b

3.59 ± 0.048

329.78 ± 3.56C

3.02 ± 0.017B

P

0.0004**

0.0003**

0.874

<.0001**

0.0055**

c.*654C > T

1

CC(497)

10,276 ± 62.96

337.95 ± 2.8

3.3 ± 0.026Aa

303.16 ± 2.04

2.95 ± 0.008

CT(479)

10,213 ± 63.44

340.69 ± 2.82

3.35 ± 0.026Bb

301.57 ± 2.05

2.96 ± 0.008

TT(107)

10,298 ± 90.26

338.05 ± 3.83

3.29 ± 0.037ab

303.44 ± 2.79

2.95 ± 0.013

P

0.3235

0.3355

0.0144*

0.4693

0.7739

2

CC(350)

10,862 ± 65.32

388.92 ± 2.89

3.58 ± 0.027

323.75 ± 2.11Aa

2.98 ± 0.009

CT(330)

10,755 ± 67.61

389.17 ± 2.98

3.61 ± 0.028

319.07 ± 2.17Bb

2.96 ± 0.009

TT(79)

10,756 ± 102.96

384.73 ± 4.33

3.58 ± 0.042

316.84 ± 3.16b

2.95 ± 0.014

P

0.1847

0.529

0.5

0.0092**

0.0922

g.10569766 T > C

1

CC(79)

10,394 ± 98.78

334.84 ± 4.14

3.26 ± 0.04

304.06 ± 3.02

2.94 ± 0.014

CT(427)

10,192 ± 65.04

336.77 ± 2.88

3.32 ± 0.027

299.51 ± 2.09

2.95 ± 0.009

TT(564)

10,191 ± 62.48

335.13 ± 2.79

3.31 ± 0.026

299.53 ± 2.03

2.95 ± 0.008

P

0.0672

0.6615

0.1899

0.2059

0.878

2

CC(60)

10,803 ± 113.4a

386.17 ± 4.72ab

3.59 ± 0.046

326.9 ± 3.44Aa

3.03 ± 0.016A

CT(309)

10,790 ± 67.29Aa

388.76 ± 2.96Aa

3.61 ± 0.028

320.1 ± 2.16Ab

2.97 ± 0.009Ba

TT(380)

10,560 ± 65.37Bb

379.99 ± 2.9Bb

3.61 ± 0.027

313.48 ± 2.11B

2.98 ± 0.009Ba

P

0.0004**

0.0015**

0.8386

<.0001**

0.0009**

g.10569779 T > C

1

CC(559)

10,286 ± 61.82

339.28 ± 2.76

3.32 ± 0.026

303.96 ± 2.01

2.96 ± 0.008

CT(434)

10,251 ± 65.2

339.93 ± 2.89

3.33 ± 0.027

302.21 ± 2.1

2.95 ± 0.009

TT(87)

10,353 ± 95.78

337.22 ± 4.03

3.28 ± 0.039

305.05 ± 2.94

2.96 ± 0.013

P

0.4605

0.7357

0.4159

0.3306

0.7423

2

CC(374)

10,598 ± 64.94Aa

382.05 ± 2.88Aa

3.62 ± 0.027

314.19 ± 2.09A

2.97 ± 0.009Aa

CT(316)

10,799 ± 66.94Bb

388.48 ± 2.95Bb

3.61 ± 0.028

319.81 ± 2.15Ba

2.97 ± 0.009Aa

TT(65)

10,726 ± 108.83ab

381.24 ± 4.54ab

3.57 ± 0.044

323.07 ± 3.31Ba

3.02 ± 0.015B

P

0.0041**

0.0197*

0.6029

0.001**

0.0035**

* indicates P < 0.05; ** indicates P < 0.01; a, b, c within the same column with different superscripts means P < 0.05; A, B, C within the same column with different superscripts means P < 0.01.

Regarding CDKN1A gene, it showed that c.271C > T (P = 0.0162) and c.*9C > G (P = 0.0193) were significantly associated with 305-days milk yield, and c.271C > T (P = 0.0377) and c.*654C > T (P = 0.0144) were markedly associated with fat percentage in the first lactation. Four identified SNPs of CDKN1A gene, c.271C > T, c.*9C > G, g.10569766 T > C, and g.10569779 T > C, were significantly associated with 305-days milk yield, fat yield, protein yield, and protein percentage (P = < 0.0001 ~ 0.0197), and c.*654C > T was only evidently associated with protein yield (P = 0.0092) in the second lactation (Table 3). Additionally, three SNPs of CDKN1A gene, c.271C > T, c.*9C > G, and c.*654C > T, were both significantly associated with milk traits in both first (P = 0.0144 ~ 0.0377) and second (P = < 0.0001 ~ 0.0197) lactations. The g.10569766 T > C and g.10569779 T > C were merely associated with milk traits in the second lactation (P = < 0.0001 ~ 0.0197), but the allelic effects of them were almost in the same direction between two lactations. Taken together, the identified SNPs of CDKN1A gene were mainly associated with the milk yield, fat yield, protein yield, and protein percentage in the second lactation of Chinese Holstein cattle in this study (Table 3).

The allele additive, dominant, and substitution effects of 19 SNPs identified in ATF3 gene were mainly significantly associated with milk yield, fat yield, and protein yield (P < 0.05), and the results in the first lactation were slightly different from that in the second lactation; nevertheless, it is interesting that only two SNPs, g.72833562G > T and g.72818819A > G, were evidently associated with fat percentage in the first lactation (P < 0.05) (Additional file 3). Nevertheless, the allele additive, dominant, and substitution effects of 5 SNPs of CDKN1A gene were mainly associated with milk yield, protein yield, and protein percentage (P < 0.05) (Additional file 4).

Associations between haplotypes and five milk traits

The pair-wise D’ measures indicated that all 19 SNPs in ATF3 gene were highly linked (D’ > 0.95), and one haplotype block comprising the 19 SNPs was inferred (Fig. 1a), in which four haplotypes were formed. The frequency of the four haplotypes, H1 (AAGTTAGTGGAGAGGATGG), H2 (AAACTAGTGGAGAGGCCTT), H3 (GGACCGACCAGCGAACCTT), and H4 (AAACTAGTGGGCGGGCCTT), were 46.3%, 28.0%, 17.7%, and 7.2%, respectively. Haplotype-based association analysis showed that the six haplotype combinations were all significantly associated with 305-days milk yield, fat yield, protein yield, and protein percentage in the first lactation (P = 0.0019 ~ 0.0398), and evidently associated with 305-days milk yield, fat yield, and protein yield in the second lactation (P < 0.0001; Table 4).
Fig. 1

Linkage disequilibrium estimated between SNPs in ATF3 (a) and CDKN1A (b) genes. The values in boxes are pair-wise SNP correlations (D’)

Table 4

Haplotypes analysis of ATF3 gene (LSM ± SE)

Lactation

Haplotype combination (No.)

Milk yield (kg)

Fat yield (kg)

Fat percentage (%)

Protein yield (kg)

Protein percentage (%)

1

H1H1 (220)

10,293 ± 73.81ab

344.45 ± 3.21Aa

3.36 ± 0.03

305.64 ± 2.34ABa

2.97 ± 0.01Aa

H1H2 (286)

10,256 ± 70.59abc

337.6 ± 3.1bc

3.31 ± 0.029

301.1 ± 2.25bc

2.94 ± 0.01Bb

H1H3 (184)

10,355 ± 77.21Aab

343.03 ± 3.34Aab

3.33 ± 0.032

305.97 ± 2.43Aa

2.96 ± 0.011ab

H1H4 (84)

10,406 ± 100.1Aa

340.62 ± 4.21abc

3.29 ± 0.041

305.61 ± 3.07ab

2.95 ± 0.014b

H2H2 (79)

10,165 ± 100.53bc

336.09 ± 4.22bc

3.32 ± 0.041

298.33 ± 3.08BCc

2.94 ± 0.014b

H2H3 (125)

10,119 ± 86.34Bc

332.39 ± 3.69Bc

3.3 ± 0.035

297.98 ± 2.69Cc

2.95 ± 0.012ab

P

0.0398*

0.0038**

0.3088

0.0019**

0.0334*

2

H1H1 (161)

10,740 ± 79.51Aab

389.62 ± 3.42Aa

3.64 ± 0.03

317.62 ± 2.49Ab

2.96 ± 0.011

H1H2 (195)

10,813 ± 76.98Aa

389.73 ± 3.34Aa

3.62 ± 0.03

322.02 ± 2.43Aab

2.98 ± 0.011

H1H3 (113)

10,625 ± 90.3b

390.54 ± 3.86Aa

3.68 ± 0.04

318.51 ± 2.81Aab

2.99 ± 0.013

H1H4 (56)

10,887 ± 116.86Aa

392.75 ± 4.86Aa

3.61 ± 0.05

325.59 ± 3.54Aa

2.99 ± 0.017

H2H2 (52)

10,293 ± 122.84Bc

369.21 ± 5.1Bb

3.6 ± 0.05

304.19 ± 3.72Bc

2.95 ± 0.017

H2H3 (84)

10,405 ± 99.79Bc

374.45 ± 4.2Bb

3.6 ± 0.04

308.09 ± 3.06Bc

2.96 ± 0.014

P

<.0001**

<.0001**

0.4721

<.0001**

0.0743

H means haplotype; H1: AAGTTAGTGGAGAGGATGG, H2: AAACTAGTGGAGAGGCCTT, H3: GGACCGACCAGCGAACCTT, and H4: AAACTAGTGGGCGGGCCTT; * indicates P < 0.05; ** indicates P < 0.01; a, b, c within the same column with different superscripts means P < 0.05; A, B, C within the same column with different superscripts means P < 0.01.

Regarding the CDKN1A haplotypes, one block was inferred (D’ > 0.98) as shown in Fig. 1b, consisting of H1 (CCCTC), H2 (CCTTC), H3 (TGCCT), and H4 (CCCCT) with frequency of 39.9%, 31.7%, 25.7%, and 1.5%, respectively. The associations (Table 5) were indicated that the haplotype combinations were markedly associated with fat percentage (P = 0.044) and protein percentage (P = 0.0351) in the first lactation, and remarkably associated with 305-days milk yield, fat yield, protein yield, and protein percentage in the second lactation (P = < 0.0001 ~ 0.0163).
Table 5

Haplotypes analysis of CDKN1A gene (LSM ± SE)

Lactation

Haplotype combination (No.)

Milk yield (kg)

Fat yield (kg)

Fat percentage (%)

Protein yield (kg)

Protein percentage (%)

1

H1H1 (175)

10,246 ± 78.7

337.02 ± 3.4

3.3 ± 0.032ab

301.01 ± 2.47

2.94 ± 0.011Bc

H1H2 (279)

10,190 ± 69.46

339.81 ± 3.04

3.35 ± 0.029a

302.54 ± 2.22

2.97 ± 0.009Aa

H1H3 (222)

10,179 ± 74.12

338.05 ± 3.22

3.33 ± 0.03ab

301.48 ± 2.35

2.97 ± 0.01ab

H2H2 (107)

10,250 ± 89.88

337.17 ± 3.81

3.3 ± 0.036ab

302.85 ± 2.78

2.96 ± 0.013abc

H2H3 (179)

10,140 ± 77.68

339.79 ± 3.35

3.36 ± 0.032Aa

298.23 ± 2.44

2.95 ± 0.011bc

H3H3 (75)

10,418 ± 100.99

336.31 ± 4.24

3.25 ± 0.041Bb

306.5 ± 3.09

2.95 ± 0.014abc

P

0.1065

0.8508

0.044*

0.0939

0.0351*

2

H1H1 (114)

10,555 ± 90.95Bc

378.57 ± 3.87Cc

3.59 ± 0.037

314.92 ± 2.82Bb

2.98 ± 0.013ABb

H1H2 (174)

10,623 ± 79.4Bc

387.32 ± 3.43BCb

3.65 ± 0.032

315.26 ± 2.5Bb

2.97 ± 0.011Bb

H1H3 (150)

11,061 ± 81.27Aa

399.1 ± 3.49Aa

3.62 ± 0.033

328.44 ± 2.54Aa

2.97 ± 0.011Bb

H2H2 (78)

10,722 ± 104.5Bbc

383.32 ± 4.39BCbc

3.58 ± 0.042

316.19 ± 3.2Bb

2.95 ± 0.015Bb

H2H3 (131)

10,717 ± 87.66Bbc

389.21 ± 3.74ABb

3.62 ± 0.036

317.87 ± 2.73Bb

2.96 ± 0.012Bb

H3H3 (53)

10,884 ± 120.25ab

388.23 ± 4.99b

3.58 ± 0.048

329.01 ± 3.64Aa

3.02 ± 0.017Aa

P

<.0001**

<.0001**

0.5127

<.0001**

0.0163*

H means haplotype; H1: CCCTC, H2: CCTTC, H3: TGCCT, and H4: CCCCT; * indicates P < 0.05; ** indicates P < 0.01; a, b, c within the same column with different superscripts means P < 0.05; A, B, C within the same column with different superscripts means P < 0.01.

Prediction of TFBSs variations in promoter region of ATF3 gene

With regard to the four SNPs on the 5’promoter region of ATF3 gene, we predicted the variation of TFBSs after mutation using JASPAR software. As the results shown in Table 6, the A allele in g.72834301C > A created the putative binding sites for the transcription factor E2F3 (E2F transcription factor 3; relative score = 0.88) and Zfp423 (zinc finger protein 423; relative score = 0.89). The binding sites for the transcription factor Bcl6 (B-cell CLL/lymphoma 6) was invented because of the A allele in g.72834229C > A (relative score = 0.87), and g.72833969A > G resulted in the appearing of the binding sites for transcription factor STAT3 (signal transducer and activator of transcription 3) after the substitution by G allele (relative score = 0.95). It was also indicated that the binding site for transcription factor Zfp423 was arisen due to the T allele in g.72833562G > T (relative score = 0.88).
Table 6

Transcription factor binding sites (TFBSs) prediction for ATF3 gene

SNPs

Allele

TFBSs

g.72834301C > A

C

-

A

E2F3, Zfp423

g.72834229C > A

C

-

A

Bcl6

g.72833969A > G

A

-

G

STAT3

g.72833562G > T

G

-

T

Zfp423

- means no predicted TFBSs.

Variant structure of CDKN1A protein caused by missense mutation

There was a missense mutation (p.Arg91Trp) on CDKN1A protein caused by c.271C > T. The results from the SOPMA SERVER revealed that α-helix was changed from 32.92% to 32.3%, β-turn from 4.35% to 5.59%, and random coil from 49.69% to 49.07% (Table 7), indicating that the CDKN1A protein secondary structure was altered from arginine to tryptophan.
Table 7

Alteration of CDKN1A protein caused by the mutation

SNPs

Allele

α-helix

Extended strand

β-turn

Random coil

c.271C > T

C

32.92

13.04

4.35

49.69

T

32.3

13.04

5.59

49.07

Discussion

This study was a follow-up investigation of our previous RNA-Seq work, in which the ATF3 and CDKN1A genes were potentially associated with milk protein and fat percentage [9]. Here, we first determined that SNPs within the ATF3 and CDKN1A genes were significantly associated with milk production traits in dairy cattle. Of these, four SNPs, g.72834301C > A, g.72834229C > A, g.72833969A > G, and g.72833562G > T, potentially changing the ATF3 promoter activity, and one SNP, c.271C > T, potentially altering the CDKN1A protein secondary structure, might be potentially causal mutations.

With regard to the associations of ATF3 and CDKN1A with five milk traits, we found that eight SNPs showed different associations between the first and second lactations (Tables 2 and 3). The possible reason may be that different number of cows were used for association analysis (1093 cows in the first lactation versus 769 cows in the second lactation) because 324 cows merely completed their milking of first lactation, which could impact the statistical significance. In addition, the physiologic status of cows between the first and second lactations are different as well, generally, cows show higher milk production in the second lactation. Further, the directions of allelic effects of the eight SNPs on the milk traits were almost consistent between the two lactations. Studies revealed that haplotype blocks in human genome is independent of their surrounding areas with regard to LD [1517], and the haplotype analyses were widely applied to the genetic variation studies [18, 19]. Our haplotypes analyses showed that the SNPs were highly linked, and the haplotypes were also significantly associated with milk yield, fat yield, fat percentage, protein yield, and protein percentage, which were consistent with the associations of SNPs with milk traits.

ATF3 is involved in the TLR4 (toll-like receptor 4) signaling pathway, and its expression was markedly increased causing by chemotaxis and diapedesis in vitro, indicating that ATF3 acts as the early adaptive-response gene having an important role in maintaining the cellular homeostasis [20]. It was reported that ATF3 activates the cyclin D1 expression, thereby stimulating the mouse hepatocellular proliferation [21]. As we know, liver plays a key role in lipid metabolism, including fatty acid uptake, synthesis and oxidation, glycerolipid synthesis, and triacylglycerol export [22]. Subsequently, Invernizzi et al. found ATF3 may modulate milk fat synthesis during lactation by participating in the endoplasmic reticulum stress pathway [23, 24]. Our results also showed a significant relationship between SNP polymorphism of ATF3 gene and fat yield, thus it can be seen that ATF3 may be associated with lipid metabolism. The CDKN1A (p21) protein regulates the cell cycle at G1 and S phase by inhibiting the activity of cyclin-CDK2, −CDK1, and –CDK4/6 complexes [25]. Li and Capuco conducted a systematic search for estrogen-responsive genes in bovine mammary gland, and identified 23 regulatory networks, of these, CDKN1A gene occupied a focal position in the network that functions as cell cycle, cellular movement and cancers, indicating that CDKN1A may play an important role in mammary gland development [26]. Together, ATF3 and CDKN1A were considered as important promising candidate genes for milk production traits.

As we know, SNPs in transcription factor binding sites could lead to allele-specific binding of transcription factors and enhancing or repressing the gene expression [27]. Studies have revealed that transcription factor E2F3 [2831], Zfp423 [32, 33], and STAT3 [34, 35] could activate or repress the gene expression, and Bcl6 might play as a repressor for gene expression [36, 37]. Our results showed that the milk yield, fat yield, fat percentage, protein yield, and protein percentage were evidently decreased or had the downtrends in genotype AA, AA, and GG severally causing by g.72834301C > A, g.72834229C > A, and g.72833969A > G, indicating that the transcription factors E2F3, Zfp423, Bcl6, and STAT3, might prejudice the milk production by repressing the expression of ATF3 gene. On the contrary, the transcription factor Zfp423 might be also beneficial to the milk production through activating the expression of ATF3 gene, because that the genotype TT causing by g.72833562G > T increased the milk yield, fat yield, fat percentage, protein yield, and protein percentage in the two lactations. Overall, our findings suggested that the four SNPs, g.72834301C > A, g.72834229C > A, g.72833969A > G, and g.72833562G > T in ATF3 gene, might be the potential mutations in milk production traits by changing promoter activity in Holstein cattle.

In the present, we found the SNP c.271C > T of CDKN1A gene was a missense mutation that caused an amino acid substitution from arginine to tryptophan, and the association analyses showed that this SNP was remarkably associated with milk yield and fat percentage in the first lactation, and milk yield, fat yield, protein yield, and protein percentage in the second lactation. Importantly, the changes of the protein structure causing by this amino acid substitution showed that the α-helix changed from 32.92% to 32.3%. Generally, the α-helix was preferably located at the core of the protein and had important functions in proteins for flexibility and conformational changes [38], and it was presumed that the CDKN1A protein might be more stable in conformation when the base was C. Hence, the SNP c.271C > T in CDKN1A gene might be another potential functional mutation for milk production through changing the protein structure in dairy cattle. Further in-depth investigation should be performed to validate the biological functions of these SNPs.

Conclusions

In this study, we totally identified 19 and five SNPs in the ATF3 and CDKN1A genes, respectively, and observed their associations with milk yield and milk composition. Of these, four SNPs in ATF3 gene altered the specific TF binding sites thereby potentially changed promoter activities, and one SNP in CDKN1A gene changed the protein secondary structure, might be the potential causal mutations. In a word, our study first determined the significant genetic effects of ATF3 and CDKN1A genes on milk yield and composition traits in dairy cattle and will be available for marker-assisted breeding based on further validation.

Abbreviations

a: 

Additive effect

ATF3: 

Activating transcription factor 3

Bcl6: 

B-cell CLL/lymphoma 6

CDKN1A: 

Cyclin dependent kinase inhibitor 1A

CREB: 

cAMP responsive element-binding

d: 

Dominant effect

DHI: 

Dairy herd improvement

E2F3: 

E2F transcription factor 3

EBVs: 

Estimate breeding values

GWAS: 

Genome-wide association study

IPA: 

Ingenuity Pathway Analysis

LD: 

linkage disequilibrium

MALDI-TOFMS: 

Matrix-assisted laser desorption/ionization time of flight mass spectrometry

QTL: 

Quantitative trait locus

RNA-Seq: 

RNA sequencing

STAT3: 

Signal transducer and activator of transcription 3

TF: 

Transcription factor

TFBSs: 

Transcription factor binding sites

TLR4: 

Toll-like receptor 4

UTR: 

Un-translated region

Zfp423: 

Zinc finger protein 423

α: 

Substitution effect

Declarations

Acknowledgements

We appreciate Beijing Dairy Cattle Center for providing the official estimate breeding values (EBVs) data.

Funding

This work was financially supported by the National Science and Technology Programs of China (2013AA102504, 2011BAD28B02, 2014ZX08009-053B), National Natural Science Foundation (31,072,016, 31,472,065), Beijing Natural Science Foundation (6152013), the Beijing Dairy Industry Innovation Team (BAIC06–2016), and the Program for Changjiang Scholar and Innovation Research Team in University (IRT1191).

Availability of data and materials

All relevant data are available within the article and its additional files.

Authors’ contributions

DS conceived and designed the experiments, WL prepared the DNA samples for SNP identification and genotyping with the help of LL and YL, BH and WL analyzed the data, and the manuscript was prepared by BH and DS. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Consent for Publication

Not applicable.

Ethics approval

All protocols for collection of the tissues of experimental individuals and phenotypic observations were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) at China Agricultural University. Tissue 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.

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Authors’ Affiliations

(1)
Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University
(2)
Beijing Dairy Cattle Center

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