SERPINA1 gene identified in RNA-Seq showed strong association with milk protein concentration in Chinese Holstein cows

The detection of candidate genes and mutations associated with phenotypic traits is important for livestock animals. A previous RNA-Seq study revealed that SERPINA1 gene was a functional candidate that may affect milk protein concentration in dairy cows. To further confirm the genetic effect of SERPINA1 on milk protein traits, genetic polymorphisms were identified and genotype-phenotype associations were performed in a large Chinese Holstein cattle population. The entire coding region and the 5′-regulatory region (5′-UTR) of SERPINA1 was sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed model with a population encompassing 1,027 Chinese Holstein cows. A total of four SNPs were identified in SERPINA1, among which rs210222822 and rs41257068 presented in exons, rs207601878 presented in an intron, and rs208607693 was in the 5′-UTR. Analyses of pairwise D′ measures of linkage disequilibrium (LD) showed strong linkage among these four SNPs (D′ = 0.99–1.00), and a 9 Kb haplotype block involving three main haplotypes with GTGT, CCCC and CCGT was inferred. An association study revealed that all four single SNPs and their haplotypes had significant genetic effects on milk protein percentage, milk protein yield and milk yield (P = 0.0458 − < 0.0001). The phenotypic variance ratio for all 11 significant SNP-trait pairs ranged from 1.01% to 7.54%. The candidate gene of SERPINA1 revealed by our previous RNA-Seq study was confirmed to have pronounced effect on milk protein traits on a genome level. Two SNPs (rs208607693 and rs210222822) presented phenotypic variances of approximately 7% and may be used as key or potential markers to assist selection for new lines of cows with high protein concentration.

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Anti-mastitis SNV identification of NFκB1 in Chinese Holstein cows and the possible anti-inflammation role of NFκB1/p105 in bovine MECs

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmaa118 ◽

2020 ◽

Vol 52 (11) ◽

pp. 1191-1201

Author(s):

Ling Chen ◽

Rongfu Tian ◽

Huilin Zhang ◽

Xiaolin Liu

Keyword(s):

Somatic Cell ◽

Mrna Expression ◽

Protein Content ◽

Milk Protein ◽

Holstein Cows ◽

Chinese Holstein ◽

Milk Protein Content ◽

Chinese Holstein Cows ◽

Anti Inflammation

Abstract NFκB1/p105 is the critical member of the NFκB family which can suppress inflammation, ageing, and cancer when p50/p50 homodimer is formed. Currently, the research about the role of NFκB1/p105 during cow mastitis is limited. Here, we analyzed the correlation of six single-nucleotide variants of the NFκB1 gene with somatic cell count, milk yield, milk fat content, and milk protein content in 547 Chinese Holstein cows, and explored the mRNA expression profiles of the NFκB family and ubiquitin ligases (βTrCP1, βTrCP2, KPC1, KPC2) in LPS-induced bovine mammary epithelial cells (MECs) by transcriptome-Seq. The association analysis showed that cows with SNV2-TT and SNV6-CC in the NFκB1 gene had significantly higher milk protein content (P < 0.05), while cows with SNV5-TT in the NFκB1 gene had significantly lower somatic cell score (SCS), but CC genotype at SNV5 locus was not detected in our Holstein cows. The transcriptome-Seq results demonstrated the mRNA expression of NFκB1 was increased and peaked at 4 h post-induction, while the mRNA expressions of both KPC1 and BCL3 that promote the anti-inflammation function of NFκB1/p105 were decreased in LPS-induced bovine MECs. TNFAIP3, an inhibitor of both degradation and processing of p105 precursor, was markedly increased by more than 3 folds. Furthermore, bta-miR-125b which targets at the 3ʹUTR of TNFAIP3 was reduced by 50%. These results indicated that SNV5-TT of the NFκB1 gene with lower SCS may be an anti-mastitis genotype that could cope with infection more efficiently in Chinese Holstein cows. In addition, the anti-inflammation role of NFκB1/p105 seemed to be inhibited in LPS-induced-bovine MECs because the formation of the p50/p50 homodimer was arrested. This study provides a new perspective to understand the inflammatory mechanism in dairy mastitis.

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Association of UDP-galactose-4-epimerase with milk protein concentration in the Chinese Holstein population

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.19.0549 ◽

2020 ◽

Vol 33 (11) ◽

pp. 1725-1731

Author(s):

Cong Li ◽

Wentao Cai ◽

Shuli Liu ◽

Chenghao Zhou ◽

Mingyue Cao ◽

...

Keyword(s):

Protein Concentration ◽

Milk Protein ◽

Association Studies ◽

Regulatory Region ◽

Protein Yield ◽

Strong Linkage Disequilibrium ◽

Phenotypic Variance ◽

Production Traits ◽

Fat Percentage ◽

Chinese Holstein

Objective: An initial RNA-Sequencing study revealed that UDP-galactose-4-epimerase (GALE) was one of the most promising candidates for milk protein concentration in Chinese Holstein cattle. This enzyme catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. To further validate the genetic effect of GALE on milk protein traits, genetic variations were identified, and genotypes-phenotypes associations were performed.Methods: The entire coding region and the 5’-regulatory region (5’-UTR) of GALE were re-sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed linear animal model with a population encompassing 1,027 Chinese Holstein cows.Results: A total of three variants in GALE were identified, including two novel variants (g.2114 A>G and g.2037 G>A) in the 5’-UTR and one previously reported variant (g.3836 G>C) in an intron. All three single nucleotide polymorphisms (SNPs) were associated with milk yield (p<0.0001), fat yield (p = 0.0006 to <0.0001), protein yield (p = 0.0232 to <0.0001) and protein percentage (p<0.0001), while no significant associations were detected between the SNPs and fat percentage. A strong linkage disequilibrium (D’ = 0.96 to 1.00) was observed among all three SNPs, and a 5 Kb haplotype block involving three main haplotypes with GAG, AGC, and AGG was formed. The results of haplotype association analyses were consistent with the results of single locus association analysis (p<0.0001). The phenotypic variance ratio above 3.00% was observed for milk protein yield that was explained by SNP-g.3836G >C.Conclusion: Overall, our findings provided new insights into the polymorphic variations in bovine GALE gene and their associations with milk protein concentration. The data indicate their potential uses for marker-assisted breeding or genetic selection schemes.

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Genetic Analyses Confirm SNPs in HSPA8 and ERBB2 are Associated with Milk Protein Concentration in Chinese Holstein Cattle

Genes ◽

10.3390/genes10020104 ◽

2019 ◽

Vol 10 (2) ◽

pp. 104 ◽

Cited By ~ 1

Author(s):

Cong Li ◽

Miao Wang ◽

Wentao Cai ◽

Shuli Liu ◽

Chenghao Zhou ◽

...

Keyword(s):

Dairy Cattle ◽

Milk Production ◽

Protein Concentration ◽

Milk Protein ◽

Genetic Effects ◽

Production Traits ◽

Rna Seq ◽

Milk Production Traits ◽

Chinese Holstein ◽

Tyrosine Kinase 2

Heat shock 70 kDa protein 8 (HSPA8) and erb-b2 receptor tyrosine kinase 2 (ERBB2) were the promising candidates for milk protein concentration in dairy cattle revealed through previous RNA sequencing (RNA-Seq) study. The objective of this post-RNA-Seq study was to confirm genetic effects of HSPA8 and ERBB2 on milk protein concentration in a large Chinese Holstein population and to evaluate the genetic effects of both genes on other milk production traits. There were 2 singlenucleotide polymorphisms (SNPs) identified for HSPA8 and 11 SNPs for ERBB2 by sequencing 17 unrelated Chinese Holstein sires. The SNP-rs136632043 in HSPA8 had significant associations with all five milk production traits (p = 0.0086 to p < 0.0001), whereas SNP-rs132976221 was remarkably associated with three yield traits (p < 0.0001). Nine (ss1996900615, rs109017161, rs109122971, ss1996900614, rs110133654, rs109941438, rs110552983, rs133031530, and rs109763505) of 11 SNPs in ERBB2 were significantly associated with milk protein percentage (p = 0.0177 to p < 0.0001). A 12 Kb haplotype block was formed in ERBB2 and haplotype associations revealed similar effects on milk protein traits. Our findings confirmed the significant genetic effects of HSPA8 and ERBB2 on milk protein concentration and other milk production traits and SNP phenotypic variances above 1% may serve as genetic markers in dairy cattle breeding programs.

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