Association of <i>MAP4K4 gene</i> single nucleotide polymorphism with mastitis and milk traits in Chinese Holstein cattle

Bhattarai, Dinesh; Chen, Xing; Rehman, Zia Ur; Hao, Xingjie; Ullah, Farman; Dad, Rahim; Talpur, Hira Sajjad; Kadariya, Ishwari; Fan, Mingxia; Zhang, Shujun

doi:10.1017/s0022029916000832

Cited by 23 publications

(16 citation statements)

References 10 publications

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“…Studies showing the important roles of SNPs for milk production traits in dairy cattle have been reported previously [8,9,10,22]. Pegolo et al discovered two SNPs, rs136905033 and rs137457402, of LPIN1 associated with milk fatty acids in bovine [23].…”

Section: Discussionmentioning

confidence: 99%

“…Genome-wide studies in dairy cows have allowed researchers to detect quantitative trait locus (QTL) harboring candidate polymorphic genes that are involved in milk production [3,4,5]. Moreover, studies have shown that the single nucleotide polymorphisms (SNPs) in the genes clearly influenced the milk yield and composition in Holsteins [6,7,8,9,10]. These results collectively suggest that loci found to affect milk production traits could be used in marker-assisted selection programs aimed at accelerating genetic progress of dairy cattle.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Effects of LPIN1 Polymorphisms on Milk Production Traits in Dairy Cattle

Han

Yuán

Liang

et al. 2019

Genes

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Our initial RNA sequencing work identified that lipin 1 (LPIN1) was differentially expressed during dry period, early lactation, and peak of lactation in dairy cows, and it was enriched into the fat metabolic Gene Ontology (GO) terms and pathways, thus we considered LPIN1 as the candidate gene for milk production traits. In this study, we detected the polymorphisms of LPIN1 and verified their genetic effects on milk yield and composition in a Chinese Holstein cow population. We found seven SNPs by re-sequencing the entire coding region and partial flanking region of LPIN1, including one in 5′ flanking region, four in exons, and two in 3′ flanking region. Of these, four SNPs, c.637T > C, c.708A > G, c.1521C > T, and c.1555A > C, in the exons were predicted to result in the amino acid replacements. With the Haploview 4.2, we found that seven SNPs in LPIN1 formed two haplotype blocks (D′ = 0.98–1.00). Single-SNP association analyses showed that SNPs were significantly associated with milk yield, fat yield, fat percentage, or protein yield in the first or second lactation (p = < 0.0001–0.0457), and only g.86049389C > T was strongly associated with protein percentage in both lactations (p = 0.0144 and 0.0237). The haplotype-based association analyses showed that the two haplotype blocks were significantly associated with milk yield, fat yield, protein yield, or protein percentage (p = < 0.0001–0.0383). By quantitative real-time PCR (qRT-PCR), we found that LPIN1 had relatively high expression in mammary gland and liver tissues. Furthermore, we predicted three SNPs, c.637T > C, c.708A > G, and c.1521C > T, using SOPMA software, changing the LPIN1 protein structure that might be potential functional mutations. In summary, we demonstrated the significant genetic effects of LPIN1 on milk production traits, and the identified SNPs could serve as genetic markers for dairy breeding.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Effects of LPIN1 Polymorphisms on Milk Production Traits in Dairy Cattle

Han

Yuán

Liang

et al. 2019

Genes

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“…Animal sampling, DNA extraction, primer design and SNP study For the initial mutation screening for exon 8 (K232A), a total of 84 blood samples including 41 cows and 43 buffaloes were used and DNA was extracted as described by Bhattarai et al (2017).…”

Section: Methodsmentioning

confidence: 99%

The functions and mechanisms of sequence differences of DGAT1 gene on milk fat synthesis between dairy cow and buffalo

Bhattarai

Dad

Worku

et al. 2020

Journal of Dairy Research

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In this research communication we describe the DGAT1 sequence and promoter region in dairy cows and buffalo and compare the activities of DGAT1 between the two species in order to increase knowledge of the cause of milk fat variation. pGL-3 basic vectors were used to construct the reporter gene. Based on the predicted promoter region, 4 truncated plasmid vectors were constructed in cow-DGAT1 and 3 plasmid vectors in buffalo-DGAT1. Each reporter plasmid was transfected into the bovine mammary epithelial cell (BMEC), 293T cell, and CHO cells to analyze the activity using Dual-Luciferase Reporter Assay System. The results show that the region between −93 to −556 bp was essential for cow promoter activity while −84 to −590 bp was essential for buffalo promoter activity revealing these regions contain core promoter. The buffalo has higher promoter activity than cow yet it was not statistically significant. Comparison of candidate mutation K232A between cow and buffalo population revealed the presence of both the allelic population in dairy cows (lysine and alanine) however, only K (lysine) allelic amino acid was found in buffalo population. The absence of the alanine allelic population from buffalo explains the higher fat content of buffalo milk.

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“…A study has revealed that the use of available loci improved the accuracy of genomic prediction in dairy cattle [19], which suggests that loci that are associated with milk production traits could be used in genomic selection programs that are aimed at accelerating genetic progress of dairy cattle. Studies have shown that the SNPs in the candidate genes significantly influenced the milk yield and composition in Holsteins [20,21,22,23,24,25]. In this study, we identified ten SNPs in NUCB2 and found that the SNPs and haplotypes of this gene were significantly associated with milk production traits.…”

Section: Discussionmentioning

confidence: 68%

Single Nucleotide Polymorphisms of NUCB2 and Their Genetic Associations with Milk Production Traits in Dairy Cows

Han

Yuán

et al. 2019

Genes

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We previously used the RNA sequencing technique to detect the hepatic transcriptome of Chinese Holstein cows among the dry period, early lactation, and peak of lactation, and implied that the nucleobindin 2 (NUCB2) gene might be associated with milk production traits due to its expression being significantly increased in early lactation or peak of lactation as compared to dry period (q value < 0.05). Hence, in this study, we detected the single nucleotide polymorphisms (SNPs) of NUCB2 and analyzed their genetic associations with milk yield, fat yield, fat percentage, protein yield, and protein percentage. We re-sequenced the entire coding and 2000 bp of 5′ and 3′ flanking regions of NUCB2 by pooled sequencing, and identified ten SNPs, including one in 5′ flanking region, two in 3′ untranslated region (UTR), and seven in 3′ flanking region. The single-SNP association analysis results showed that the ten SNPs were significantly associated with milk yield, fat yield, fat percentage, protein yield, or protein percentage in the first or second lactation (p values <= 1 × 10−4 and 0.05). In addition, we estimated the linkage disequilibrium (LD) of the ten SNPs by Haploview 4.2, and found that the SNPs were highly linked in one haplotype block (D′ = 0.98–1.00), and the block was also significantly associated with at least one milk traits in the two lactations (p values: 0.0002–0.047). Further, we predicted the changes of transcription factor binding sites (TFBSs) that are caused by the SNPs in the 5′ flanking region of NUCB2, and considered that g.35735477C>T might affect the expression of NUCB2 by changing the TFBSs for ETS transcription factor 3 (ELF3), caudal type homeobox 2 (CDX2), mammalian C-type LTR TATA box (VTATA), nuclear factor of activated T-cells (NFAT), and v-ets erythroblastosis virus E26 oncogene homolog (ERG) (matrix similarity threshold, MST > 0.85). However, the further study should be performed to verify the regulatory mechanisms of NUCB2 and its polymorphisms on milk traits. Our findings first revealed the genetic effects of NUCB2 on the milk traits in dairy cows, and suggested that the significant SNPs could be used in genomic selection to improve the accuracy of selection for dairy cattle breeding.

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Association of MAP4K4 gene single nucleotide polymorphism with mastitis and milk traits in Chinese Holstein cattle

Cited by 23 publications

References 10 publications

Genetic Effects of LPIN1 Polymorphisms on Milk Production Traits in Dairy Cattle

Genetic Effects of LPIN1 Polymorphisms on Milk Production Traits in Dairy Cattle

The functions and mechanisms of sequence differences of DGAT1 gene on milk fat synthesis between dairy cow and buffalo

Single Nucleotide Polymorphisms of NUCB2 and Their Genetic Associations with Milk Production Traits in Dairy Cows

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