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

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 449 ◽  
Author(s):  
Bo Han ◽  
Yuwei Yuan ◽  
Yanhua Li ◽  
Lin Liu ◽  
Dongxiao Sun
Keyword(s):  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Genetic Associations ◽  
Milk Production Traits ◽  
Fat Percentage ◽  
Dry Period ◽  
Milk Traits ◽  
Single Nucleotide ◽  
Flanking Region ◽  
Fat Yield

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.

scholarly journals Identification of single nucleotide polymorphisms of PIK3R1 and DUSP1 genes and their genetic associations with milk production traits in dairy cows

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Bo Han ◽  
Yuwei Yuan ◽  
Lijun Shi ◽  
Yanhua Li ◽  
Lin Liu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dairy Cows ◽  
Milk Production ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Genetic Associations ◽  
Milk Production Traits ◽  
Single Nucleotide ◽  
Association Analyses ◽  
Flanking Region

Abstract Background Previously, phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) and dual specificity phosphatase 1 (DUSP1) were identified as promising candidate genes for milk production traits due to their being differentially expressed between the dry period and the peak of lactation in livers of dairy cows. Hence, in this study, the single nucleotide polymorphisms (SNPs) of PIK3R1 and DUSP1 genes were identified and their genetic associations with milk yield, fat yield, fat percentage, protein yield, and protein percentage, were investigated using 1067 Chinese Holstein cows from 40 sire families. Results By re-sequencing the entire coding region and 2000 bp of the 5′ and 3′ flanking regions of the two genes, one SNP in the 5′ untranslated region (UTR), three in the 3′ UTR, and two in the 3′ flanking region of PIK3R1 were identified, and one in the 5′ flanking region, one in the 3′ UTR, and two in the 3′ flanking region of DUSP1 were found. Subsequent single-locus association analyses showed that five SNPs in PIK3R1, rs42590258, rs210389799, rs208819656, rs41255622, rs133655926, and rs211408208, and four SNPs in DUSP1, rs207593520, rs208460068, rs209154772, and rs210000760, were significantly associated with milk, fat and protein yields in the first or second lactation (P values ≤ 0.0001 and 0.0461). In addition, by the Haploview 4.2 software, the six and four SNPs in PIK3R1 and DUSP1 respectively formed one haplotype block, and the haplotype-based association analyses showed significant associations between their haplotype combinations and the milk traits in both two lactations (P values ≤ 0.0001 and 0.0364). One SNP, rs207593520(T/G), was predicted to alter the transcription factor binding sites (TFBSs) in the 5′ flanking region of DUSP1. Further, the dual-luciferase assay showed that the transcription activity of allele T in rs207593520 was significantly higher than that of allele G, suggesting the activation of transcriptional activity of DUSP1 gene by allele T of rs207593520. Thus, the rs207593520 SNP was highlighted as a potential causal mutation that should be further verified. Conclusions We demonstrated novel and significant genetic effects of the PIK3R1 and DUSP1 genes on milk production traits in dairy cows, and our findings provide information for use in dairy cattle breeding.

Study on candidate genes for milk production traits of Red Chittagong Cattle

2020 ◽  
Vol 26 (1-2) ◽  
pp. 1-7
Author(s):  
MP Mostari ◽  
MYA Khan
Keyword(s):  
Candidate Genes ◽  
Milk Production ◽  
Milk Fat ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Single Nucleotide ◽  
Lactating Cows ◽  
Pooled Dna ◽  
Fat Yield

The study was carried out on Stearoyl-CoA desaturase (SCD,) diacylglycerolacyltransferase-1 (DGAT1) and ATP-binding cassette G2 (ABCG2) genes which are responsible for variation in milk production traits (milk yield, fat yield, protein yield, and SNF yield) in cattle. These genes were used as candidate genes in Red Chittagong Cattle (RCC) breed of Bangladesh Livestock Research Institute (BLRI) herd for detection of single nucleotide polymorphisms (SNPs) causing variation in milk production traits. Focusing on the effects of SNPs on milk production traits, phenotypic variation within RCC breed was identified and categorized based on milk production traits. Average lactation yield varied from 527 to 1436 kg (n=29) per lactation. About 18% of lactating cows showed an average of >1000 kg per lactation. Average fat percent ranged from 4.71 to 6.25 (n=15). Eighteen (18) set of primers were designed to amplify targeted regions of SCD, DGAT1 and ABCG2 genes, where 8 set from DGAT1, 6 set from SCD and 4 set from ABCG2 gene. Pooled DNA from 50 RCC cows and 5 RCC bulls were used in sequencing. In sequence analysis, the SCD, DGAT1 and ABCG2 alleles found fixed in RCC. This study suggests an evidence that RCC breed has fixed alleles with respect to SCD, DGAT1 and ABCG2 genes reported to be responsible for higher milk fat yield, higher fat and protein percent. Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 1-7

scholarly journals Association of single nucleotide polymorphisms in the fatty acid synthase, LOC514211, and fat mass and obesity-associated genes with milk traits in Indonesian-Holstein dairy cattle

2019 ◽  
Vol 12 (7) ◽  
pp. 1160-1166
Author(s):  
Amalia Puji Rahayu ◽  
Tety Hartatik ◽  
Agung Purnomoadi ◽  
Edy Kurnianto
Keyword(s):  
Fatty Acid ◽  
Single Nucleotide Polymorphisms ◽  
Fat Mass ◽  
Milk Protein ◽  
Fatty Acid Synthase ◽  
Nucleotide Polymorphisms ◽  
Fat Percentage ◽  
Fto Gene ◽  
Milk Traits ◽  
Single Nucleotide

Aim: The study aimed to identify fatty acid synthase (FASN), LOC514211, and fat mass and obesity-associated (FTO) gene polymorphisms and to investigate their associations with milk traits in an Indonesian-Holstein dairy cow population. Materials and Methods: A total of 100 Indonesian-Holstein cows consisting of 50 heads (0th generation; G0) and 50 heads of their daughters (1st generation; G1) were used. Polymerase chain reaction-restriction fragment length polymorphism was performed to genotype three single nucleotide polymorphisms: rs41919985 in the FASN gene, rs42688595 in the LOC514211 gene, and g.1371T>A in the FTO gene. Results: FASN rs41919985 was associated with milk protein percentage (p<0.05), FTO g.1371T>A was associated with milk fat percentage (p<0.05), and LOC514211 rs42688595 was not associated with any trait (p>0.05). Heterozygote variants showed a higher protein percentage for FASN and the highest fat percentage for FTO. These associations were consistent in the G0 and G1 populations. Conclusion: Our results indicate that the milk protein and fat percentages can be improved by increasing the frequency of the AG genotype of FASN and the AT genotype of FTO, respectively.

scholarly journals Associations between polymorphisms of SLC22A7, NGFR, ARNTL and PPP2R2B genes and Milk production traits in Chinese Holstein

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruike Jia ◽  
Yihan Fu ◽  
Lingna Xu ◽  
Houcheng Li ◽  
Yanhua Li ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Milk Production ◽  
Association Analysis ◽  
Milk Yield ◽  
Production Traits ◽  
Milk Production Traits ◽  
Fat Percentage ◽  
Protein Percentage ◽  
Fat Yield ◽  
Percentage Protein

Abstract Background Our preliminary work confirmed that, SLC22A7 (solute carrier family 22 member 7), NGFR (nerve growth factor receptor), ARNTL (aryl hydrocarbon receptor nuclear translocator like) and PPP2R2B (protein phosphatase 2 regulatory subunit Bβ) genes were differentially expressed in dairy cows during different stages of lactation, and involved in the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, so we considered these four genes as the candidates affecting milk production traits. In this study, we detected polymorphisms of the four genes and verified their genetic effects on milk yield and composition traits in a Chinese Holstein cow population. Results By resequencing the whole coding region and part of the flanking region of SLC22A7, NGFR, ARNTL and PPP2R2B, we totally found 20 SNPs, of which five were located in SLC22A7, eight in NGFR, three in ARNTL, and four in PPP2R2B. Using Haploview4.2, we found three haplotype blocks including five SNPs in SLC22A7, eight in NGFR and three in ARNTL. Single-SNP association analysis showed that 19 out of 20 SNPs were significantly associated with at least one of milk yield, fat yield, fat percentage, protein yield or protein percentage in the first and second lactations (P < 0.05). Haplotype-based association analysis showed that the three haplotypes were significantly associated with at least one of milk yield, fat yield, fat percentage, protein yield or protein percentage (P < 0.05). Further, we used SOPMA software to predict a SNP, 19:g.37095131C > T in NGFR, changed the structure of NGFR protein. In addition, we used Jaspar software to found that four SNPs, 19:g.37113872C > G,19:g.37113157C > T, and 19:g.37112276C > T in NGFR and 15:g.39320936A > G in ARNTL, could change the transcription factor binding sites and might affect the expression of the corresponding genes. These five SNPs might be the potential functional mutations for milk production traits in dairy cattle. Conclusions In summary, we proved that SLC22A7, NGFR, ARNTL and PPP2R2B have significant genetic effects on milk production traits. The valuable SNPs can be used as candidate genetic markers for genomic selection of dairy cattle, and the effects of these SNPs on other traits need to be further verified.

scholarly journals Polymorphisms of the PRLR Gene and Their Association with Milk Production Traits in Egyptian Buffaloes

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1237
Author(s):  
Mohammed A. El-Magd ◽  
Aziza Fathy ◽  
Khaled A. Kahilo ◽  
Ayman A. Saleh ◽  
Ahmed I. El Sheikh ◽  
...  
Keyword(s):  
Milk Production ◽  
Association Studies ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Milk Traits ◽  
Water Buffaloes ◽  
Protein Levels ◽  
Milk Performance

Prolactin (PRL) and its receptor (PRLR) were considered as potential genetic markers for milk production and quality traits in cattle. However, little information is available regarding PRLR genetic diversity and association studies with milk traits in Egyptian water buffaloes. Therefore, the present study was conducted to search for mutations in PRLR and determine their associations with milk performance in these animals. Exon3 (E3) and E10 of PRLR were screened for polymorphisms using single strand conformation polymorphism (SSCP) and sequencing in 400 buffaloes. The associations between haplotypes and milk production (fat%, protein%, lactose%, and solid%) traits as well as mRNA and protein levels of PRL and PRLR were studied. Two single nucleotide polymorphisms (SNPs) in E10 were detected: g.11685G>A (p.Ala494Thr) and g.11773T>C (p.Val523Aal). The G and T alleles were wild (ancestral) alleles, while the A and C alleles were mutant alleles. These SNPs resulted in four haplotypes; AC, AT, GC, and GT. Buffaloes with wild GT haplotypes showed significantly higher milk yield, fat% and protein%, mRNA and protein levels of PRL and PRLR in milk somatic cells than other animals. Animals carrying mutant AC haplotype had inferior milk traits and lowest levels of associated mRNAs and proteins. With these results, we could conclude that the selection of buffaloes with wild GT haplotypes for g.11685G>A and g.11773T>C SNPs of the PRLR gene might improve the milk production traits of Egyptian water buffaloes.

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

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 265 ◽  
Author(s):  
Bo Han ◽  
Yuwei Yuan ◽  
Ruobing Liang ◽  
Yanhua Li ◽  
Lin Liu ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Genetic Effects ◽  
Production Traits ◽  
Milk Production Traits ◽  
Association Analyses ◽  
Protein Percentage ◽  
Haplotype Blocks ◽  
Flanking Region ◽  
Fat Yield

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.

Effects of polymorphism in the 5′-flanking region of the IGF-I gene on milk-production traits in Chinese Holstein cattle

2012 ◽  
Vol 52 (9) ◽  
pp. 795 ◽  
Author(s):  
M. A. Alim ◽  
Yan Xie ◽  
Yipeng Fan ◽  
Xiaoping Wu ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Milk Production ◽  
Holstein Cattle ◽  
Production Traits ◽  
Milk Production Traits ◽  
Chinese Holstein ◽  
Chinese Holstein Cattle ◽  
Igf I ◽  
Flanking Region ◽  
Fat Yield ◽  
I Gene

Milk and milk products are major components of human dietary intake and have a potential influence on health. In our experiment, associations between insulin-like growth factor 1 (IGF-I) gene polymorphism and milk-production traits were analysed in Chinese Holstein cattle. A polymorphism, transition at position g.1407 T > C, was identified in the 5′-flanking region of the IGF-I gene by pooled DNA sequencing. The identified single-nucleotide polymorphism (SNP) was genotyped by matrix-assisted laser desorption–ionisation time-of-flight mass spectrometry (MALDI–TOF MS) methods from 752 individuals. Significant associations between IGF-I genotypes and 305-day milk yield, fat yield and protein yield were found. Homozygous cows with TT genotype showed the highest milk, fat and protein yields, with increases of 532.75 kg, 23.57 kg and 14.69 kg, respectively, as compared with homozygous CC cows. Heterozygous CT cows had intermediate yields. Allele substitution showed that the C allele decreased milk yield (255.23 kg), fat yield (11.37 kg) and protein yield (7.05 kg), whereas it increased protein percentage (0.01%). The results suggest that IGF-I is a candidate gene that influences milk-production traits, and provides useful information to be implemented in breeding programs to improve the performance of the Chinese Holstein.

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