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.

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.

Using quantile regression for fitting lactation curve in dairy cows

2019 ◽  
Vol 86 (1) ◽  
pp. 19-24
Author(s):  
Hossein Naeemipour Younesi ◽  
Mohammad Mahdi Shariati ◽  
Saeed Zerehdaran ◽  
Mehdi Jabbari Nooghabi ◽  
Peter Løvendahl
Keyword(s):  
Quantile Regression ◽  
Dairy Cows ◽  
Milk Production ◽  
Milk Yield ◽  
Information Criterion ◽  
Production Traits ◽  
Milk Production Traits ◽  
Fat Percentage ◽  
Protein Percentage ◽  
Breeding Center

AbstractThe main objective of this study was to compare the performance of different ‘nonlinear quantile regression’ models evaluated at theτth quantile (0·25, 0·50, and 0·75) of milk production traits and somatic cell score (SCS) in Iranian Holstein dairy cows. Data were collected by the Animal Breeding Center of Iran from 1991 to 2011, comprising 101 051 monthly milk production traits and SCS records of 13 977 cows in 183 herds. Incomplete gamma (Wood), exponential (Wilmink), Dijkstra and polynomial (Ali & Schaeffer) functions were implemented in the quantile regression. Residual mean square, Akaike information criterion and log-likelihood from different models and quantiles indicated that in the same quantile, the best models were Wilmink for milk yield, Dijkstra for fat percentage and Ali & Schaeffer for protein percentage. Over all models the best model fit occurred at quantile 0·50 for milk yield, fat and protein percentage, whereas, for SCS the 0·25th quantile was best. The best model to describe SCS was Dijkstra at quantiles 0·25 and 0·50, and Ali & Schaeffer at quantile 0·75. Wood function had the worst performance amongst all traits. Quantile regression is specifically appropriate for SCS which has a mixed multimodal distribution.

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.

AGPAT3 Gene polymorphisms are associated with milk production traits in Chinese Holstein cows

2021 ◽  
pp. 1-6
Author(s):  
Xiaomei Sun ◽  
Yan Liang ◽  
Qisong Gao ◽  
Jiahe Guo ◽  
Cheng Tang ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Fat Percentage ◽  
Urea Nitrogen ◽  
Protein Percentage ◽  
Milk Urea ◽  
Milk Urea Nitrogen

Abstract The current study reports the identification of previously undiscovered single-nucleotide polymorphisms (SNPs) in the bovine AGPAT3 gene and further investigates their associations with milk production traits. Our results demonstrate that the major allele C of the SNP g.12264 C > T is positively correlated with test-day milk yield, protein percentage and 305-day milk yield. Importantly, in silico analysis showed that the C/T transition at this locus gives rise to two new transcription factor binding sites (TFBS), E2F1 and Nkx3-2. Polymorphism g.18658 G > A was the only SNP associated with milk urea nitrogen (MUN) with the G allele related to an increase in milk urea nitrogen as well as fat percentage. The GG genotype of SNP g.28731 A > G was associated with the highest fat and protein percentage and lowest 305-day milk yield and somatic cell score (SCS). The association between AGPAT3 locus and milk production traits could be utilized in marker-assisted selection for the genetic improvement of milk production traits and, probably in conjunction with other traits, for selection to improve fitness of dairy cattle.

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.

An association analysis between PRL genotype and milk production traits in Italian Mediterranean river buffalo

2017 ◽  
Vol 84 (4) ◽  
pp. 430-433 ◽  
Author(s):  
Jun Li ◽  
Aixin Liang ◽  
Zipeng Li ◽  
Chao Du ◽  
Guohua Hua ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Milk Fat ◽  
Fat Content ◽  
Phenotypic Variance ◽  
River Buffalo ◽  
Production Traits ◽  
Milk Production Traits ◽  
Exon 2 ◽  
Mediterranean River

This Research Communication describes the association between genetic variation within the prolactin (PRL) gene and the milk production traits of Italian Mediterranean river buffalo (Bufala mediterranea Italiana). High resolution melting (HRM) techniques were developed for genotyping 465 buffaloes. The association of genetic polymorphism with milk production traits was performed and subsequently the effects of parity and calving season were evaluated. Single nucleotide polymorphisms (SNPs) were identified at exons 2 and 5 and at introns 1 and 2. All the SNPs were in Hardy–Weinberg equilibrium, and statistical analysis showed that the polymorphism of intron1 was significantly (P < 0·05) associated with milk yield, milk protein content and peak milk yield. The average contribution of the intron1 genotype (r2intron1) to total phenotypic variance in milk production traits was 0·09, and the TT genotype showed lower values than CC and CT genotypes. A nonsynonymous SNP was identified in exon 2, which resulted in an amino acid change from arginine to cysteine. Moreover, the polymorphism of exon 2 was associated significantly with milk fat content (P < 0·05), and the buffaloes with TT genotype showed higher total fat content than the buffaloes with CT genotype. These findings provide evidence that polymorphisms of the buffalo PRL gene are associated with milk production traits and PRL can be used as a candidate gene for marker-assisted selection in Italian Mediterranean river buffalo breeding.

scholarly journals Sequence Variations in the Bovine Growth Hormone Gene Characterized by Single-Strand Conformation Polymorphism (SSCP) Analysis and Their Association with Milk Production Traits in Holsteins

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1809-1816 ◽  
Author(s):  
Jianbo Yao ◽  
Samuel E Aggrey ◽  
David Zadworny ◽  
J Flan Hayes ◽  
Urs Kühnlein
Keyword(s):  
Growth Hormone ◽  
Milk Production ◽  
Milk Yield ◽  
Single Strand Conformation Polymorphism ◽  
Sscp Analysis ◽  
Bovine Growth Hormone ◽  
Production Traits ◽  
Milk Production Traits ◽  
Sequence Variations ◽  
Conformation Polymorphism

Sequence variations in the bovine growth hormone (GH) gene were investigated by single strand conformation polymorphism (SSCP) analysis of seven amplified fragments covering almost the entire gene (2.7 kb). SSCPs were detected in four of these fragments and a total of six polymorphisms were found in a sample of 128 Holstein bulls. Two polymorphisms, a T→C transition in the third intron (designated GH4.1) and an A→C transversion in the fifth exon (designated GH6.2), were shown to be associated with milk production traits. GH4.1c/GH4.1c bulls had higher milk yield than GH4.1c/GH4.1t (P ≤ 0.005) and GH4.1t/GH4.1t (P ≤ 0.0022) bulls. GH4.1c/GH4.1c bulls had higher kg fat (P ≤ 0.0076) and protein (P ≤ 0.0018) than GH4.1c/GH4.1t bulls. Similar effects on milk production traits with the GH6.2 polymorphism were observed with the GH6.2a allele being the favorable allele. The average effects of the gene substitution for GH4.1 and GH6.2 are similar, with ±300 kg for milk yield, ±8 kg for fat content and ±7 kg for protein content per lactation. The positive association of GH4.1c and GH6.2a with milk production traits may be useful for improving milk performance in dairy cattle.

Investigation of myostatin and calpain 3 gene polymorphisms and their association with milk-production traits in Sfakia sheep

2020 ◽  
Vol 60 (3) ◽  
pp. 347
Author(s):  
Adel H. M. Ibrahim ◽  
Nikolaos Tzanidakis ◽  
Smaragda Sotiraki ◽  
Huitong Zhou ◽  
Jonathan Hickford
Keyword(s):  
Nucleotide Sequence ◽  
Milk Production ◽  
Milk Yield ◽  
Milk Fat ◽  
Fat Content ◽  
Solid Content ◽  
Production Traits ◽  
Milk Production Traits ◽  
Banding Patterns ◽  
Milk Solid

Context Genetic selection based on genetic markers for economically important traits in Sfakia sheep. Aims The aim of the present study was to investigate variation in the ovine myostatin gene (MSTN) and calpain 3 gene (CAPN3), and their association with milk-production traits. Methods Records for milk yield, milk fat content, protein content, lactose content, and non-fat solid content, pH and somatic-cell score (log), were obtained from 376 Sfakia ewes. Polymerase chain reaction–single-strand conformational polymorphism (PCR–SSCP) analyses were used to detect variation in intron 1 of MSTN and exon 10 of CAPN3. General linear models were then used to test for associations between the variation in MSTN and CAPN3, and milk-production traits. Key results The SSCP banding patterns for MSTN showed four variants (A1, A2, A3 and A4), which contained nine nucleotide sequence differences. Four SSCP banding patterns (C1, C2, C3 and C4) were observed for CAPN3 and these contained eight nucleotide-sequence differences. The MSTN variation was associated (P &lt; 0.05) with variation in milk yield and non-fat milk solid content. Variation in CAPN3 was associated with milk yield (P &lt; 0.001), fat content (P &lt; 0.05) and lactose content (P &lt; 0.05). Association analyses between the presence/absence of MSTN and CAPN3 variants and milk-production traits showed that a variant of MSTN that had previously between associated with muscle hypertrophy was associated with decreased milk yield (P &lt; 0.05) and a lower non-fat milk solid content (P &lt; 0.01). A CAPN3 variant that had previously been associated with increased sheep-carcass loin lean-meat yield was associated with a decreased milk yield (P &lt; 0.01) and a decreased milk fat content (P &lt; 0.05). Conclusions Our results have provided an insight into the effects of variation in ovine MSTN and CAPN3 on milk-production traits in sheep. Implications To preserve the dual-purpose characteristics of Sfakia sheep, breeding goals should take into account the possible antagonism between meat and milk traits.

scholarly journals Analyses of genetic relationships between linear type traits, fat-to-protein ratio, milk production traits, and somatic cell count in first-parity Czech Holstein cows

2014 ◽  
Vol 59 (No. 12) ◽  
pp. 539-547 ◽  
Author(s):  
V. Zink ◽  
L. Zavadilová ◽  
J. Lassen ◽  
M. Štípková ◽  
M. Vacek ◽  
...  
Keyword(s):  
Somatic Cell ◽  
Milk Yield ◽  
Somatic Cell Score ◽  
Protein Yield ◽  
Production Traits ◽  
Linear Type ◽  
Protein Percentage ◽  
Phenotypic Correlations ◽  
Type Traits ◽  
Fat Yield

Genetic and phenotypic correlations between production traits, selected linear type traits, and somatic cell score were estimated. The results could be useful for breeding programs involving Czech Holstein dairy cows or other populations. A series of bivariate analyses was applied whereby (co)variance components were estimated using average information (AI-REML) implemented via the DMU statistical package. Chosen phenotypic data included average somatic cell score per a 305-day standard first lactation as well as the production traits milk yield, fat yield, protein yield, fat percentage, and protein percentage per the standard first lactation. Fifteen classified linear type traits were added, as they were measured at first lactation in the Czech Holstein population. All phenotypic data were collected within the progeny testing program of the Czech-Moravian Breeders Corporation from 2005 to 2009. The number of animals for each linear type trait was 59&nbsp;454, except for locomotion, for which 53 424 animals were recorded. The numbers of animals with records of&nbsp;milk production data were 43 992 for milk yield, fat percentage, protein percentage, and fat-to-protein percentage ratio and 43 978 for fat yield and protein yield. In total, 27 098 somatic cell score records were available. The strongest positive genetic correlation between production traits and linear type traits was estimated between udder width and fat yield (0.51 &plusmn; 0.04), while the strongest negative correlation estimated was between body condition score and fat yield (&minus;0.45 &plusmn; 0.03). Other estimated correlations were between those two extremes but generally they were close to zero or positive. The strongest negative phenotypic correlations were estimated between udder depth and milk yield and protein yield (both &minus;0.17), while the strongest positive phenotypic correlations were estimated between milk yield, protein yield, and udder width (both 0.32). &nbsp;

Relationship between udder and teat conformation and milk yield performance in dairy cows pre- and post-milking

2007 ◽  
Vol 87 (3) ◽  
pp. 285-289 ◽  
Author(s):  
Nilufer Sabuncuoglu ◽  
Omer Coban
Keyword(s):  
Dairy Cows ◽  
Milk Production ◽  
Milk Yield ◽  
Relative Reduction ◽  
Production Traits ◽  
Milk Production Traits ◽  
Simple Method ◽  
Absolute Reduction ◽  
Daily Milk Yield ◽  
Daily Milk

The objectives of this study were to determine the relationship between udder floor area (UFA) and milk production traits in dairy cows, pre- and post-milking, as well as to examine the usefulness of a simple method of measuring UFA. The absolute reduction (AR, cm2) and relative reduction (RR, %) in UFA post-milking relative to pre-milking was calculated. Absolute reduction was influenced by breed and lactation stage, but not by parity of the cows (P < 0.05). There was no effect of breed and stage of lactation on the RR of UFA. Moderate correlations were observed between absolute reduction of UFA and daily milk yield (r2 = 0.422), lactation milk yield (r2 = 0.426), and absolute fat yield (r2 = 0.515) (P < 0.01 and P < 0.05). Moderate and weak correlations were found between RR of UFA and daily milk yield (r2 = 0.335) (P < 0.01), AR of the udder area and the 305-d lactation milk yield (r2 = 0.326) (P < 0.10). It was concluded that measuring UFA using the method described may be useful for the selection of dairy cattle mammary conformation traits. Key words: Dairy cow, udder and teat conformation, milk production traits, measurement technique

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