Mediterranean river buffalo CSN1S1 gene: search for polymorphisms and association studies

The aim of the present study was to investigate the variability at CSN1S1 locus of the Italian Mediterranean river buffalo and to study possible allele effects on milk yield and its composition. Effects of parity, calving season and month of production were also evaluated. Three single-nucleotide polymorphisms were detected. The first mutation, located at position 89 of the 17th exon (c.628C>T), is responsible for the amino acid change p.Ser178 (B allele)/Leu178 (A allele). The other two polymorphisms, detected at the positions 144 (c.882G>A) and 239 (c.977A>G) of 19th exon, respectively, are silent (3ʹ UTR, untranslated region). Associations between the CSN1S1 genotypes and milk production traits were investigated using 4122 test day records of 503 lactations from 175 buffalo cows. Milk yield, fat and protein percentages were analysed using a mixed linear model. A significant association between the c.628C>T SNP and the protein percentage was found. In particular, the CC genotype showed an average value ~0.04% higher than the CT and TT genotypes. The allele substitution effect of cytosine into thymine was –0.014, with a quite low (0.3%) protein percentage contribution to total phenotypic variance. A large dominance effect was detected. Characterisation of the CSN1S1 transcripts and a method based on MboI amplification created restriction site PCR for a rapid genotyping of c.628C>T are provided.

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

Journal of Dairy Research ◽

10.1017/s0022029917000693 ◽

2017 ◽

Vol 84 (4) ◽

pp. 430-433 ◽

Cited By ~ 6

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.

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Genetic variability detected at the lactoferrin locus (LTF) in the Italian Mediterranean river buffalo

Animal Production Science ◽

10.1071/an14612 ◽

2016 ◽

Vol 56 (1) ◽

pp. 102

Author(s):

Alfredo Pauciullo ◽

Luigi Ramunno ◽

Nicolò P. P. Macciotta ◽

Giustino Gaspa ◽

Angelo Coletta ◽

...

Keyword(s):

Genetic Variability ◽

Milk Yield ◽

Large Scale ◽

Milk Composition ◽

Potential Candidate ◽

River Buffalo ◽

Nucleotide Polymorphisms ◽

Functional Protein ◽

Mediterranean River ◽

Ruminant Species

Lactoferrin (LTF) is a multi-functional protein belonging to the whey protein fractions of milk. The gene LTF encoding for such protein is considered a potential candidate for body measurement, milk composition and yield. This study reports on the genetic variability at the LTF locus in the Italian Mediterranean river buffalo and its possible association with milk yield. Eleven polymorphic sites were found in the DNA fragment spanning exons 15–16. In particular, intron 15 was extremely polymorphic with nine single nucleotide polymorphisms (SNPs) detected, whereas the remaining two SNPs were exonic mutations (g.88G > A at exon 15 and g.1351G > A at exon 16) and both synonymous. The genotyping of the informative samples evidenced three haplotypes, whose frequencies were 0.6, 0.3 and 0.1, respectively, whereas the analysis of the exonic SNPs showed a perfect condition of linkage disequilibrium (g.88A/g.1351G and g.88G/g.1351A). The association study carried out by using the SNP g.88G > A showed that buffalo LTF gene has no statistically significant influence on daily milk yield. This study adds knowledge to the genetic variability of a species less investigated than the other ruminant species. These findings may serve as a useful tool for large-scale screening of buffalo populations.

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

Journal of Dairy Research ◽

10.1017/s0022029921000546 ◽

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.

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Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle

Genetics Selection Evolution ◽

10.1186/s12711-020-00575-1 ◽

2020 ◽

Vol 52 (1) ◽

Cited By ~ 1

Author(s):

Thierry Tribout ◽

Pascal Croiseau ◽

Rachel Lefebvre ◽

Anne Barbat ◽

Mekki Boussaha ◽

...

Keyword(s):

Dairy Cattle ◽

Candidate Genes ◽

Milk Production ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Production Traits ◽

Milk Production Traits ◽

Udder Health ◽

Gwas Approach

Abstract Background Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important traits. However, in general this approach does not allow to validate the effects of candidate mutations or determine if they are truly causative for the trait(s) in question. To address these questions, we applied a two-step, within-breed GWAS approach on 15 traits (5 linked with milk production, 2 with udder health, and 8 with udder morphology) in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cattle. We detected the most-promising candidate variants (CV) using imputed WGS of 2515 MON, 2203 NOR, and 6321 HOL bulls, and validated their effects in three younger populations of 23,926 MON, 9400 NOR, and 51,977 HOL cows. Results Bull sequence-based GWAS detected 84 QTL: 13, 10, and 30 for milk production traits; 3, 0, and 2 for somatic cell score (SCS); and 8, 2 and 16 for udder morphology traits, in MON, NOR, and HOL respectively. Five genomic regions with effects on milk production traits were shared among the three breeds whereas six (2 for production and 4 for udder morphology and health traits) had effects in two breeds. In 80 of these QTL, 855 CV were highlighted based on the significance of their effects and functional annotation. The subsequent GWAS on MON, NOR, and HOL cows validated 8, 9, and 23 QTL for production traits; 0, 0, and 1 for SCS; and 4, 1, and 8 for udder morphology traits, respectively. In 47 of the 54 confirmed QTL, the CV identified in bulls had more significant effects than single nucleotide polymorphisms (SNPs) from the standard 50K chip. The best CV for each validated QTL was located in a gene that was functionally related to production (36 QTL) or udder (9 QTL) traits. Conclusions Using this two-step GWAS approach, we identified and validated 54 QTL that included CV mostly located within functional candidate genes and explained up to 6.3% (udder traits) and 37% (production traits) of the genetic variance of economically important dairy traits. These CV are now included in the chip used to evaluate French dairy cattle and can be integrated into routine genomic evaluation.

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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

Czech Journal of Animal Science ◽

10.17221/7793-cjas ◽

2014 ◽

Vol 59 (No. 12) ◽

pp. 539-547 ◽

Cited By ~ 5

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 59 454, except for locomotion, for which 53 424 animals were recorded. The numbers of animals with records of 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 ± 0.04), while the strongest negative correlation estimated was between body condition score and fat yield (−0.45 ± 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 −0.17), while the strongest positive phenotypic correlations were estimated between milk yield, protein yield, and udder width (both 0.32).  

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Using quantile regression for fitting lactation curve in dairy cows

Journal of Dairy Research ◽

10.1017/s0022029919000013 ◽

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.

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Variation at CPE but not CEBPA appears to be associated with intramuscular fat deposition in the longissimus muscle of cattle

Animal Production Science ◽

10.1071/ea08307 ◽

2009 ◽

Vol 49 (7) ◽

pp. 558 ◽

Cited By ~ 6

Author(s):

William Barendse ◽

Rowan J. Bunch ◽

Blair E. Harrison

Keyword(s):

Substitution Effect ◽

Intramuscular Fat ◽

High Linkage Disequilibrium ◽

Substitution Effects ◽

Phenotypic Variance ◽

Nucleotide Polymorphisms ◽

Allele Substitution Effect ◽

Single Nucleotide ◽

Enhancer Binding Protein ◽

Allele Substitution

An important step in the localisation of quantitative trait loci is the confirmation of trait-marker associations in independent studies. In this report, we test three single nucleotide polymorphisms (SNP) of two genes for associations to intramuscular fat (IMF) measurements in cattle. We genotyped SNP of carboxypeptidase E (CPE) and ccaat/enhancer binding protein, α (CEBPA) in a sample of a total of 813 cattle of taurine, composite and indicine breeds. All three polymorphisms showed significant differences between breeds, with the widest range found in CEBPA:g.271A > C where the A allele frequency ranged from P = 0.07 in Brahman to 0.88 in Shorthorn. The taurine breeds showed high linkage disequilibrium between the pair of CPE SNP, with all four breeds showing r2 = 1.0. The Brahman and Santa Gertrudis showed r2 ≤ 0.17. Both CPE:g.445C > T and CPE:g.601C > T SNP showed significant allele substitution effects to IMF in animals of taurine ancestry, with an allele substitution effect of α = 0.22, P = 0.020 for CPE:g.445C > T, explaining 0.4% of the phenotypic variance.

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Effects of cow families on production traits in dairy cattle

Animal Science ◽

10.1017/s1357729800054886 ◽

2000 ◽

Vol 71 (1) ◽

pp. 49-57 ◽

Cited By ~ 4

Author(s):

T. Roughsedge ◽

P. M. Visscher ◽

S. Brotherstone

Keyword(s):

Milk Yield ◽

Genetic Relationships ◽

Phenotypic Variance ◽

Production Traits ◽

Maternal Lineage ◽

Environment Effects ◽

Holstein Friesian ◽

Lactation Curve ◽

Two Measures ◽

The Uk

AbstractThe components of phenotypic variance attributable to maternal lineage for production traits of the UK Holstein Friesian dairy population were estimated. First lactation production records of 55 230 cows calving between 1996-1998 in the UK Holstein Friesian population were used in the analysis. Maternal pedigree records were traced back to 1960 to establish maternal lineages. The tracing resulted in 36 320 cows being assigned to 11 786 cow families with more than one cow per maternal lineage. Using test day records it was possible to explore aspects of the lactation curve in terms of persistency and different periods of production. The traits analysed were 305-day milk yield and composition traits, the first three milk yield tests of lactation and two measures of persistency. A contemporary record design was used to minimize pair-wise additive direct genetic relationships between cows within a maternal lineage and to remove both the effect of heterogeneous variance over time and the complications of permanent environment effects. No significant component of variance attributable to maternal lineage was found for yield traits. When data were restricted to maternal lineages with five or more records, persistency, as a ratio of cumulative yield in the last third to that in the first third of a 300-day lactation, was estimated to have a 4·4% component due to maternal lineage variance significant at the 5% level. The study also investigated the preferential treatment of cow families. Some evidence of maternal lineage×herd interaction was found.

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Single-Nucleotide Polymorphism Variations Associated With Specific Genes Putatively Identified Enhanced Genetic Predisposition for 305-Day Milk Yield in the Girolando Crossbreed

Frontiers in Genetics ◽

10.3389/fgene.2020.573344 ◽

2021 ◽

Vol 11 ◽

Author(s):

Alex Silva da Cruz ◽

Danilo Conrado Silva ◽

Lysa Bernardes Minasi ◽

Larissa Kamídia de Farias Teixeira ◽

Flávia Melo Rodrigues ◽

...

Keyword(s):

Milk Production ◽

Milk Yield ◽

Genetic Predisposition ◽

Fixed Effects ◽

Genome Wide Association Study ◽

Significant Snps ◽

Nucleotide Polymorphisms ◽

Production Traits ◽

Single Nucleotide ◽

A Genome

Milk production phenotypes are the main focus of genetic selection in dairy herds, and although there are many genes identified as related to the biology of these traits in pure breeds, little is known about crossbreed animals. This study aimed to identify potential genes associated with the 305-day milk yield in 337 crossbreed Gir × Holstein (Girolando) animals. Milk production records were genotyped for 45,613 single-nucleotide polymorphisms (SNPs). This dataset was used for a genome-wide association study (GWAS) using the 305-day milk yield adjusted for the fixed effects of herd and year and linear and quadratic effects of age at calving (in days) and calving factor averaged per animal. Genes within the significant SNPs were retrieved from the Bos taurus ARS-UCD1.2 assembly (bosTau9) for gene ontology analysis. In summary, the GWAS identified 52 SNPs associated [p ≤ 10–4, false discovery rate (FDR) = 8.77%] with milk production, including NUB1 and SLC24A2, which were previously described as related to milk production traits in cattle. The results suggest that SNPs associated mainly with NUB1 and SLC24A2 could be useful to understand milk production in Girolando and used as predictive markers for selecting genetic predisposition for milk yield in Girolando.

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Random regression models to estimate genetic parameters for test-day milk yield and composition in Iranian buffaloes

Archives Animal Breeding ◽

10.7482/0003-9438-56-027 ◽

2013 ◽

Vol 56 (1) ◽

pp. 276-284 ◽

Cited By ~ 1

Author(s):

M. Madad ◽

N. Ghavi Hossein-Zadeh ◽

A. A. Shadparvar ◽

D. Kianzad

Keyword(s):

Milk Yield ◽

Milk Fat ◽

Milk Protein ◽

Genetic Parameters ◽

Genetic Correlations ◽

Random Regression ◽

Production Traits ◽

Environmental Correlations ◽

Protein Percentage ◽

Heritability Estimates

Abstract. The objective of this study was to estimate genetic parameters for milk yield and milk percentages of fat and protein in Iranian buffaloes. A total of 9,278 test-day production records obtained from 1,501 first lactation buffaloes on 414 herds in Iran between 1993 and 2009 were used for the analysis. Genetic parameters for productive traits were estimated using random regression test-day models. Regression curves were modeled using Legendre polynomials (LPs). Heritability estimates were low to moderate for milk production traits and ranged from 0.09 to 0.33 for milk yield, 0.01 to 0.27 for milk protein percentage and 0.03 to 0.24 for milk fat percentage, respectively. Genetic correlations ranged from −0.24 to 1 for milk yield between different days in milk over the lactation. Genetic correlations of milk yield at different days in milk were often higher than permanent environmental correlations. Genetic correlations for milk protein percentage ranged from −0.89 to 1 between different days in milk. Also, genetic correlations for milk percentage of fat ranged from −0.60 to 1 between different days in milk. The highest estimates of genetic and permanent environmental correlations for milk traits were observed at adjacent test-days. Ignoring heritability estimates for milk yield and milk protein percentage in the first and final days of lactation, these estimates were higher in the 120 days of lactation. Test-day milk yield heritability estimates were moderate in the course of the lactation, suggesting that this trait could be applied as selection criteria in Iranian milking buffaloes.

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