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.

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.

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.

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

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.

DGAT1 polymorphism in Riverine buffalo, Swamp buffalo and crossbred buffalo

2018 ◽  
Vol 85 (4) ◽  
pp. 412-415 ◽  
Author(s):  
Jun Li ◽  
Shenhe Liu ◽  
Zipeng Li ◽  
Shujun Zhang ◽  
Guohua Hua ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Buffalo Milk ◽  
Production Performance ◽  
Production Traits ◽  
Coding Region ◽  
Fat Percentage ◽  
Protein Percentage ◽  
Dgat1 Gene ◽  
Swamp Buffalo

This Research Communication describes the polymorphisms in the coding region of DGAT1 gene in Riverine buffalo, Swamp buffalo and crossbred buffalo, and associations between polymorphisms and milk production performance in Riverine buffalo. Two polymorphisms of DGAT1were identified, located in exon 13 and exon 17, respectively. The distribution of the genotypes of the two SNP loci in different buffalo population varied, especially the polymorphism located in exon 13 which was not found in the Swamp buffalo. Moreover, SNP located in exon 17 was a nonsynonymous switch resulting in the animo acid sequence changed from an arginine (Arg) to a histidine (His) at position 484. Both SNPs were in Hardy–Weinberg equilibrium, and the polymorphism of g.8330T>C in the exon 13 was significantly associated with peak milk yield, total milk yield and protein percentage. The C variant was associated with an increase in milk yield and peak yield but less in protein percentage compared with the T variant. The polymorphisms of g.9046T>C in exon 17 were significantly associated with fat percentage, in that the buffaloes with TT genotype had a significantly higher fat percentage than those with CC genotype. These findings reveal the difference in the genetic evolution of the DGAT1 between Riverine buffalo and Swamp buffalo, and provide evidence that the DGAT1 gene has potential effects for Riverine buffalo milk production traits, which can be used as a candidate gene for marker-assisted selection in buffalo breeding.

Effect of Breed and Some Non - Genetic Factors on Milk Production and Some Proportions of Its Chemical Components in Two Breeds of Local Sheep

2020 ◽  
Vol 10 (1) ◽  
pp. 227-231
Author(s):  
Rahman Hussein AL-Qasimi ◽  
Shatha Mohammed Abbas ◽  
Allawi L.D. AL-Khauzai
Keyword(s):  
Milk Production ◽  
Genetic Factors ◽  
Chemical Components ◽  
Lactation Period ◽  
Production Traits ◽  
Milk Production Traits ◽  
Fat Percentage ◽  
Awassi Sheep ◽  
Total Milk ◽  
Milk Components

The study was carried out on 19 ewes of local Awassi sheep and 12ewes local Arabi sheep in the Al-kafeel sheep station Karbala, to determine the effect of breed and some non-genetic factors such as (sex of the lamb, type of birth, age and weight of ewes at birth) on daily and total milk production and lactation period and some of milk components (fat, protein and lactose). The results showed that a significant effect (P <0.05) of the breed on milk production traits where Awassi sheep recorded the highest mean (0.91 kg , 101.63 kg , 104.86 day) compared to the Arabi sheep she was means (0.77 kg , 88.15 kg , 99.15 day) respectively. As well as in proportions of milk components with mean( 5.1 , 4.90 , 5.51) % respectively compared to the Arabi sheep (4.70 . 4.20 . 4.89) ewes with male lambs also exceeded superior ewes with female lambs in daily and total milk production and the lactation period the sex of the lamb did not affect the proportions of milk components the weight of the ewes had a significant effect (P <0.05) in milk production attributes with superior weight of ewes on lower ewes and did not affect the proportions of milk ingredients except for lactose. The type of birth and the age of the ewes did not have a significant effect in all the studied traits except for the superiority (P<0.05) of young ewes on age ewes in the fat percentage of milk.

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.

Genotype Environment Interaction on Milk Production Traits of Crossbred Dairy Cows under Tropical Climatic Condition of India

2021 ◽  
Author(s):  
Rajalaxmi Behera ◽  
Ajoy Mandal ◽  
Saroj Rai ◽  
M. Karunakaran ◽  
Mohan Mondal ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Milk Production ◽  
Milk Yield ◽  
Vital Role ◽  
Genetic Group ◽  
Environment Interaction ◽  
Production Traits ◽  
Crossbred Cows ◽  
Genotype Environment Interaction ◽  
Heat Tolerant

Background: Genotype environment interaction plays vital role in animal productivity. Heat stress is one of the major environmental stressor affecting milk production and measured in terms of temperature humidity index (THI). Indian milk industry largely depends on crossbred cows bearing different degree of exotic inheritance. Thus, the role of genotype (genetic group) of the crossbred cows and environment (THI) interaction plays vital role in Indian climate which is mostly tropical in nature. Therefore, study was undertaken to examine the existence of genetic group × THI in crossbred dairy cows reared at institute herd of ICAR-National Dairy Research Institute, Eastern Regional Station, Kalyani, West Bengal. Methods: A total of 12364 records each of monthly milk yield (MMY) and average daily milk yield in a month (AMY) of crossbred cows spanned over twenty two years (1994-2015) and weather parameters(temperature and relative humidity) for the corresponding years were collected from institute records. The data were classified into 8 genetic groups according to the genetic composition and 3 THI groups (THI less than 72, THI 72-78 and THI above 78). The interaction model was used to study the G×E interaction study using least squares analysis. Result: Effect of non-genetic factors (parity, period of calving and stage of lactation) was found to be highly significant (P less than 0.01) and genetic group × THI was significant (P less than 0.05) of on both MMY and AMY. Genetic group bearing 50% Jersey and 50% Red Sindhi or Tharparkar were the most heat tolerant breeds. Jersey crossbred cows were more heat tolerant than Holstein crossbred cows. Crossbred cows with 50% Jersey inheritance performed better than higher Jersey inheritance during periods of THI above 72.

scholarly journals QTL mapping for production traits in Czech Fleckvieh cattle

2013 ◽  
Vol 58 (No. 9) ◽  
pp. 396-403 ◽  
Author(s):  
J. Matějíčková ◽  
M. Štípková ◽  
G. Sahana ◽  
T. Kott ◽  
J. Kyseľová ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Qtl Mapping ◽  
Milk Production ◽  
Variance Component ◽  
Variance Component Analysis ◽  
Production Traits ◽  
Milk Production Traits ◽  
Chromosome 14 ◽  
Fat Percentage ◽  
Mapping Model

The objective of this study was to find QTL for milk production traits in Czech Fleckvieh cattle on chromosomes 6, 7, 11, 14, and 23 where QTL were previously identified in other dairy cattle populations. Sixteen grandsire families were genotyped for 38 microsatellite markers on the selected chromosomes. A QTL mapping model based on variance component analysis was implemented via restricted maximum likelihood (REML) to estimate QTL positions and their effects. A significant QTL affecting fat percentage was found at the beginning of chromosome 14 (0 cM), near marker ILSTS039. Suggestive QTL associated with milk production traits appeared on other studied chromosomes (BTA6, BTA7, BTA11, and BTA23). This first QTL search on five chromosomes in Czech Fleckvieh population showed several suggestive QTL that can be promising for further studies and contribute to better understanding of genetics of milk production in the Czech Fleckvieh cattle. &nbsp;

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