scholarly journals Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

2017 ◽  
Author(s):  
Hubert Pausch ◽  
Reiner Emmerling ◽  
Birgit Gredler-Grandl ◽  
Ruedi Fries ◽  
Hans D. Daetwyler ◽  
...  
Keyword(s):  
Association Studies ◽  
Meta Analysis ◽  
Substitution Effects ◽  
Sequence Variant ◽  
Production Traits ◽  
Milk Production Traits ◽  
Cattle Breeds ◽  
Allelic Substitution ◽  
Nucleotide Resolution ◽  
Mapping Populations

AbstractBackgroundGenotyping and whole-genome sequencing data have been collected in many cattle breeds. The compilation of large reference panels facilitates imputing sequence variant genotypes for animals that have been genotyped using dense genotyping arrays. Association studies with imputed sequence variant genotypes allow characterization of quantitative trait loci (QTL) at nucleotide resolution particularly when individuals from several breeds are included in the mapping populations.ResultsWe imputed genotypes for more than 28 million sequence variants in 17,229 animals of the Braunvieh (BV), Fleckvieh (FV) and Holstein (HOL) cattle breeds in order to generate large mapping populations that are required to identify sequence variants underlying milk production traits. Within-breed association tests between imputed sequence variant genotypes and fat and protein percentages in milk uncovered between six and thirteen QTL (P<1e-8) per breed. Eight of the detected QTL were significant in more than one breed. We combined the association studies across three breeds using meta-analysis and identified 25 QTL including six that were not significant in the within-breed association studies. Closer inspection of the QTL revealed that two well-known causal missense mutations in the ABCG2 (p.Y581S, rs43702337, P=4.3e-34) and GHR (p.F279Y, rs385640152, P=1.6e-74) genes were the top variants at two QTL on chromosomes 6 and 20. Another true causal missense mutation in the DGAT1 gene (p.A232K, rs109326954, P=8.4e-1436) was the second top variant at a QTL on chromosome 14 but its allelic substitution effects were not consistent across three breeds analyzed. It turned out that the conflicting allelic substitution effects resulted from flaws in the imputed genotypes due to the use of a multi-breed reference population for genotype imputation.ConclusionsMany QTL for milk production traits segregate across breeds. Metaanalysis of association studies across breeds has greater power to detect such QTL than within-breed association studies. True causal mutations can be readily detected among the most significantly associated variants at QTL when the accuracy of imputation is high. However, true causal mutations may show conflicting allelic substitution effects across breeds when the imputed sequence variant genotypes contain flaws. Validating the effect of known causal variants is highly recommended in order to assess the ability to detect true causal mutations in association studies with imputed sequence variant genotypes.

scholarly journals Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Hubert Pausch ◽  
Reiner Emmerling ◽  
Birgit Gredler-Grandl ◽  
Ruedi Fries ◽  
Hans D. Daetwyler ◽  
...  
Keyword(s):  
Association Studies ◽  
Meta Analysis ◽  
Cattle Breeds ◽  
Nucleotide Resolution

scholarly journals Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Irene van den Berg ◽  
Ruidong Xiang ◽  
Janez Jenko ◽  
Hubert Pausch ◽  
Mekki Boussaha ◽  
...  
Keyword(s):  
Milk Fat ◽  
Meta Analysis ◽  
Sequence Variant ◽  
Protein Percentage ◽  
Cattle Breeds

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

2020 ◽  
Vol 52 (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.

Effect of DGAT1 and TG gene polymorphisms on intramuscular fat and on milk production traits in different cattle breeds in Hungary

2008 ◽  
Vol 56 (2) ◽  
pp. 181-186 ◽  
Author(s):  
István Anton ◽  
Katalin Kovács ◽  
László Fésüs ◽  
József Várhegyi ◽  
László Lehel ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Fat ◽  
Longissimus Dorsi ◽  
Production Traits ◽  
Milk Production Traits ◽  
Fat Percentage ◽  
Longissimus Dorsi Muscle ◽  
Cattle Breeds ◽  
Pcr Rflp ◽  
The Difference

The objective of this study was to estimate the effect of the thyroglobulin (TG) locus on beef quality traits in some beef cattle breeds and to investigate the effect of the DGAT1 locus on milk production traits in the Hungarian Holstein Friesian population. TG and DGAT1 genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. At the TG locus TT bulls showed the highest fat percentage values in the longissimus dorsi muscle (m. longissimus dorsi); the difference between CC and TT genotypes was significant. DGAT1 GC/GC cows had the highest milk, fat and protein yield values. Due to the relatively small number of GC/GC cows the difference proved to be significant only between AA/AA and AA/GC genotypes.

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 Genome‐wide association studies for milk production traits in Valle del Belice sheep using repeated measures

2019 ◽  
Vol 50 (3) ◽  
pp. 311-314 ◽  
Author(s):  
A. M. Sutera ◽  
V. Riggio ◽  
S. Mastrangelo ◽  
R. Di Gerlando ◽  
M. T. Sardina ◽  
...  
Keyword(s):  
Milk Production ◽  
Repeated Measures ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Production Traits ◽  
Milk Production Traits ◽  
Genome Wide

Meta-analysis of mammary RNA seq datasets reveals the molecular understanding of bovine lactation biology

Genome ◽  
2019 ◽  
Vol 62 (7) ◽  
pp. 489-501
Author(s):  
Periyasamy Vijayakumar ◽  
Sanniyasi Bakyaraj ◽  
Arunasalam Singaravadivelan ◽  
Thangavelu Vasanthakumar ◽  
Ramalingam Suresh
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Milk Production ◽  
Meta Analysis ◽  
Mammary Tissue ◽  
Secretory Cells ◽  
Molecular Pathways ◽  
Production Traits ◽  
Rna Seq ◽  
Milk Production Traits

A better understanding of the biology of lactation, both in terms of gene expression and the identification of candidate genes for the production of milk and its components, is made possible by recent advances in RNA seq technology. The purpose of this study was to understand the synthesis of milk components and the molecular pathways involved, as well as to identify candidate genes for milk production traits within whole mammary transcriptomic datasets. We performed a meta-analysis of publically available RNA seq transcriptome datasets of mammary tissue/milk somatic cells. In total, 11 562 genes were commonly identified from all RNA seq based mammary gland transcriptomes. Functional annotation of commonly expressed genes revealed the molecular processes that contribute to the synthesis of fats, proteins, and lactose in mammary secretory cells and the molecular pathways responsible for milk synthesis. In addition, we identified several candidate genes responsible for milk production traits and constructed a gene regulatory network for RNA seq data. In conclusion, this study provides a basic understanding of the lactation biology of cows at the gene expression level.

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