Functional validation of GPIHBP1 and identification of a functional mutation in GPIHBP1 for milk fat traits in dairy cattle

Yang, Jie; Li, Xuan; Wang, Dan; Ning, Chao; Wang, Haifei; Zhang, Qin; Jiang, Li

doi:10.1038/s41598-017-08668-6

Cited by 15 publications

(12 citation statements)

References 27 publications

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“…The well-known DGAT1 p.A232K-variant [35] can be excluded as the causal variant for the milk production QTL on BTA14 because it does not segregate in Brown Swiss cattle [11]. For a QTL for milk production traits in close vicinity to DGAT1 on BTA14, the GPIHBP1 gene has been postulated as candidate gene [34,36].…”

Section: Milk Productionmentioning

confidence: 99%

“…Another two QTL for milk production traits were located on BTA14 and BTA16. Both regions have recently been described to harbor QTL for milk production traits in several cattle breeds including Brown Swiss [11,33,34]. The well-known DGAT1 p.A232K-variant [35] can be excluded as the causal variant for the milk production QTL on BTA14 because it does not segregate in Brown Swiss cattle [11].…”

Section: Milk Productionmentioning

confidence: 99%

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Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Fang

Pausch

2019

Preprint

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Background:The Brown Swiss dual-purpose cattle breed is renowned for high milk and protein yield and long productive lifetime under different production conditions. However, little is known about the genetic architecture of those traits because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS had been performed for single traits, thus preventing insights into potentially existing pleiotropic effects of trait-associated loci. Results: To compile a comprehensive catalogue of large-effect QTL segregating in BrownSwiss cattle, we carried out association tests between partially imputed genotypes at 598,016SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4,578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 x 10 -8 ) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL. Conclusions:Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the daughter-derived phenotypes and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by traitassociated variants. BackgroundGenome-wide association studies (GWAS) between economically important traits and dense single nucleotide polymorphism (SNP) genotypes identified hundreds of quantitative trait loci (QTL) and thousands of trait-associated genetic variants in many cattle breeds [1]. Prioritizing trait-associated variants in genomic prediction models may accelerate genetic gain, particularly when large reference populations are not available, e.g., for traits that are either expensive or difficult to measure [2]. Furthermore, characterizing the spectrum of traits that are affected by pleiotropic QTL may contribute to a better understanding of the physiological underpinnings of economically important traits and help unravelling moleculargenetic mechanism through which QTL acts. This knowledge could further facilitate an improved prediction of correlated res...

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Section: Milk Productionmentioning

confidence: 99%

Section: Milk Productionmentioning

confidence: 99%

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Fang

Pausch

2019

Preprint

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“…Another two QTL for milk production traits were located on BTA14 and BTA16. Both regions have recently been described to harbor QTL for milk production traits in several cattle breeds including Brown Swiss [11, 16, 17]. The well-known DGAT1 p.A232K-variant [18] can be excluded as the causal variant for the milk production QTL on BTA14 because it does not segregate in Brown Swiss cattle [11], but mutations in DGAT1 other than the p.A232K-variant might segregate in Brown Swiss.…”

Section: Resultsmentioning

confidence: 99%

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Fang

Pausch

2019

BMC Genomics

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Background Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci. Results To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 × 10 − 8 ) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL. Conclusions Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants. Electronic supplementary material The online version of this article (10.1186/s12864-019-6066-6) contains supplementary material, which is available to authorized users.

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“…The unannotated gene is LOC104973964, while the rest are protein-coding genes: LOC112441461, LOC787628, LY6H, GPIHBP1 LY6E, LY6L, GML, and CYP11B1. In previous research, Yang et al (Yang et al, 2017) found the gene GPIHBP1 related to the fat milk trait in dairy cattle. Further investigation of the relationship of the listed genes with the phenotype of interest (beyond the scope of this paper) would be needed.…”

Section: Classification With Decision Treesmentioning

confidence: 99%

Research Article Genome-wide classification of dairy cows using decision trees and artificial neural network algorithms

Rodríguez¹,

Waissman²,

Mahadevan³

et al. 2019

Genet. Mol. Res.

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We compared two techniques of machine learning for the identification of cows that will be good producers of milk based on their genome-wide information. Data from a genome-wide genotyping panel, consisting of 164312 single nucleotide polymorphism markers (SNPs), within the 29 autosomal chromosomes, from 1092 Holstein cow samples were used for this study. Sample cows were divided as high-milk producers and lowmilk producers based on their estimated breeding value of the 305 day average milk yield. Seven data sets were generated that grouped chromosomes with the highest number of SNPs related to milk production for prediction. Decision trees and artificial neural network algorithms were trained and tested, and the performance of prediction was computed. The mean prediction accuracy obtained with the decision tree algorithm was 92.44%, with a maximum of 94.5%, while the mean prediction accuracy obtained with the artificial neural network algorithm was 82.19%, with a maximum of 87.3%. Also, the decision tree algorithm permitted the identification ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (4): gmr18407 E. Rodríguez et al. 2 of the most dominant single nucleotide polymorphism for prediction, which is situated within a milk-related quantitative trait locus in chromosome 14. Finally, our results add new evidence to support that machine learning algorithms may be used for managing genomewide SNP markers, for implementing classification and prediction tools in the cattle industry.

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Functional validation of GPIHBP1 and identification of a functional mutation in GPIHBP1 for milk fat traits in dairy cattle

Cited by 15 publications

References 27 publications

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Research Article Genome-wide classification of dairy cows using decision trees and artificial neural network algorithms

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