Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

Mazzoni, Gianluca; Pedersen, Helene Helboe; Oliveira, G.A.; Razza, E. M.; Callesen, Henrik; Hyttel, Poul; Nogueira, Marcelo Fábio Gouveia; Ferraz, José Bento Sterman; Kadarmideen, Haja N.

doi:10.21451/1984-3143-ar993

Cited by 3 publications

(1 citation statement)

References 47 publications

(26 reference statements)

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“…between the phenotype and the genome. Therefore, eQTL analysis can identify interesting genetic variants even with a low sample size [12,13]. The identification of genomic regions influencing the expressions of the candidate genes could give a better perspective to use the information in animal selection as well as provide a better explanation about the way genomic regions control traits of interest.…”

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confidence: 99%

Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Salleh

Mazzoni²,

Nielsen

et al. 2018

J Genet Genome Res

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Background: Residual feed intake (RFI) is the difference between actual and predicted feed intake and an important factor determining feed efficiency (FE). Recently, 170 candidate genes were associated with RFI, but no expression quantitative trait loci (eQTL) mapping has hitherto been performed on FE related genes in dairy cows. In this study, an integrative systems genetics approach was applied to map eQTLs in Holstein and Jersey cows fed two different diets to improve identification of candidate genes for FE. Methods: Liver RNA-seq transcriptomics data from nine Holstein and ten Jersey cows that had been fed control (C) or high concentrate (HC) diets were integrated with genomic data (from 777k BovineHD Illumina BeadChip) by using the Matrix eQTL R package. A total of 170 previously identified candidate genes for FE (89 differentially expressed genes (DEGs) between high and low RFI groups and 81 hub genes (HG) in a group of co-expressed genes) were used in the data integration analysis. Results: From the 241,542 SNPs used in the analysis, we identified 20 significant (FDR < 0.05) local-eQTLs targeting seven candidate genes and 16 significant (FDR < 0.05) local-eQTLs targeting five candidate genes related to RFI for the C and HC diet group analysis, respectively, in a breed-specific way. Conclusions: Interestingly, Holstein and Jersey cows appear to rely on different strategies (lipid and cholesterol metabolism versus immune and inflammatory function) to achieve low RFI. The eQTLs overlapped with QTLs previously associated with FE trait (e.g. dry matter intake, longevity, body weight gain and net merit). The eQTLs and biological pathways identified in this study improve our understanding of the complex biological and genetic mechanisms that determine FE traits in dairy cattle. The identified eQTLs/genetic variants can potentially be used in new genomic selection methods that include biological/functional information on SNPs.

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confidence: 99%

Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Salleh

Mazzoni²,

Nielsen

et al. 2018

J Genet Genome Res

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Transcriptomics–genomics data integration and expression quantitative trait loci analyses in oocyte donors and embryo recipients for improving invitro production of dairy cattle embryos

Kadarmideen

Mazzoni

2019

Reprod. Fertil. Dev.

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In this paper we first provide a brief review of main results from our previously published studies on genome-wide gene expression (transcriptomics) in donor and recipient cattle used in invitro production (IVP) of embryos and embryo transfer (ET). Then, we present novel results from applying integrative systems genomics and biological analyses where transcriptomics data are combined with genomic data in both donor and recipient cattle to map expression quantitative trait loci (eQTLs). The eQTLs are genetic markers that can regulate or control the expression of genes in the entire genome, via complex molecular mechanisms, and thus can act as a powerful tool for genomic and gene-assisted selection. We identified significant eQTLs potentially controlling the expression of 13 candidate genes for donor cow quality (IVP parameters; e.g. cyclin B1 (CCNB1), outer dense fiber of sperm tails 2 like (ODF2L)) and 19 candidate genes for recipient cows quality (endometrial receptivity; e.g. ER membrane protein complex subunit 9 (EMC9), mannosidase beta (MANBA), peptidase inhibitor 16 (PI16)). Annotation and colocation of detected eQTLs show that some of the eQTLs are in the same genomic regions previously reported as QTLs for reproduction-related traits. However, eQTLs and the candidate genes identified should be further validated in larger populations before implementation as genetic markers or used in genomic selection for improving IVP and ET performance.

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Genomics to Systems Biology in Livestock Management: its Applications and Future Perspective

Patil,

Kanthe,

Parvatikar

et al. 2023

Systems Biology, Bioinformatics and Livestock Science

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The recurrent and comprehensive study of biological systems as a single entity in response to stimuli is known as systems biology. The introduction of high-throughput technology for studying an animal's DNA, proteome, and metabolome was a blow to reductionism in livestock science. It is based on ideas formalized in models derived from global functional genomics investigations of the genome, transcriptome, proteome, metabolome, and other complex biological systems. The mapping of entire sets of genes, transcripts, proteins, and metabolites from a variety of organisms has driven the creation of novel '-omic' technologies for gathering and analyzing vast amounts of data. This widely defined systems approach is being used to address a wide range of issues and organizational scales, along with several elements of livestock research. It is well established that the tools that relate genetic variations to their cellular activities, pathways, and other biological roles will become even more essential in the future. For each animal genomics research issue, a vision, current state of the art, research needed to progress the field, expected outputs, and partnerships are required. Modern computational tools capable of finding functional implications and biologically meaningful networks complement the ever-increasing ability to generate massive molecular, microbial, and metabolite data sets. The intricate inter-tissue responses to physiological status and nutrition can now be seen at the same time. The knowledge acquired from the application of functional analysis of systems biology data sets to livestock management in order to improve productivity, quality, and yield.

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Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

Cited by 3 publications

References 47 publications

Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Transcriptomics–genomics data integration and expression quantitative trait loci analyses in oocyte donors and embryo recipients for improving invitro production of dairy cattle embryos

Genomics to Systems Biology in Livestock Management: its Applications and Future Perspective

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