Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits

Imumorin, Ikhide G.; Kim, Eun‐Hee; Lee, Yun-Mi; Koning, Dirk-Jan de; Arendonk, J.A.M. van; Donato, Marcos De; Taylor, Jeremy F.; Kim, Jong-Joo

doi:10.3389/fgene.2011.00044

Cited by 55 publications

(46 citation statements)

References 99 publications

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“…Another study 8 mapping body weight and growth in a murine intercross found little overlap between known imprinted genes and imprinted QTL (only 2 of 10 loci overlapped confirmed imprinted genes) but all imprinted QTL contained multiple genes predicted to be imprinted by bioinformatic approaches (discussed below in the Identifying molecular signatures of imprinted loci section) 30 . Similar patterns, where most QTL map to regions that do not contain known imprinted genes but do contain bioinformatically predicted imprinted genes, were found in a study of bovine growth and body composition 31 .…”

Section: Imprinting Effects On Complex Traitssupporting

confidence: 65%

Genomic imprinting and parent-of-origin effects on complex traits

2013

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Parent-of-origin effects occur when the phenotypic effect of an allele depends on whether it is inherited from an individual’s mother or father. Several phenomena can cause parent-of-origin effects, with the best characterized being parent-of-origin dependent gene expression associated with genomic imprinting. Imprinting plays a critical role in a diversity of biological processes and in certain contexts it structures epigenetic relationships between DNA sequence and phenotypic variation. The development of new mapping approaches applied to the growing abundance of genomic data has demonstrated that imprinted genes can be important contributors to complex trait variation. Therefore, to understand the genetic architecture and evolution of complex traits, including complex diseases and traits of agricultural importance, it is crucial to account for these parent-of-origin effects. Here we discuss patterns of phenotypic variation associated with imprinting, evidence supporting its role in complex trait variation, and approaches for identifying its molecular signatures.

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Section: Imprinting Effects On Complex Traitssupporting

confidence: 65%

Genomic imprinting and parent-of-origin effects on complex traits

2013

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“…The MAM is an extracellular domain that mediates protein-protein interactions, and is found in a variety of proteins, of which many are known to function in cell adhesion [96]. The remaining 16 SNPs, which were not described in detail here, accounted for 19.14% of dEBV variation for backfat thickness and, as seen in Table 2, most of them present some fat-related QTL described within their regions [29,65,66,85,97-99], and are of further interest for future investigations on how these SNPs can be influencing backfat thickness deposition in Canchim beef cattle.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

et al. 2013

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BackgroundMeat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal’s life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.ResultsThe set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.ConclusionsThese results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.

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“…Nonetheless, there is an increasing body of knowledge on the roles of imprinted genes in livestock production. For example, in a recent genome scan, Imumorin et al (2011) detected quantitative trait loci (QTL) with parent-of-origin effects on growth and carcass traits in the Angus × Brahman cattle crossbred population. A single nucleotide polymorphism (SNP) in IGF2 was found to be associated with an increase in rib eye area and percentage of grade fat (Goodall and Schmutz, 2007).…”

Section: Introductionmentioning

confidence: 99%

Maternal Diet during Pregnancy Induces Gene Expression and DNA Methylation Changes in Fetal Tissues in Sheep

Lan¹,

Cretney²,

Schmidt³

et al. 2013

Front. Genet.

104

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Studies in rats and mice have established that maternal nutrition induces epigenetic modifications, sometimes permanently, that alter gene expression in the fetus, which in turn leads to phenotypic changes. However, limited data is available on the influence of maternal diet on epigenetic modifications and gene expression in sheep. Therefore, the objectives of this study were to investigate the impact of different maternal dietary energy sources on the expression of imprinted genes in fetuses in sheep. Ewes were naturally bred to a single sire and from days 67 ± 3 of gestation until necropsy (days 130 ± 1), they were fed one of three diets of alfalfa haylage (HY; fiber), corn (CN; starch), or dried corn distiller’s grains (DG; fiber plus protein plus fat). A total of 26 fetuses were removed from the dams and longissimus dorsi, semitendinosus, perirenal adipose depot, and subcutaneous adipose depot tissues were collected for expression and DNA methylation analyses. Expression analysis of nine imprinted genes and three DNA methyltransferase (DNMTs) genes showed significant effects of the different maternal diets on the expression of these genes. The methylation levels of CpG islands of both IGF2R and H19 were higher in HY and DG than CN fetuses in both males and females. This result is consistent with the low amino acid content of the CN diet, a source of methyl group donors, compared to HY and DG diets. Thus, results of this study provide evidence of association between maternal nutrition during pregnancy and transcriptomic and epigenomic alterations of imprinted genes and DNMTs in the fetal tissues.

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Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits

Cited by 55 publications

References 99 publications

Genomic imprinting and parent-of-origin effects on complex traits

Genomic imprinting and parent-of-origin effects on complex traits

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Maternal Diet during Pregnancy Induces Gene Expression and DNA Methylation Changes in Fetal Tissues in Sheep

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