Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle

January 2011
BMC Genetics;2011, Vol. 12 Issue 1, p80
Academic Journal
The article presents a study conducted to calculate accuracy of direct genomic estimated breeding values (DGEBV) using best linear unbiased genomic prediction (GBLUP) for different marker densities, heritabilities and sizes of the training set (TS) in simulated populations that mimicked previously reported extent and pattern of linkage disequilibrium (LD) in beef cattle. The study suggests that the size of the TS and the extent of LD have major impact on the accuracy of DGEBV.


Related Articles

  • The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Habier, David; Tetens, Jens; Seefried, Franz-Reinhold; Lichtner, Peter; Thaller, Georg // Genetics Selection Evolution;Feb2010, Vol. 42 Issue 2, p1 

    Background: The impact of additive-genetic relationships captured by single nucleotide polymorphisms (SNPs) on the accuracy of genomic breeding values (GEBVs) has been demonstrated, but recent studies on data obtained from Holstein populations have ignored this fact. However, this impact and the...

  • Isolated populations as treasure troves in genetic epidemiology: the case of the Basques. Garagnani, Paolo; Laayouni, Hafid; González-Neira, Anna; Sikora, Martin; Luiselli, Donata; Bertranpetit, Jaume; Calafell, Francesc // European Journal of Human Genetics;Nov2009, Vol. 17 Issue 11, p1490 

    The Basques are a culturally isolated population, living across the western border between France and Spain and speaking a non-Indo-European language. They show outlier allele frequencies in the ABO, RH, and HLA loci. To test whether Basques are a genetic isolate with the features that would...

  • Genome-Wide Linkage-Disequilibrium Profiles from Single Individuals. Lynch, Michael; Sen Xu; Takahiro Maruki; Xiaoqian Jiang; Pfaffelhuber, Peter; Haubold, Bernhard // Genetics;Sep2014, Vol. 198 Issue 1, p269 

    Although the analysis of linkage disequilibrium (LD) plays a central role in many areas of population genetics, the sampling variance of LD is known to be very large with high sensitivity to numbers of nucleotide sites and individuals sampled. Here we show that a genome-wide analysis of the...

  • A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations. Meng-Hua Li; Terhi Iso-Touru; Laurén, Hannele; Kantanen, Juha // Genetics Selection Evolution;Aug2010, Vol. 42 Issue 8, p1 

    Background: Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has...

  • Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle. Abo-Ismail, Mohammed K.; Voort, Gordon Vander; Squires, James J.; Swanson, Kendall C.; Mandell, Ira B.; Xiaoping Liao; Stothard, Paul; Moore, Stephen; Plastow, Graham; Miller, Stephen P. // BMC Genetics;2014, Vol. 15 Issue 1, p1 

    Background This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the...

  • The Extent of Linkage Disequilibrium in Rice (Oryza sativa L.). Mather, Kristie A.; Caicedo, Ana L.; Polato, Nicholas R.; Olsen, Kenneth M.; McCouch, Susan; Purugganan, Michael D. // Genetics;Dec2007, Vol. 177 Issue 4, p2223 

    Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association...

  • How Population Growth Affects Linkage Disequilibrium. Rogers, Alan R. // Genetics;8/1/2014, Vol. 197 Issue 4, p1329 

    The "LD curve" relates the linkage disequilibrium (LD) between pairs of nucleotide sites to the distance that separates them along the chromosome. The shape of this curve reflects natural selection, admixture between populations, and the history of population size. This article derives new...

  • Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle. Shinichiro Ogawa; Hirokazu Matsuda; Yukio Taniguchi; Toshio Watanabe; Shota Nishimura; Yoshikazu Sugimoto; Hiroaki Iwaisaki // BMC Genetics;2014, Vol. 15 Issue 1, p1 

    Background Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including...

  • Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle. Santana, Miguel H. A.; Utsunomiya, Yuri T.; Neves, Haroldo H. R.; Gomes, Rodrigo C.; Garcia, José F.; Fukumasu, Heidge; Silva, Saulo L.; Oliveira Junior, Gerson A.; Alexandre, Pâmela A.; Leme, Paulo R.; Brassaloti, Ricardo A.; Coutinho, Luiz L.; Lopes, Thiago G.; Meirelles, Flávio V.; Eler, Joanir P.; Ferraz, José B. S. // BMC Genetics;2014, Vol. 15 Issue 1, p1 

    Background Feed intake plays an important economic role in beef cattle, and is related with feed efficiency, weight gain and carcass traits. However, the phenotypes collected for dry matter intake and feed efficiency are scarce when compared with other measures such as weight gain and carcass...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics