Efficient Methods to Compute Genomic Predictions
TLDR
Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously, and a blend of first- and second-order Jacobi iteration using 2 separate relaxation factors converged well for allele frequencies and effects.About:
This article is published in Journal of Dairy Science.The article was published on 2008-11-01 and is currently open access. It has received 4196 citations till now. The article focuses on the topics: Best linear unbiased prediction & Allele frequency.read more
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BookDOI
Plant Functional Genomics
Jose M. Alonso,Anna Stepanova +1 more
TL;DR: This chapter describes an approach to map chromatin features in specifi c cell types of Arabidopsis thaliana using nuclei purifi cation from individual cell types with the INTACT method followed by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq).
Journal ArticleDOI
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
Maria Izabel A. Cavassim,Sara Moeskjær,Camous Moslemi,Bryden Fields,Asger Bachmann,Bjarni J. Vilhjálmsson,Mikkel H. Schierup,J. Peter W. Young,Stig U. Andersen +8 more
TL;DR: Investigating inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv.
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Genomic prediction for growth and reproduction traits in pig using an admixed reference population
Hailiang Song,J Y Zhang,Y. Jiang,H. Gao,S. Tang,S. Mi,F. Yu,Q. Meng,W. Xiao,Qin Zhang,Xiangdong Ding +10 more
TL;DR: The results indicated ssGBLUP using an admixed reference population is also meaningful for national joint genetic evaluation of Chinese pig breeding and in most situations, BayesR performed comparably to GBLUP for most traits.
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Genome-Wide Association Analyses Based on Broadly Different Specifications for Prior Distributions, Genomic Windows, and Estimation Methods.
TL;DR: It is determined that it is advantageous to use variable selection specifications based on adaptively constructed genomic window lengths for GWA studies, and it is found that SSVS and BayesA lead to the best receiver operating curve properties in almost all cases.
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Evaluation on the genomic selection in Litopenaeus vannamei for the resistance against Vibrio parahaemolyticus
TL;DR: Genetic selection (GS) could be an alternative approach to improve the genetic gains in L. vannamei for the resistance to V. parahaemolyticus, and analysis based on real and simulation data showed that the genomic best linear unbiased prediction (GBLUP) can result in more accurate prediction than the traditional pedigree-based best linear biased prediction (PBLUP).
References
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Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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Coefficients of Inbreeding and Relationship
TL;DR: The importance of having a coefficient by means of which the degree of inbreeding may be expressed has been brought out by Pearl' in a number of papers published between 1913 and 1917.
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Strategy for applying genome-wide selection in dairy cattle.
TL;DR: Genome-wide selection may become a popular tool for genetic improvement in livestock after a strategy that utilizes these advantages was compared with a traditional progeny testing strategy under a typical Canadian-like dairy cattle situation.
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Derivation, calculation, and use of national animal model information.
Paul M. VanRaden,G.R. Wiggans +1 more
TL;DR: New terms and definitions were developed to explain national USDA genetic evaluations computed by an animal model, whereiability is the squared correlation of predicted and true transmitting ability.
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Accuracy of Genomic Selection Using Different Methods to Define Haplotypes
TL;DR: It was concluded that genomic selection is considerably more accurate than traditional selection, especially for a low-heritability trait.