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
Citations
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Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein–Friesian dairy cattle
TL;DR: Investigation of effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein–Friesian cows found inbreeding depression was observed and there was evidence of purging for yield traits and based on pedigree.
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An R2R3-type MYB transcription factor, GmMYB29, regulates isoflavone biosynthesis in soybean.
Shanshan Chu,Shanshan Chu,Jiao Wang,Ying Zhu,Shu-Lin Liu,Xiaoqiong Zhou,Huairen Zhang,Chun-e Wang,Wenming Yang,Zhixi Tian,Hao Cheng,Deyue Yu +11 more
TL;DR: Overexpression and RNAi-mediated silencing of GmMYB29 in soybean hairy roots resulted in increased and decreased isoflavone content, respectively, and a candidate-gene association analysis revealed that 11 natural GmmyB29 polymorphisms were significantly associated with is oflavone contents, and regulation of Gb29 expression could partially contribute to the observed phenotypic variation.
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Multi-environment Genomic Prediction of Plant Traits Using Deep Learners With Dense Architecture
Abelardo Montesinos-López,Osval A. Montesinos-López,Daniel Gianola,José Crossa,Carlos M. Hernández-Suárez +4 more
TL;DR: This study corroborates the view that there are no universally best prediction machines and believes that DL should be added to the data science toolkit of scientists working on animal and plant breeding.
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Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle.
Bart Buitenhuis,Luc Janss,Nina Aagaard Poulsen,Lotte Bach Larsen,Mette Krogh Larsen,Peter Sørensen +5 more
TL;DR: There was a clear similarity between the underlying genetics of FA in the milk between DH and DJ and the biological pathway analysis suggested that fat digestion and absorption KEGG04975 is important for the traits FP, C14:1, C16 index and C16:1.
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Genomic Estimated Breeding Values Using Genomic Relationship Matrices in a Cloned Population of Loblolly Pine
TL;DR: Estimation of genomic relationships could be a powerful tool in forest tree breeding because it accurately accounts both for genetic relationships among individuals and for nuisance effects such as location and replicate effects, and makes more accurate selection possible within full-sib crosses.
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.