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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Journal ArticleDOI
Incorporating Gene Annotation into Genomic Prediction of Complex Phenotypes
Ning Gao,Ning Gao,Johannes W. R. Martini,Zhe Zhang,Xiaolong Yuan,Hao Zhang,Henner Simianer,Jiaqi Li +7 more
TL;DR: This study proposes a novel strategy to incorporate gene annotation into GP of complex phenotypes by defining haploblocks according to gene positions, and is believed to be the first work that incorporates epistatic interaction or gene annotations into haplotype-based prediction approaches.
Journal ArticleDOI
Genomic correlation: harnessing the benefit of combining two unrelated populations for genomic selection.
Laercio R. Porto-Neto,William Barendse,John M. Henshall,Sean McWilliam,Sigrid A. Lehnert,Antonio Reverter +5 more
TL;DR: It is found that, by carefully selecting the subset of SNPs, the missing heritability can be largely recovered and accuracies in genomic predictions can be improved six-fold, however, the increases in accuracy might come at the expense of large biases.
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Genome Wide Association Study to Identify the Genetic Base of Smallholder Farmer Preferences of Durum Wheat Traits
Yosef Gebrehawaryat Kidane,Yosef Gebrehawaryat Kidane,Chiara Mancini,Dejene K. Mengistu,Dejene K. Mengistu,Elisabetta Frascaroli,Carlo Fadda,Mario Enrico Pè,Matteo Dell’Acqua +8 more
TL;DR: The results of the GWA study show that smallholder farmers' traditional knowledge can yield QTL eluding metric measurements of phenotypes, and the potential of including farmer evaluations based on traditional knowledge in crop breeding is discussed, arguing for the utilization of this untapped resource to develop better adapted genetic materials for local agriculture.
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Prospects of GWAS and predictive breeding for European winter wheat's grain protein content, grain starch content, and grain hardness.
Quddoos H. Muqaddasi,Jonathan Brassac,Erhard Ebmeyer,Sonja Kollers,Viktor Korzun,Odile Argillier,Gunther Stiewe,Jörg Plieske,Martin W. Ganal,Marion S. Röder +9 more
TL;DR: It is observed that all of the investigated traits hold a wide and significant genetic variation, and a significant negative correlation exists between GPC and GSC plus grain yield, and the prospects of predictive breeding for the investigated trait suggested its efficient use in the breeding programs.
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Using crop growth model stress covariates and AMMI decomposition to better predict genotype-by-environment interactions
Renaud Rincent,Renaud Rincent,Marcos Malosetti,Behnam Ababaei,Behnam Ababaei,Gaëtan Touzy,Agathe Mini,Matthieu Bogard,Pierre Martre,J. Le Gouis,J. Le Gouis,F.A. van Eeuwijk +11 more
TL;DR: This study showed that selecting a subset of ECs, and estimating covariance matrices using an AMMI decomposition to benefit from the information brought by the phenotypic records of the training set are promising approaches to better predict genotype-by-environment interactions (G × E).
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.