Combined Multistage Linear Genomic Selection Indices To Predict the Net Genetic Merit in Plant Breeding. 2020

J Jesus Cerón-Rojas, and Jose Crossa
Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, México City, México and.

A combined multistage linear genomic selection index (CMLGSI) is a linear combination of phenotypic and genomic estimated breeding values useful for predicting the individual net genetic merit, which in turn is a linear combination of the true unobservable breeding values of the traits weighted by their respective economic values. The CMLGSI is a cost-saving strategy for improving multiple traits because the breeder does not need to measure all traits at each stage. The optimum (OCMLGSI) and decorrelated (DCMLGSI) indices are the main CMLGSIs. Whereas the OCMLGSI takes into consideration the index correlation values among stages, the DCMLGSI imposes the restriction that the index correlation values among stages be zero. Using real and simulated datasets, we compared the efficiency of both indices in a two-stage context. The criteria we applied to compare the efficiency of both indices were that the total selection response of each index must be lower than or equal to the single-stage combined linear genomic selection index (CLGSI) response and that the correlation of each index with the net genetic merit should be maximum. Using four different total proportions for the real dataset, the estimated total OCMLGSI and DCMLGSI responses explained 97.5% and 90%, respectively, of the estimated single-stage CLGSI selection response. In addition, at stage two, the estimated correlations of the OCMLGSI and the DCMLGSI with the net genetic merit were 0.84 and 0.63, respectively. We found similar results for the simulated datasets. Thus, we recommend using the OCMLGSI when performing multistage selection.

UI MeSH Term Description Entries
D008957 Models, Genetic Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Genetic Models,Genetic Model,Model, Genetic
D010641 Phenotype The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. Phenotypes
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D000069600 Plant Breeding The purposeful manipulation of plant species with the goal of creating desired genotypes and phenotypes, using techniques such as controlled pollination and or genetic engineering, followed by artificial selection of progeny. Breeding, Plant
D012641 Selection, Genetic Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population. Natural Selection,Genetic Selection,Selection, Natural
D016678 Genome The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA. Genomes
D023281 Genomics The systematic study of the complete DNA sequences (GENOME) of organisms. Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. Functional Genomics,Structural Genomics,Comparative Genomics,Genomics, Comparative,Genomics, Functional,Genomics, Structural

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