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Factors affecting genomic selection revealed by empirical evidence in maize

Author: Xiaogang Liu
Author: Hongwu Wang
Author: Hui Wang
Author: Zifeng Guo
Author: Xiaojie Xu
Author: Jiacheng Liu
Author: Shanhong Wang
Author: Wen-Xue, Li
Author: Cheng Zou
Author: Prasanna, B.M.
Author: Olsen, M.
Author: Changling Huang
Author: Yunbi Xu
Year: 2018
ISSN: ISSN:  2214-5141
URI: https://hdl.handle.net/10883/19915
Abstract: Genomic selection (GS) as a promising molecular breeding strategy has been widely implemented and evaluated for plant breeding, because it has remarkable superiority in enhancing genetic gain, reducing breeding time and expenditure, and accelerating the breeding process. In this study the factors affecting prediction accuracy (rMG) in GS were evaluated systematically, using six agronomic traits (plant height, ear height, ear length, ear diameter, grain yield per plant and hundred-kernel weight) evaluated in one natural and two biparental populations. The factors examined included marker density, population size, heritability, statistical model, population relationships and the ratio of population size between the training and testing sets, the last being revealed by resampling individuals in different proportions from a population. Prediction accuracy continuously increased as marker density and population size increased and was positively correlated with heritability; rMG showed a slight gain when the training set increased to three times as large as the testing set. Low predictive performance between unrelated populations could be attributed to different allele frequencies, and predictive ability and prediction accuracy could be improved by including more related lines in the training population. Among the seven statistical models examined, including ridge regression best linear unbiased prediction (RR-BLUP), genomic BLUP (GBLUP), BayesA, BayesB, BayesC, Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), and reproducing kernel Hilbert space (RKHS), the RKHS and additive-dominance model (Add + Dom model) showed credible ability for capturing non-additive effects, particularly for complex traits with low heritability. Empirical evidence generated in this study for GS-relevant factors will help plant breeders to develop GS-assisted breeding strategies for more efficient development of varieties.
Format: PDF
Language: English
Publisher: Elsevier
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
Type: Article
Place of Publication: Netherlands
Pages: 341–352
Issue: 4
Volume: 6
DOI: 10.1016/j.cj.2018.03.005
Keywords: Marker Density
Keywords: Population Size
Keywords: Population Relationship
Agrovoc: GENOMIC FEATURES
Agrovoc: MAIZE
Agrovoc: MOLECULAR GENETICS
Journal: The Crop Journal


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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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