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Prospects for Genomewide Selection for Quantitative Traits in Maize

Prospects for Genomewide Selection for Quantitative Traits in Maize,10.2135/cropsci2006.11.0690,Crop Science,Rex Bernardo,Jianming Yu

Prospects for Genomewide Selection for Quantitative Traits in Maize   (Citations: 36)
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The availability of cheap and abundant molecu- lar markers in maize (Zea mays L.) has allowed breeders to ask how molecular markers may best be used to achieve breeding progress, with- out conditioning the question on how breeding has traditionally been done. Genomewide selec- tion refers to marker-based selection without fi rst identifying a subset of markers with signifi - cant effects. Our objectives were to assess the response due to genomewide selection com- pared with marker-assisted recurrent selection (MARS) and to determine the extent to which phenotyping can be minimized and genotyping maximized in genomewide selection. We simu- lated genomewide selection by evaluating dou- bled haploids for testcross performance in Cycle 0, followed by two cycles of selection based on markers. Individuals were genotyped for NM mark- ers, and breeding values associated with each of the NM markers were predicted and were all used in genomewide selection. We found that across different numbers of quantitative trait loci (20, 40, and 100) and levels of heritability, the response to genomewide selection was 18 to 43% larger than the response to MARS. Responses to selection were maintained when the number of doubled haploids phenotyped and genotyped in Cycle 0 was reduced and the number of plants gen- otyped in Cycles 1 and 2 was increased. Such schemes that minimize phenotyping and maxi- mize genotyping would be feasible only if the cost per marker data point is reduced to about 2 cents. The convenient but incorrect assumption of equal marker variances led to only a minimal loss in the response to genomewide selection. We conclude that genomewide selection, as a brute-force and black-box procedure that exploits cheap and abundant molecular markers, is superior to MARS in maize.
Journal: Crop Science - CROP SCI , vol. 47, no. 3, 2007
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    • ..., 2004; Bernardo and Yu, 2007; Rutkoski et al...

    Majid R. Fooladet al. Marker-Assisted Selection in Tomato Breeding

    • ...A study comparing GS to MARS in a simulated maize breeding program found GS to have increased response from selection, especially for traits of low heritability (Bernardo and Yu 2007)...
    • ...Overall, increased marker densities have been shown to increase accuracy (Solberg et al. 2008) as long as the number of phenotypes also increases to allow accurate estimation of the marker effects (Bernardo and Yu 2007; Muir 2007; Hayes et al. 2009b; Lorenzana and Bernardo 2009)...
    • ...Recent studies in plants evaluated TPs consisting of biparental crosses (Lorenzana and Bernardo 2009), doubled haploid testcrosses (Bernardo and Yu 2007) and intermated inbred lines (Zhong et al. 2009) where the validation population was directly related to the TP. The ideal situation may be to generate a new TP for each family derived from each bi-parental cross in the breeding program...
    • ...However, in a simulation study by Bernardo and Yu (2007) of GS in maize comparing scenarios where h 2 = 0.2, 0.5 and 0.8, GS...
    • ...According to simulations, the use of GS to select individuals in recurrent selection programs leads to greater responses to selection relative to MARS (Bernardo and Yu 2007)...

    Jessica E. Rutkoskiet al. Genomic selection for durable stem rust resistance in wheat

    • ...Therefore, genome wide marker approaches, such as MARS and GS should be more effective approaches as compared to marker-assisted backcrossing (MABC) in case of groundnut to develop the varieties with enhanced drought tolerance through molecular breeding (Charmet et al. 1999; Bernardo and Charcosset 2006; Bernardo and Yu 2007; Mayor and Bernardo 2009)...

    K. Raviet al. Identification of several small main-effect QTLs and a large number of...

    • ...This method, which has already shown its efficiency in animal breeding, is being proposed for plants (Bernardo and Yu, 2007; Heffner et al...

    S. Negrãoet al. Recent Updates on Salinity Stress in Rice: From Physiological to Molec...

    • ...One should, however, recognize that currently MAS is largely practiced for simple traits that are difficult to score, and not for the complex polygenic quantitative traits like yield, for which MAS involving marker-assisted recurrent selection (MARS) and genome-wide selection (GS) seem to be more appropriate (Bernardo and Yu 2007; Heffner et al. 2009)...

    P. K. Guptaet al. Marker-assisted wheat breeding: present status and future possibilitie...

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