Genomewide prediction of genotypic values and genetic variances within 969 maize biparental populations
2014-09
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Genomewide prediction of genotypic values and genetic variances within 969 maize biparental populations
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2014-09
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In plant breeding, selecting within biparental crosses and selecting parents to make new crosses are both important. My first study investigated the accuracy of genomewide selection (<italic>r</italic><sub>MG</sub>) within 969 biparental maize populations (<italic>Zea mays</italic> L.). My objectives were to determine: (i) the mean and variability of <italic>r</italic><sub>MG</sub>, (ii) if <italic>r</italic><sub>MG</sub> can be predicted, and (iii) how training population size (<italic>N</italic>), heritability (<italic>h</italic><super>2</super>), and number of markers (<italic>N</italic><sub>M</sub>) affect <italic>r</italic><sub>MG</sub>. I modified an equation for expected <italic>r</italic><sub>MG</sub> [E(<italic>r</italic><sub>MG</sub>)] to account for linkage disequilibrium (<italic>r</italic><super>2</super>) between markers and quantitative trait loci. Across the 969 populations, the mean and range (in parentheses) of observed <italic>r</italic><sub>MG</sub> was 0.45 (&minus0.59, 1.03) for yield, 0.59 (&minus0.34, 0.96) for moisture, and 0.55 (&minus0.24, 1.10) for test weight. The observed <italic>r</italic><sub>MG</sub>values were centered around E(<italic>r</italic><sub>MG</sub>) when <italic>r</italic><super>2</super> was accounted for, but had a large spread around E(<italic>r</italic><sub>MG</sub>). The <italic>r<super>2</super>(Nh<super>2</super>)<super>&half</super></italic> had the strongest association with the observed <italic>r</italic><sub>MG</sub>. In the second study, my objective was to determine whether related populations could be used to predict the genetic variance (V<sub>G</sub>) of a segregating population from two parents (A and B). For each of 85 A/B populations, 2&ndash23 A/* and B/* populations were used as training populations, where * denotes a random parent. In the genomewide selection model, the testcross V<sub>G</sub> in A/B was predicted as the variance among the predicted genotypic values of progeny from the simulated A/B population. In the mean variance model, V<sub>G</sub> was estimated as the mean of V<sub>G</sub> in A/* and B/* populations. The correlations between observed and predicted V<sub>G</sub> were not significant (P = 0.05) for the genomewide selection model but were significant for the mean variance model (0.26 for yield, 0.46 for moisture, and 0.50 for test weight). The V<sub>G</sub> of A/B population could therefore be predicted as the mean of V<sub>G</sub> in A/* and B/* populations. Overall, the results indicated that genomewide selection can identify the best individuals within a cross, but it cannot reliably predict which parents would lead to the largest genetic variance.
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University of Minnesota Ph.D. dissertation. September 2014. Major: Applied Plant Sciences. Advisor: Rex Bernardo. 1 computer file (PDF); ix, 61 pages, appendices p. 56-61.
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Lian, Lian. (2014). Genomewide prediction of genotypic values and genetic variances within 969 maize biparental populations. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/168264.
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