Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

Abstract

Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent 3 Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudooverdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in testcrosses.H YBRID breeding was pioneered in maize (Shull 1908) and plays an ever increasing role in other globally important field (Duvick 1999) and vegetable crops (Silva Dias 2010). Maize has also served as a model species for research in heterosis, the phenomenon behind the success of hybrid varieties, for which the genetic mechanisms have been elusive (Duvick 1999;Lippman and Zamir 2006). In recent years, evidence emerged for the importance of (pseudo-)overdominance in the manifestation of heterosis in maize (Lippman and Zamir 2006;Schön et al. 2010) and the particular role of the centromeres in this process (Gore et al. 2009;McMullen et al. 2009). Today, the availability of high-density marker data and whole-genome regression methods developed in the context of genomic prediction (Meuwissen et al. 2001) allows us to revisit this hypothesis by studying key genome properties such as allele frequencies and linkage phases.Consistency of linkage phases between quantitative trait loci (QTL) and markers is a key prerequisite for pooling of diverse breeds and germplams to increase sample size for genetic studies and transferability of their results to different populations (De Roos et al. 2008). Weber et al. (2012) used whole-genome estimates of marker effects of several cattle breeds to investigate across-breed marker-QTL linkage phase consistency. Such a study is still missing for maize and other important crops. For o...

Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding

“…1 and SI Appendix, Note b). This value is higher than previously observed for a population comprising 90 wheat hybrids (20), but corresponds to findings reported for 1,254 factorial crosses in a public maize breeding program (14). Thus, the high prediction accuracy observed in our study can be explained by a large population size of 1,604 single crosses, the phenotyping in 11 environments, as well as efficient exploitation of genetic relatedness for hybrid prediction.…”

“…The enhanced relevance of additive genetic variance contributes to an increase in recurrent selection gain (16). Moreover, predictions based on additive effects are more accurate than those based on dominance effects (14). Thus, breeding based on the identified heterotic pattern also increases the prediction accuracies in genomic prediction.…”

“…Intense selection increases short-term selection gain, but a reduction in the effective population size carries a cost in terms of long-term response (23). This could be of particular relevance for hybrid breeding, where ongoing reciprocal recurrent selection likely leads to divergent chromosomal regions caused by dominance or overdominance (14). Consequently, once a heterotic pattern has been identified and enhanced through interpopulation selection, the introgression of novel germplasm potentially disrupts coevolved gene complexes.…”

“…The germplasm was not structured into heterotic groups, but with the introduction of single-cross hybrids, available inbred lines were clustered into a female pool and a male pool according to production traits, such as seed yield. With ongoing hybrid breeding, the male and female groups coevolved and diverged (13), most likely owing to differential fixation of quantitative trait locus (QTL) alleles caused by dominance or overdominance (14).…”

“…Molecular marker-based genetic distance has been promoted as a proxy for heterosis and ultimately hybrid performance, although this is not the case for unrelated parental lines (12). Alternatively, genome-wide approaches can be used to predict hybrid performance (3,10,14). Genomic prediction is particularly promising for the complex trait of grain yield, because pedigree information, cosegregation, and linkage disequilibrium between markers and QTLs are jointly exploited.…”