Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize

Frisch, Matthias; Thiemann, Alexander; Fu, Junjie; Schrag, Tobias; Scholten, Stefan; Melchinger, Albrecht E.

doi:10.1007/s00122-009-1204-1

Cited by 99 publications

(95 citation statements)

References 19 publications

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“…Besides metabolite profiling, there are other promising genomics data sources with the potential to enhance the prediction accuracy of hybrid performance exploiting, for instance, structural variation (30) or transcriptome profiling (31). It would be of interest to integrate these data sources into the existing genomic selection models to increase the accuracy of prediction of hybrid performance for unrelated genotypes.…”

Section: Expanding the Search For Promising Heterotic Patterns Towardmentioning

confidence: 99%

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

Zhao

Zuo

Liu

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

183

188

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Hybrid breeding promises to boost yield and stability. The single most important element in implementing hybrid breeding is the recognition of a high-yielding heterotic pattern. We have developed a three-step strategy for identifying heterotic patterns for hybrid breeding comprising the following elements. First, the full hybrid performance matrix is compiled using genomic prediction. Second, a high-yielding heterotic pattern is searched based on a developed simulated annealing algorithm. Third, the long-term success of the identified heterotic pattern is assessed by estimating the usefulness, selection limit, and representativeness of the heterotic pattern with respect to a defined base population. This three-step approach was successfully implemented and evaluated using a phenotypic and genomic wheat dataset comprising 1,604 hybrids and their 135 parents. Integration of metabolomic-based prediction was not as powerful as genomic prediction. We show that hybrid wheat breeding based on the identified heterotic pattern can boost grain yield through the exploitation of heterosis and enhance recurrent selection gain. Our strategy represents a key step forward in hybrid breeding and is relevant for self-pollinating crops, which are currently shifting from pure-line to high-yielding and resilient hybrid varieties.hybrid breeding | genomic prediction | heterotic pattern

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Section: Expanding the Search For Promising Heterotic Patterns Towardmentioning

confidence: 99%

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

Zhao

Zuo

Liu

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

183

188

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“…Additionally, the identity, the genetic function and interaction of specific genes associated with heterosis of different traits is mostly unknown. More detailed information may be obtained by inspection of other molecular traits, like transcript or metabolite levels, which integrate genetic and environmental influences [17], [18]. The first complementary testing of large-scale genomic and metabolite data to predict important agronomical traits in hybrid maize test-crosses concluded that the prediction accuracies of heterotic traits in adult maize plants using metabolite profiles of the young leaves were only slightly lower than with Small Nucleotide Polymorphisms (SNPs), although metabolites represent approximately 300 times smaller number of variables compared to SNPs [19].…”

Section: Introductionmentioning

confidence: 99%

Deducing Hybrid Performance from Parental Metabolic Profiles of Young Primary Roots of Maize by Using a Multivariate Diallel Approach

et al. 2014

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Heterosis, the greater vigor of hybrids compared to their parents, has been exploited in maize breeding for more than 100 years to produce ever better performing elite hybrids of increased yield. Despite extensive research, the underlying mechanisms shaping the extent of heterosis are not well understood, rendering the process of selecting an optimal set of parental lines tedious. This study is based on a dataset consisting of 112 metabolite levels in young roots of four parental maize inbred lines and their corresponding twelve hybrids, along with the roots' biomass as a heterotic trait. Because the parental biomass is a poor predictor for hybrid biomass, we established a model framework to deduce the biomass of the hybrid from metabolite profiles of its parental lines. In the proposed framework, the hybrid metabolite levels are expressed relative to the parental levels by incorporating the standard concept of additivity/dominance, which we name the Combined Relative Level (CRL). Our modeling strategy includes a feature selection step on the parental levels which are demonstrated to be predictive of CRL across many hybrid metabolites. We demonstrate that these selected parental metabolites are further predictive of hybrid biomass. Our approach directly employs the diallel structure in a multivariate fashion, whereby we attempt to not only predict macroscopic phenotype (biomass), but also molecular phenotype (metabolite profiles). Therefore, our study provides the first steps for further investigations of the genetic determinants to metabolism and, ultimately, growth. Finally, our success on the small-scale experiments implies a valid strategy for large-scale experiments, where parental metabolite profiles may be used together with profiles of selected hybrids as a training set to predict biomass of all possible hybrids.

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“…This has fostered the proposal that more bio-logically meaningful markers need to be exploited for this purpose. Therefore, it has been suggested that parental differences in gene expression levels from a genomewide perspective (transcriptome) will likely produce more reliable markers for the prediction of heterosis, and indeed, some promising results were obtained (Stupar et al, 2008;Swanson-Wagner et al, 2009;Frisch et al, 2010;Thiemann et al, 2010). Nonetheless, trans-criptome-based molecular makers are expensive to develop and, at the current stage, unrealistic to be readily used by breeders.…”

Section: Discussionmentioning

confidence: 99%

Parental epigenetic difference in DNA methylation-level may play contrasting roles for different agronomic traits related to yield heterosis in maize

Yang¹,

Yu²,

Yang³

et al. 2011

Afr. J. Biotechnol.

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Although, maize is the crop wherein heterosis or hybrid vigor has been exploited to nearly the fullest extent, the molecular and genetic basis underlying this remarkable biological phenomenon remains largely an enigma.To further explore the issue from an epigenetic perspective, we sought to probe for possible relationships between the parental epigenetic difference in the form of DNA methylation revealed by the epigenetic marker MSAP, among a set of 11 maize inbred lines and heterosis in four agronomic traits manifested by a set of 30 F1 hybrids resulting from a half-diallel crossing among the inbred lines. We found that a specific type of DNA methylation-level difference, that is, relative CHG (H denotes A, C or T) methylation levels at the 5'-CCGG-3' sites exhibits a statistically significant negative correlation with heterosis in the number of rows per ear (NRE) and a positive correlation with the number of kernels per row (NKR), whereas, no correlation was detected between any of the DNA methylation-level differences and the rest two studied traits, 100-kernel weight (HKW) and kernel weight per ear (KWE). In a sharp contrast, parental genetic distance revealed by the genetic marker AFLP did not show any correlation with heterosis for any of the four studied agronomic traits. Our results suggest that parental epigenetic difference in particular types of DNA methylation-level difference plays some significant roles in the manifestation of heterosis of specific traits in maize, but the effects can be in opposite directions, and hence, offsetting each other and cumulating to cryptic effects on yield, itself.

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Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize

Cited by 99 publications

References 19 publications

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

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

Deducing Hybrid Performance from Parental Metabolic Profiles of Young Primary Roots of Maize by Using a Multivariate Diallel Approach

Parental epigenetic difference in DNA methylation-level may play contrasting roles for different agronomic traits related to yield heterosis in maize

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