Small RNA-based prediction of hybrid performance in maize
| Autor: | Stefan Scholten, Matthias Frisch, Tobias A. Schrag, Alexander Thiemann, Dominika Rybka, Albrecht E. Melchinger, Felix Seifert |
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| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
0301 basic medicine Small RNA lcsh:QH426-470 Hybrid performance lcsh:Biotechnology SNP Genomics Computational biology Breeding Biology Polymorphism Single Nucleotide Zea mays 01 natural sciences Transcriptome 03 medical and health sciences Hybrid trait prediction lcsh:TP248.13-248.65 Gene expression Genetics RNA Messenger Grain yield Gene Gene Expression Profiling Maize Gene expression profiling lcsh:Genetics 030104 developmental biology Hybridization Genetic RNA Small Untranslated Epigenetics DNA microarray Research Article 010606 plant biology & botany Biotechnology Reference genome |
| Zdroj: | BMC Genomics BMC Genomics, Vol 19, Iss 1, Pp 1-14 (2018) |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/s12864-018-4708-8 |
| Popis: | Background Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program. Results Correlation of genomic differences and messenger RNA (mRNA) or sRNA expression differences between parental lines with hybrid performance of their hybrids revealed that sRNAs showed an inverse relationship in contrast to the other two data types. We associated differences for SNPs, mRNA and sRNA expression between parental inbred lines with the performance of their hybrid combinations and developed two prediction approaches using distance measures based on associated markers. Cross-validations revealed parental differences in sRNA expression to be strong predictors for hybrid performance for grain yield in maize, comparable to genomic and mRNA data. The integration of both positively and negatively associated markers in the prediction approaches enhanced the prediction accurary. The associated sRNAs belong predominantly to the canonical size classes of 22- and 24-nt that show specific genomic mapping characteristics. Conclusion Expression profiles of sRNA are a promising alternative to SNPs or mRNA expression profiles for hybrid prediction, especially for plant species without reference genome or transcriptome information. The characteristics of the sRNAs we identified suggest that association studies based on breeding populations facilitate the identification of sRNAs involved in hybrid performance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4708-8) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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