Small RNA-based prediction of hybrid performance in maize

Abstract

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.

Keywords: Epigenetics; Grain yield; Hybrid performance; Hybrid trait prediction; Maize; SNP; Small RNA; Transcriptome.

Fig. 1

Correlation r of hybrid performance for grain yield with parental differences for SNP (a), mRNA (b) or sRNA (c) data

Fig. 2

Permutation analysis with shuffled hybrid trait values with SNP, transcriptome (mRNA), or sRNA data. The lowest p-values of each permutation run (black violin plot) and of the actual genotype-trait allocation (red dot) are represented. The dotted line indicates the threshold to reach significance at 5% FDR

Fig. 3

Prediction types (a) type-2 prediction, both parents have test crosses; (b, c) type-1 prediction, only one of the parental groups has test crosses; (d) type-0 prediction, none of the parents has been tested

Fig. 4

Prediction accuracy for SNP, mRNA and sRNA based prediction of hybrid performance for grain yield for (a) type-2 prediction, (b) type-1 prediction, (c) type-0 prediction

Fig. 5

Enrichment of hpa-sRNAs for lengths of 22-nt and 24-nt. Size distribution of positively/negatively hpa-sRNAs and random sets of sRNAs. Enrichment analysis by bootstrapping (p < 0.001)

Fig. 6

Genome-wide distribution and enrichment of sRNAs. Genomic coverage of hpa-sRNAs (1), all sRNAs (2), genes (3), repeats (4), intergenic regions (5) and recombination rates (6) throughout the B73 reference genome. Distribution of 22-nt sRNAs (7a), positively 22-nt hpa-sRNAs (7b), negatively 22-nt hpa-sRNAs (7d), 24-nt sRNAs (8a), positively 24-nt hpa-sRNAs (8b), negatively 24-nt hpa-sRNAs (8d) on the B73 reference genome. -log₁₀ plot of enrichment probabilities of positively 22-nt hpa-sRNAs (7c), negatively 22-nt hpa-sRNAs (7e), positively 24-nt hpa-sRNAs (8c) and negatively 24-nt hpa-sRNAs (8e). Peaks in green background zone show significant enrichment (p < 0.05). All distributions are shown in 1 Mb resolution. Centromeres according to Jiao et al. [31] are indicated red in the rulers. Whole-genome visualization was created with Circos [43]. Annotations in (2) to (4) are according to genome assembly AGPv4.36

Fig. 7

Relation of hpa-sRNAs to genomic features. Size distribution of hpa-sRNAs mapping to single or multiple annotated features of the maize genome; 22-nt hpa-sRNAs map primarily to multiple annotations (repeat/intergenic, gene/repeat/intergenic), while 24-nt hpa-sRNAs map primarily to single annotations (intergenic or repeat)