Abstract
BackgroundPolyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported.ResultsHere, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid.ConclusionsThis study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.
Highlights
Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny
213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid, and 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, were nonadditively expressed in the F1 hybrid. miRNA synteny analysis revealed some miRNA loss and gain events in the genome of the F1 hybrid
Small RNA sequencing of B. napus, B. rapa and their triploid hybrid Total RNA from developing embryos of B. napus, B. rapa and their F1 hybrid was isolated for the preparation of small RNA libraries
Summary
Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. Few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported. Natural triploid plants have great potential in polyploid breeding, and introgression of genetic resources of B. rapa (AA genome) into B. napus will broaden the genetic basis of the latter and have important application significance [34,35,36]. Triploids from crosses of B. napus and B. rapa are ideal models to assess homologous pairing and recombination occurring between their genomes. These triploid hybrids have been used for the production of monosomic addition lines and for gene flow assessment after backcrossing to either parent [38]. The genomes of B. napus and B. rapa have been recently sequenced [39, 40], providing available genome information to globally identify miRNAs and analyze miRNA expression patterns among B. napus, B. rapa and their hybrid
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