Abstract
Main conclusion
Using a genome-wide analysis of miRNAs in ‘Yali’ pear (Pyrus bretschneideri) via the next-generation high-throughput sequencing of small RNAs with a bioinformatics analysis, we found that pbr-miR156, pbr-miR164, pbr-miR399, and pbr-miR482 and their target genes function in viral defense in ‘Duli’ and ‘Hongbaoshi’. pbr-miR160, pbr-miR168, pbr-miR171, and pbr-miR319 and their targets function in auxin signaling pathways in ‘Zhongai 4’ and ‘Zhongai 5’.
Successful fruit production in pear (Pyrus spp.) depends on the use of optimal combinations of rootstocks and scions. Deciphering plant–pathogen defense mechanisms and hormone signaling pathways is an important step towards develo** pear rootstocks and varieties with improved qualities. In the current study, we combined next-generation sequencing of small RNAs with a bioinformatics analysis to systematically identify and characterize 298 miRNAs in the pear scion cultivar ‘Yali’ (Pyrus bretschneideri). We also analyzed miRNAs in three rootstock varieties (‘Duli’, ‘Zhongai 4’, and ‘Zhongai 5’) and one scion cultivar (‘Hongbaoshi’). We found that pbr-miR156, pbr-miR164, pbr-miR399, and pbr-miR482 are induced following infection with the pear virus Apple stem pitting virus (ASPV), and identified their target genes (pbRPS6, pbNAC, pbTLR, and pbRX-CC, respectively), which participate in viral defense pathways in ‘Duli’ and ‘Hongbaoshi’. Furthermore, we identified pbr-miR160, pbr-miR168, pbr-miR171, and pbr-miR319, and found that the production of these miRNAs was suppressed under low levels of synthetic auxin. The targets of these miRNAs (pbARF, pbAEC, pbSCL, and pbTCP4) respond to auxin signaling pathways in ‘Zhongai 4’ and ‘Zhongai 5’. Our results lay the foundation for breeding improved pear cultivars.
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Abbreviations
- R gene:
-
Resistance gene
- TLRs:
-
Toll-like receptors
- ARF:
-
Auxin response factor
- AEC:
-
Auxin efflux carrier
- ASGV:
-
Apple stem grooving virus
- ASPV:
-
Apple stem pitting virus
- ACLSV:
-
Apple chlorotic leaf spot virus
- NAA:
-
1-naphthaleneacetic acid; synthetic auxin
- SCL:
-
Scarecrow-like
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This study was financially supported by the earmarked fund for China Pear Modern Agro-industry Technology Research System CARS 28-08.
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Supplementary Fig. S1
Characteristic fold-back RNA secondary structure of 21 novel miRNAs. The hairpin structure precursors of 21 potential novel miRNAs identified in a small RNA library constructed from ‘Yali’ leaves. Highlighted in red are the novel miRNA sequences and in blue are the miRNA* sequences (PDF 897 kb)
Supplementary Fig. S2
Conserved domains of pbr-miR156 (a), pbr-miR164 (b), pbr-miR399 (c), and pbr-miR482 (d) target genes pbRPS6, pbNAC, pbTLR, and pbRX-CC, respectively (JPEG 1581 kb)
Supplementary Fig. S3
Conserved domains of pbr-miR160 (a), pbr-miR168 (b), pbr-miR171 (c), and pbr-miR319 (d) target genes pbARF, pbAEC, pbSCL, and pbTCP4, respectively (JPEG 1617 kb)
Supplementary Fig. S4
Diagram of multiple PCR analysis of three viruses (ASGV, ASPV, and ACLSV) (PNG 191 kb)
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Zhang, Q., Zhang, Y., Wang, S. et al. Characterization of genome-wide microRNAs and their roles in development and biotic stress in pear. Planta 249, 693–707 (2019). https://doi.org/10.1007/s00425-018-3027-2
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DOI: https://doi.org/10.1007/s00425-018-3027-2