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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #311185
Title: Novel and recently evolved miRNA clusters regulate expansive F-box gene networks through phasiRNAs in wild diploid strawberry

Author
item YE, SONGQING - University Of Maryland
item XIA, RUI - University Of Delaware
item Liu, Zongrang
item MEYERS, BLAKE - University Of Delaware
item LIU, ZHONGCHI - University Of Maryland

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2015
Publication Date: 7/4/2015
Citation: Ye, S., Xia, R., Liu, Z., Meyers, B., Liu, Z. 2015. Novel and recently evolved miRNA clusters regulate expansive F-box gene networks through phasiRNAs in wild diploid strawberry. Plant Physiology. DOI: 10.1104/pp.15.00253.

Interpretive Summary: Micro RNAs (miRNAs), one of the small RNA species discovered recently, play an important role in regulation of growth, development and fruit productivity in Arabidopsis plants. To understand whether these small RNAs control fruit growth and productivity in strawberry, we studied and characterized miRNAs in different fruit tissues and identified a large number of miRNAs that are differentially regulated among various fruit tissues and during plant development. We also identified two new miRNAs, which specifically target and cleave a large gene family that code for F-box genes, suggesting a new function of these two miRNAs on control of fruit production. Our discovery also supports a new hypothesis on how miRNAs in strawberry act and function. Implication of this work on improvement of strawberry productivity and other practical applications is discussed.

Technical Abstract: The wild strawberry, Fragaria vesca, has recently emerged as an excellent model for investigating flower and fruit traits in economically important fruit crops. Its history of physiological studies combined with sequenced genome and a full complement of molecular genetic tools facilitate investigations into mechanisms of its unique biological processes such as fleshy fruit development from the enlarged stem tip called receptacle. Sequencing of nine small RNA libraries encompassing vegetative, flower, and fruit tissues led to the identification of 22 conserved and 10 less-conserved miRNAs as well as 41 novel miRNAs that are likely specific to strawberry. High throughput Parallel Analyses of RNA ends (PARE) were performed to identify miRNA-guided cleavage events and corresponding target genes. We found that most conserved miRNAs developed species-specific target genes in addition to conserved targets, highlighting the dynamic and fluid nature of the miRNA-target relations. Significantly, we discovered two novel clusters of miRNAs, which together target up to 94 F-box genes. Within one of the clusters is a 22 nt novel miRNA, miRN39, that was expressed preferentially in the developing receptacle fruit, and triggered phased siRNA production from six primary FBX PHAS loci. This miRN39-phasiFBX pathway may be involved in regulating disease resistance in the receptacle fruit. In addition, a modified “two-hit” mode of tasiRNA processing was identified in F. vesca, suggesting flexibility in applying previously set rules. A major theme that emerges from this work is that novel miRNAs and miRNA-phasiRNA networks may have evolved to regulate recently expanded gene families so as to control species-specific biological or physiological processes.