MicroRNA Sequencing Revealed Citrus Adaptation to Long-Term Boron Toxicity through Modulation of Root Development by miR319 and miR171

Abstract

Boron (B) toxicity in Citrus is a common physiological disorder leading to reductions in both productivity and quality. Studies on how Citrus roots evade B toxicity may provide new insight into plant tolerance to B toxicity. Here, using Illumina sequencing, differentially expressed microRNAs (miRNAs) were identified in B toxicity-treated Citrus sinensis (tolerant) and C. grandis (intolerant) roots. The results showed that 37 miRNAs in C. grandis and 11 miRNAs in C. sinensis were differentially expressed when exposed to B toxicity. Among them, miR319, miR171, and miR396g-5p were confirmed via 5′-RACE and qRT-PCR to target a myeloblastosis (MYB) transcription factor gene, a SCARECROW-like protein gene, and a cation transporting ATPase gene, respectively. Maintenance of SCARECROW expression in B treated Citrus roots might fulfill stem cell maintenance, quiescent center, and endodermis specification, thus allowing regular root elongation under B-toxic stress. Down-regulation of MYB due to up-regulation of miR319 in B toxicity-treated C. grandis roots might decrease the number of root tips, thereby dramatically changing root system architecture. Our findings suggested that miR319 and miR171 play a pivotal role in Citrus adaptation to long-term B toxicity by targeting MYB and SCARECROW, respectively, both of which are responsible for root growth and development.

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“…Expression of the novel miRNAs is tissue-specific, and two precursors, ppe-miR171a and ppe-miR171b , of the miR171 family were found. In another study, peach sRNAs (miRNAs) from different tissues were comprehensively analyzed and characterized for their expression in roots, leaves, flowers and fruit using sRNA-seq and RNA blots [67]. Size distribution analysis showed that 90% of sRNAs belong to 20 to 24 bp, with the 24-nt class most abundant.…”

“…Furthermore, peach sRNA sequences were classified into two major families: conserved miRNAs (23 miRNA families) and less-conserved miRNAs (24 miRNA families) [68]. Most of the conserved miRNAs, such as miR156-miR169 , miR319 , miR390 and miR396 , are expressed at high levels in all tissue i.e., leaf, flower, fruit, root, and bark tissues of peach as compared less-conserved miRNAs such as miR828 , miR858 and miR2118 [67].…”

“…The miRNA precursors ranges from 90 to 130 bp. Some miRNAs (miRC26) were observed to be highly accumulated than the precursor in young fruit as compared to bark tissue [67]. Thus, these miRNAs might be processed differently in different tissues.…”

“…In the peach, over 50 target genes for known miRNAs were identified (Table 1) [67]. Overall, 15 most conserved miRNA families target more than thirty genes, nine less-conserved miRNA families target 29 target genes.…”

“…Based on the abundance of the targets transcript, five categories have been formed: (I) conserved miRNAs and their conserved targets, (II) novel targets for conserved miRNAs, (III) targets for other known miRNAs, and (IV) peach-specific miRNAs. Most of the determined targets are belong to the transcription factor gene families, including ARF , NAC , SPL , MYB , and GRF , while others are relevant to auxin signaling ( TIR/AFB ), sRNA binding ( AGO ), sulfate transport ( AST ), redox reactions ( LAC and ARPN ), disease resistance (NBS-LRR), RNA editing, splicing and translation (pentatricopeptide repeat-containing proteins (PPR), protein kinase, FAR1-related, plant defense and growth [67].…”