Abstract
BackgroundMicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. However, the regulatory mechanism of miRNA-mediated abiotic stress response in sweet potato remains unclear.ResultsIn this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed sweet potato cultivars and its untreated control. Twelve small non-coding RNA libraries from NaCl-free (CK) and NaCl-treated (Na150) sweet potato leaves and roots were constructed for salt-responsive miRNA identification in sweet potatoes. A total of 475 known miRNAs (belonging to 66 miRNA families) and 175 novel miRNAs were identified. Among them, 51 (22 known miRNAs and 29 novel miRNAs) were significantly up-regulated and 76 (61 known miRNAs and 15 novel miRNAs) were significantly down-regulated by salinity stress in sweet potato leaves; 13 (12 known miRNAs and 1 novel miRNAs) were significantly up-regulated and 9 (7 known miRNAs and 2 novel miRNAs) were significantly down-regulated in sweet potato roots. Furthermore, 636 target genes of 314 miRNAs were validated by degradome sequencing. Deep sequencing results confirmed by qRT-PCR experiments indicated that the expression of most miRNAs exhibit a negative correlation with the expression of their targets under salt stress.ConclusionsThis study provides insights into the regulatory mechanism of miRNA-mediated salt response and molecular breeding of sweet potatoes though miRNA manipulation.
Highlights
MicroRNAs, a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses
Sequencing, annotation and sequence characterisation of small RNA To explore the regulatory mechanisms of miRNAs in response to salt stress in sweet potato, we established four different sample groups, namely, NaCl-treated (Na150) group of roots (SRN) and leaves (SLN) and the NaCl-free group of roots (SRC) and leaves (SLC)
After filtering low-quality data and 3′ joint contamination data and sequences with length less than 18 nt or greater than 25 nt and excluding non-coding RNAs, the remaining unannotated data were used for miRNA identification
Summary
MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. The regulatory mechanism of miRNAmediated abiotic stress response in sweet potato remains unclear. One of the major environmental factors, reduces the productivity of crops worldwide [1]. Previous studies showed that miRNAs regulate diverse processes in plants, including leaf morphogenesis and polarity, root initiation and development, flower differentiation and development, stem and vascular development, phase switch from vegetative growth to reproductive growth and response to abiotic and biotic stresses [7, 11, 12]
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