High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.)

Abstract

Background: 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. However, the regulatory mechanism of miRNAmediated abiotic stress response in sweet potato remains unclear. Results: In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinityexposed 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. Conclusions:This study provides insights into the regulatory mechanism of miRNA-mediated salt response and molecular breeding of sweet potatoes though miRNA manipulation.

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

“…Nitrogen starvation [149] miR156, miR164, miR167, miR168, miR528, miR820, miR821, miR1318 Low-nitrogen stress [150] multiple miRNAs Abiotic stress [151] osa-miR414, osa-miR164e, osa-miR408 Salt stress [152] Soybean (Glycine max) multiple miRNAs Water deficit [153] Sugarcane (Saccharum L.) multiple miRNAs Water-deficit stress [154] multiple miRNAs Low temperature stress [155] multiple miRNAs Waterlogging condition [156] multiple miRNAs Drought stress [157] multiple miRNAs Drought stress [158] Sweet Potato (Ipomoea batatas) multiple miRNAs Drought and CO 2 stress [159] multiple miRNAs Salt stress [160] Switchgrass (Panicum virgatum) multiple miRNAs Drought and heat stress [161] multiple miRNAs Salt stress [162] Tobacco (Nicotiana tabacum) multiple miRNAs Salt and alkali stress [163] Tomato (Solanum lycopersicum) multiple miRNAs Drought and heat stress [164] multiple miRNAs Drought stress [165] Turnip (Brassica rapa) miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u, Bra-novel-miR3153-5p and Bra-novel-miR3172-5p…”

Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam]

“…When the seedlings had five to six functional leaves and adventitious roots of 8 to 10 cm, these seedlings were subjected to six different stresses, respectively. To study the expression patterns under these stresses, the adventitious roots of seedlings were submerged in the solution containing 150 mM NaCl, 20% PEG 6000, 100 mM ABA, 50 mg/L uniconazole, and 50 mg/L gibberellic acid (GA 3 ) respectively [ 54 ]. For black spot pathogen treatment, C. fimbriata conidia was collected after growing in potato dextrose agar (PDA) at 28 °C for 7 days, then were diluted to 1 × 10 4 spores/mL with sterile water, and then the roots of sweetpotato seedlings were cultivated in the 1 × 10 4 spores/mL conidia suspension.…”

Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops

“…Fu et al identified 1,077 miRNAs in Zea mays, comprising the highest number of identified miRNAs in various crops among the reports (Fu et al, 2017). Moreover, 882, 876, 693, and 650 miRNAs were identified in Mesembryanthemum crystallinum, Medicago truncatula, Vicia faba, and Ipomoea batatas, respectively (Jian et al, 2016;Cao et al, 2018;Alzahrani et al, 2019;Yang et al, 2020). The numbers of identified miRNA vary from dozens to hundreds, which may be due to the plant species, tissue specificity, development stage, and salt stress treatment methods.…”