Abstract
Salinity is a serious environmental issue. It has a substantial effect on crop yield, as many crop species are sensitive to salinity due to climate change, and it impact is continuing to increase. Plant microRNAs (miRNAs) contribute to salinity stress response in bread wheat. However, the underlying molecular mechanisms by which miRNAs confer salt tolerance in wheat are unclear. We conducted a genome-wide discovery study using Illumina high throughput sequencing and comprehensive in silico analysis to obtain insight into the underlying mechanisms by which small RNAs confer tolerance to salinity in roots of two contrasting wheat cvv., namely Suntop (salt-tolerant) and Sunmate (salt-sensitive). A total of 191 microRNAs were identified in both cultivars, consisting of 110 known miRNAs and 81 novel miRNAs; 181 miRNAs were shared between the two cultivars. The known miRNAs belonged to 35 families consisted of 23 conserved and 12 unique families. Salinity stress induced 43 and 75 miRNAs in Suntop and Sunmate, respectively. Among them, 14 and 29 known and novel miRNAs were expressed in Suntop and 37 and 38 in Sunmate. In silico analysis revealed 861 putative target mRNAs for the 75 known miRNAs and 52 putative target mRNAs for the 15 candidate novel miRNAs. Furthermore, seven miRNAs including tae-miR156, tae-miR160, tae-miR171a-b, tae-miR319, tae-miR159a-b, tae-miR9657 and novel-mir59 that regulate auxin responsive-factor, SPL, SCL6, PCF5, R2R3 MYB, and CBL-CIPK, respectively, were predicted to contribute to salt tolerance in Suntop. This information helps further our understanding of how the molecular mechanisms of salt tolerance are mediated by miRNAs and may facilitate the genetic improvement of wheat cultivars.
Highlights
Non-coding RNAs are functional RNAs with low protein-coding potential and are divided into three main groups based on length: small (18–30 nt), medium (31–200 nt), and long (>201 nt) [1]
MicroRNAs and putative target genes expression patterns of salt-tolerant Suntop and salt-sensitive Sunmate in responses to salinity were analyzed by high throughput sequencing
110 known and 81 novels miRNAs were identified belonging to 35 families, among them, 181 miRNAs were shared by both cultivars
Summary
Non-coding RNAs are functional RNAs with low protein-coding potential and are divided into three main groups based on length: small (18–30 nt), medium (31–200 nt), and long (>201 nt) [1]. Small RNAs (sRNAs) are 21–24 nt long, are predominantly derive from intergenic region [2], and are vital regulators of protein-coding transcript expression at both RNA and DNA levels. These regulatory sRNAs mainly function in two ways: by posttranscriptional gene silencing (PTGS) through mRNA degradation, mRNA cleavage, or translational repression; and by transcriptional gene silencing (TGS) due to histone modifications [3,4,5]. Some miRNAs are conserved among species while others are non-conserved, called novel miRNAs and are often tissue or species-specific [16] Due to their involvement in stress responses, an understanding of the expression of miRNAs is important, especially for breeding crops that are tolerant of abiotic stress
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