Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

Abstract

BackgroundPollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of the miRNA pathway in pollen development remains limited, and the dynamic profile of miRNAs in developing pollen is unknown.ResultsUsing next-generation sequencing technology, we pyrosequenced small RNA populations from rice uninucleate microspores to tricellular pollen and control sporophytic tissues at the genome-wide level. We identified 292 known miRNAs, including members of all 20 families conserved in plants, and 75 novel miRNAs. Of the 292 known miRNAs, 202 were expressed, with 103 enriched, in developing pollen. More than half of these novel miRNAs displayed pollen-or stage-specific expression. Furthermore, analyzing the 367 miRNAs and their predicted targets indicated that correlation in expression profiles of pollen-enriched known miRNAs and their targets significantly differs from that of sporophyte-enriched known miRNAs and their targets in some functional terms, while novel miRNAs appeared to negatively regulate their targets. Importantly, gene ontology abundance analysis demonstrated chromatin assembly and disassembly was important in the targets of bicellular pollen-expressed novel miRNAs. Principal component analysis revealed pollen of all three stages was discriminated from sporophytes, largely because of the novel and non-conserved known miRNAs.ConclusionsOur study, for the first time, revealed the differences in composition and expression profiles of miRNAs between developing pollen and sporophytes, with novel and non-conserved known miRNAs the main contributors. Our results suggest the important roles of the miRNA pathway in pollen development.

Comparative analysis of microRNA profiles of rice anthers between cool-sensitive and cool-tolerant cultivars under cool-temperature stress

“…In addition, we identified two cultivar-specific miRNAs (osa-miR531a/c and nov-miR039) that accumulated to more than 10 RPM in one cultivar and less than 1 RPM in the other cultivar; osa-miR531 and nov-miR039 were specifically expressed in Sasanishiki and Hitomebore, respectively (Table 3). It is noteworthy that seven osamiRNAs, out of the 13 differentially expressed and two cultivar-specific miRNAs, have previously been reported to be expressed in developing rice pollen (Wei et al, 2011). Thus, we considered that these 15 miRNAs were candidates for rice miRNAs related to cool tolerance in immature anthers.…”

“…Although previous papers have suggested a relationship between miRNA profiles and rice anther or pollen development (Wei et al, 2011;Peng et al, 2012;Yan et al, 2015), further investigation is needed to understand the complete picture of the molecular genetic system(s) active in this tissue, and in particular the role of miRNAs in developing rice anthers under cool stress. Here, we focused on miRNA accumulation in immature anthers of rice under cool stress related to cool-temperature injury at the booting stage, and compared the miRNA profiles between cool-sensitive Sasanishiki and cool-tolerant Hitomebore cultivars.…”

Identification of microRNAs potentially involved in male sterility of Brassica campestris ssp. chinensis using microRNA array and quantitative RT-PCR assays

“…In 2011, Wei et al conducted deep sequencing of rice on a genome-wide scale to explore the composition and expression patterns of miRNAs in developing pollen, including uninucleate microspores, bicellular and tricellular pollen, and sporophytic tissues, and 292 known miRNAs and 75 novel miRNAs were identified. Of the 292 known miRNAs, 103 were found in abundance in developing pollen, and more than half of the novel miRNAs displayed pollen-or stage-specific expression [36]. Their research revealed differences in the composition and expression profiles of miRNAs for developing pollen and sporophytes, which suggest the important roles of the miRNA pathway in pollen development.…”

Differential expression of microRNAs may regulate pollen development in Brassica oleracea

“…For example, miR157, miR171, miR172, and miR824 were identified in mature Arabidopsis pollen using 454 sequencing and a miRCURY array (Chambers and Shuai, 2009;Grant-Downton et al, 2009b). miR171a and miR398 have been detected in male loblolly pine (Pinus taeda) gametophytes and rice pollen, respectively, by microarray analysis (Wei et al, 2011;Quinn et al, 2014). miR172b expression has been detected in the flower buds of Brassica campestris (Jiang et al, 2013).…”

“…Significant progress has been made in pollen research by employing a variety of resources and novel techniques (Jiang et al, 2014), which have provided important information regarding the molecular mechanism of pollen development and the control of crop fertility. Recently, it has been demonstrated that miRNAs are differentially expressed during the various periods of pollen development, and play specific roles in regulatory function in model plants ( Le Trionnaire and Twell, 2010;Wei et al, 2011). For example, miRNAs have been shown to function in mature Arabidopsis pollen, together with some of the most important genes involved in the miRNA silencing pathway, such as DCL1, AGO1, and RDR6 (Grant-Downton et al, 2009a).…”