Comparative profiling of miRNA expression in developing seeds of high linoleic and high oleic safflower (Carthamus tinctorius L.) plants.

Shijiang Cao,Xiaochun Zhao,Wanxia Shen,Surinder P Singh,Ming-Bo Wang,Lixia Liu,Qing Liu,Xiaoming Jiao,Qian-Hao Zhu

doi:10.3389/fpls.2013.00489

Abstract

Vegetable oils high in oleic acid are considered to be advantageous because of their better nutritional value and potential industrial applications. The oleic acid content in the classic safflower oil is normally 10–15% while a natural mutant (ol) accumulates elevated oleic acid up to 70% in seed oil. As a part of our investigation into the molecular features of the high oleic (HO) trait in safflower we have profiled the microRNA (miRNA) populations in developing safflower seeds expressing the ol allele in comparison to the wild type high linoleic (HL) safflower using deep sequencing technology. The small RNA populations of the mid-maturity developing embryos of homozygous ol HO and wild type HL safflower had a very similar size distribution pattern, however, only ~16.5% of the unique small RNAs were overlapping in these two genotypes. From these two small RNA populations we have found 55 known miRNAs and identified two candidate novel miRNA families to be likely unique to the developing safflower seeds. Target genes with conserved as well as novel functions were predicted for the conserved miRNAs. We have also identified 13 miRNAs differentially expressed between the HO and HL safflower genotypes. The results may lay a foundation for unraveling the miRNA-mediated molecular processes that regulate oleic acid accumulation in the HO safflower mutant and developmental processes in safflower embryos in general.

Highlights

MicroRNAs are small endogenous non-coding RNAs of ∼21 nucleotides in length and have been identified in animal, plant, virus and a single-celled eukaryote (Bartel, 2004; Jones-Rhoades et al, 2006)
Safflower is an important oilseed crop grown for edible oil production and understanding the functions of miRNAs in regulating oil accumulation in the developing embryos of safflower could be of great value for the development of safflower germplasm with enhanced oil production and improved nutritional value
We have characterized the small RNA (sRNA) transcriptomes of a high oleic (HO) mutant and the high linoleic (HL) wild type safflower

Summary

Introduction

MicroRNAs (miRNAs) are small endogenous non-coding RNAs of ∼21 nucleotides (nt) in length and have been identified in animal, plant, virus and a single-celled eukaryote (Bartel, 2004; Jones-Rhoades et al, 2006). MiRNAs have been clearly shown to regulate a number of developmental and physiological processes by mediating target gene silencing at transcriptional and/or post-transcriptional levels (Bartel, 2004; Wu et al, 2010). Some miRNA targets are themselves regulators, such as those encoding transcription factors and F-box proteins (Bartel, 2004; Jones-Rhoades et al, 2006; Mallory and Vaucheret, 2006). The mature miRNA strand is incorporated into the RNA-induced silencing complex (RISC) to recognize its target(s), whereas the miRNA∗ strand is subject to degradation (Bartel, 2004; Sunkar and Zhu, 2004)

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