Linkage mapping and expression analysis of miRNAs and their target genes during fiber development in cotton

Abstract

BackgroundMicroRNAs (miRNAs) are small, endogenously expressed, non-coding RNA molecules involved in gene transcription and expression that combine with specific mRNA site of target genes to inhibit protein synthesis or degrade mRNA. Since the first plant miRNA was reported in 2002, numerous new miRNAs and their targets have been discovered via high-throughput sequencing and computational approaches. However, the genetic variation of miRNA genes is poorly understood due to the lack of miRNA-specific DNA markers.ResultsTo study the genetic variation and map miRNAs and their putative target genes in cotton, we designed specific primers based on pre-miRNAs and published putative target genes. A total of 83 pre-miRNA primers and 1,255 putative target gene primers were surveyed, and 9 pre-miRNA polymorphic loci were mapped on 7 of the 26 tetraploid cotton chromosomes. Furthermore, 156 polymorphic loci of the target genes were mapped on the cotton genome. To map more miRNA loci, miRNA-based SRAP (sequence-related amplified polymorphism) markers were used to map an additional 54 polymorphic loci on the cotton genome with the exception of Chr01, Chr22, and Chr24. Finally, a network between miRNAs and their targets was constructed. All pre-miRNAs and 98 putative target genes were selected for RT-PCR analysis, revealing unique expression patterns across different fiber development stages between the mapping parents.ConclusionsOur data provide an overview of miRNAs, their putative targets, and their network in cotton as well as comparative expression analyses between Gossypium hirsutum and G. barbadense. These data provide a foundation for understanding miRNA regulation during cotton fiber development.

Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton

“…Overall, the result provided a good data resource for better understanding of fibre development. Several other studies also show that many miRNAs were differentially expressed during cotton fibre initiation and development ( Pang et al , 2009 ; Chen et al , 2013 ; Gong et al , 2013 ; Zhang et al , 2013 ).…”

“…MicroRNAs (miRNAs) may play a role during cotton response to drought and salinity stress. Using both computational and deep sequencing technology, some conserved and new miRNAs have recently been identified in cotton ( Qiu et al , 2007 ; Zhang et al , 2007 ; Pang et al , 2009 ; Chen et al , 2013 ; Gong et al , 2013 ; Yang et al , 2013 ; Zhang et al , 2013 ). Some of these miRNAs and their predicted targets were also found to be expressed differentially in terms of dose dependence and tissue dependence under salinity and drought conditions, such as miR156-SPL2, miR162-DCL1, miR159-TCP3, miR395-APS1, and miR396-GRF1 ( Yin et al , 2012 ; Wang et al , 2013 ).…”

Differential expression of microRNAs during fiber development between fuzzless-lintless mutant and its wild-type allotetraploid cotton

“…Liu et al (2014) identified 54 miRNAs including 47 conserved and 7 new miRNAs from island cotton using deep sequencing; their study also show that miR160, miR167, miR171, miR172 and miR827 were highly expressed in fiber initiation stage comparing to the elongation and secondary wall biosynthesis stage 37 . At the same time, several laboratories reported hundreds of miRNAs in cotton ovules and fibers 25 , 38 – 40 . Xie et al (2015) identified 65 conserved miRNA families in cotton ovules with initiated fiber and leaves using the first-generation deep sequencing technology; among these miRNAs, the expression of 32 miRNA families were difference between ovule and leaf tissues 41 .…”

Profiling of 21 novel microRNA clusters and their targets in an important grain: wheat (Triticum aestivum L.)

“…MicroRNAs (miRNAs) are class of RNAs which do not take part in protein coding having short length from 18 to 26 nucleotide (nt) long. Chen et al, (2013) revealed that long hairpin precursor is processed to produce mature miRNA sequence. The gene expression is regulated by miRNAs via messenger RNA's (mRNA) decomposition or translation (Khvorova et al, 2007).…”