Comparative expression of miRNA genes and miRNA-based AFLP marker analysis in cultivated tetraploid cottons

Pang, Mingxiong; Xing, Chaozhu; Adams, Nick; Rodriguez‐Uribe, Laura; Hughs, S. E.; Hanson, Stephen F.; Zhang, Jinfa

doi:10.1016/j.jplph.2010.10.006

Cited by 24 publications

(19 citation statements)

References 41 publications

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“…Exceptions were miR319-SRAP primer combinations which generated only 0–2 scorable bands. These results are consistent with those obtained from miRNA-based AFLP marker techniques [32]. Fifty-five primers produced 59 polymorphic loci (Additional file 4: Table S4), and the rate of primer polymorphism was 1.87%.…”

Section: Resultssupporting

confidence: 87%

“…Pang et al [32] explored the possibility of using miRNA genes as markers and identified DNA sequences of potential pre-miRNA. miRNA-AFLP analysis provides a reliable targeted genotyping strategy to assess genetic diversity among cotton species.…”

Section: Resultsmentioning

confidence: 99%

“…Pang et al [32] developed conserved miRNA gene markers and explored the possibility of an miRNA-AFLP marker technique. Then, the amplified products were sequenced and compared for homology using cotton expressed sequence tags.…”

Section: Resultsmentioning

confidence: 99%

“…Because the polymorphism is low in cotton, to genetically map more miRNAs, SRAP primers, including 64 forward primers and 64 reverse primers [44] were combined with 23 miRNA degenerate primers [32] in the form of miRNA-SRAP analysis. Finally, a total of 2,944 primer combinations were applied in this study.…”

Section: Methodsmentioning

confidence: 99%

“…Only one report in the literature described miRNA markers- miRNA-AFLP (amplified fragment length polymorphism) [32], but no miRNAs or their target genes have been genetically mapped in cotton.…”

Section: Introductionmentioning

confidence: 99%

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

Gao

Zhang

et al. 2013

BMC Genomics

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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.

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Gao

Zhang

et al. 2013

BMC Genomics

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Overexpression of miRNA in Cotton via Agrobacterium-Mediated Transformation

Wang¹,

Sun²,

Wang³

et al. 2018

Methods in Molecular Biology

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Overexpression of miR 156 in Cotton via Agrobacterium-Mediated Transformation

Zhang

Wang

Li³

et al. 2012

Methods in Molecular Biology

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microRNAs (miRNAs) are an extensive class of newly identified endogenous small regulatory molecules. Many studies show that miRNAs play a critical role in almost all biological and metabolic progresses through targeting protein-coding genes for mRNA cleavage or translation inhibition. Many miRNAs are also identified from cotton using computational and/or experimental approaches, including the next generation deep sequencing technology. However, the function of the majority of miRNAs are unclear. In this chapter, we describe a detailed method for overexpressing miR 156 in cotton using Agrobacterium-mediated genetic transformation. This provides an approach to investigate the function and regulatory mechanism of miRNAs in cotton.

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Comparative expression of miRNA genes and miRNA-based AFLP marker analysis in cultivated tetraploid cottons

Cited by 24 publications

References 41 publications

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

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

Overexpression of miRNA in Cotton via Agrobacterium-Mediated Transformation

Overexpression of miR 156 in Cotton via Agrobacterium-Mediated Transformation

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