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

Chen X, Gao W, Zhang J, Zhang X, Lin Z - BMC Genomics (2013)

Bottom Line: Finally, a network between miRNAs and their targets was constructed.Our 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, Hubei, China. linzhongxu@mail.hzau.edu.cn.

ABSTRACT

Background: MicroRNAs (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.

Results: To 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.

Conclusions: Our 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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Related in: MedlinePlus

RT-PCR analysis of target genes between mapping parents. Numbers at the top represent 0DPA, 5DPA, 10DPA, 15DPA, 20DPA and 25DPA of Emian22 and 3–79, respectively. Similar expression tendencies between Emian22 and 3–79 were classified into similar expression patterns. Obvious differential expression tendencies between Emian22 and 3–79 were classified into differential expression patterns. Obvious differential expression levels between Emian22 and 3–79 were classified into obvious difference. Minor differential expression levels between Emian22 and 3–79 were classified accordingly. Gene primers and their corresponding miRNA families are labeled on the left, and only one miRNA family is listed. More family information was shown in Additional file 8.
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Figure 4: RT-PCR analysis of target genes between mapping parents. Numbers at the top represent 0DPA, 5DPA, 10DPA, 15DPA, 20DPA and 25DPA of Emian22 and 3–79, respectively. Similar expression tendencies between Emian22 and 3–79 were classified into similar expression patterns. Obvious differential expression tendencies between Emian22 and 3–79 were classified into differential expression patterns. Obvious differential expression levels between Emian22 and 3–79 were classified into obvious difference. Minor differential expression levels between Emian22 and 3–79 were classified accordingly. Gene primers and their corresponding miRNA families are labeled on the left, and only one miRNA family is listed. More family information was shown in Additional file 8.

Mentions: Regarding target genes, 66 (67.3%) were expressed in cotton fiber (Additional file 8: Table S6). Among them, 50 were obviously differentially expressed; 14 had minor differences; and 2 were not different (Figure 4). Overall, 75.8% of the expressed target genes were significantly different at various fiber development stages (0, 5, 10, 15, 20, and 25 DPA), when comparing Emian22 and 3–79. Three target genes were weakly expressed or not expressed at all stages in both Emian22 and 3–79 (defined as no expression differences in this study). Furthermore, 39 target genes had similar expression patterns. Of the 25 target genes with different expression patterns, 13 were up-regulated and 12 were down regulated in 3–79, compared with Emian22. To further confirm RT-PCR data, target genes belonging to different categories were randomly chosen for qRT-PCR analysis (Additional file 9: Figure S3). Consistent results were observed between both RT-PCR and qRT-PCR analyses.


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

Chen X, Gao W, Zhang J, Zhang X, Lin Z - BMC Genomics (2013)

RT-PCR analysis of target genes between mapping parents. Numbers at the top represent 0DPA, 5DPA, 10DPA, 15DPA, 20DPA and 25DPA of Emian22 and 3–79, respectively. Similar expression tendencies between Emian22 and 3–79 were classified into similar expression patterns. Obvious differential expression tendencies between Emian22 and 3–79 were classified into differential expression patterns. Obvious differential expression levels between Emian22 and 3–79 were classified into obvious difference. Minor differential expression levels between Emian22 and 3–79 were classified accordingly. Gene primers and their corresponding miRNA families are labeled on the left, and only one miRNA family is listed. More family information was shown in Additional file 8.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4007520&req=5

Figure 4: RT-PCR analysis of target genes between mapping parents. Numbers at the top represent 0DPA, 5DPA, 10DPA, 15DPA, 20DPA and 25DPA of Emian22 and 3–79, respectively. Similar expression tendencies between Emian22 and 3–79 were classified into similar expression patterns. Obvious differential expression tendencies between Emian22 and 3–79 were classified into differential expression patterns. Obvious differential expression levels between Emian22 and 3–79 were classified into obvious difference. Minor differential expression levels between Emian22 and 3–79 were classified accordingly. Gene primers and their corresponding miRNA families are labeled on the left, and only one miRNA family is listed. More family information was shown in Additional file 8.
Mentions: Regarding target genes, 66 (67.3%) were expressed in cotton fiber (Additional file 8: Table S6). Among them, 50 were obviously differentially expressed; 14 had minor differences; and 2 were not different (Figure 4). Overall, 75.8% of the expressed target genes were significantly different at various fiber development stages (0, 5, 10, 15, 20, and 25 DPA), when comparing Emian22 and 3–79. Three target genes were weakly expressed or not expressed at all stages in both Emian22 and 3–79 (defined as no expression differences in this study). Furthermore, 39 target genes had similar expression patterns. Of the 25 target genes with different expression patterns, 13 were up-regulated and 12 were down regulated in 3–79, compared with Emian22. To further confirm RT-PCR data, target genes belonging to different categories were randomly chosen for qRT-PCR analysis (Additional file 9: Figure S3). Consistent results were observed between both RT-PCR and qRT-PCR analyses.

Bottom Line: Finally, a network between miRNAs and their targets was constructed.Our 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, Hubei, China. linzhongxu@mail.hzau.edu.cn.

ABSTRACT

Background: MicroRNAs (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.

Results: To 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.

Conclusions: Our 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.

Show MeSH
Related in: MedlinePlus