Identification of Genes Related to White and Black Plumage Formation by RNA-Seq from White and Black Feather Bulbs in Ducks

Li, Shijun; Wang, Cui; Yu, Wenhua; Zhao, Shuhong; Gong, Yanzhang

doi:10.1371/journal.pone.0036592

Cited by 80 publications

(78 citation statements)

References 59 publications

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“…Based on these results, although feathers are elaborate skin appendages, the mechanism for melanogenesis between skin and feather in black-bone chicken is significantly different. Li et al showed that the expression of TYR and MITF was associated with the formation of black and white plumage in ducks [58]. Melanin pigmentation is an important component of vertebrate colouration that is often under strong genetic control [3].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

Wang

Liao

et al. 2018

Cell Physiol Biochem

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Background/Aims: Melanin is a major and ubiquitous component of plumage colouration, and patterns of melanin pigmentation in birds are extremely varied. However, the molecular mechanism of pigmentation in avian plumage is still largely unknown. Methods: To elucidate the molecular mechanisms involved in the formation of black and white plumage, this study takes advantage of high-throughput sequencing technology to compare differences in the transcriptome between black and white chicken feather bulbs. In total, we constructed six cDNA libraries from black (Group B) and white (Group W) feather bulbs in the dorsal plumage of Muchuan black-boned chickens. Results: A comparison between Groups B and W revealed 61 differentially expressed genes, with 47 displaying higher, and 14 displaying lower, levels of expression in white feather bulbs. Our results revealed a set of candidate genes and two potential metabolic pathways involved in black-bone chicken plumage melanogenesis. These include four homeobox genes (HOXB9, HOXC8, HOXA9, and HOXC 9), two glutathione (GSH) metabolism-related genes (CHAC1 and GPX3), and the transforming growth factor beta (TGF-β) signalling pathway. Two known genes, TYR and MITF, were also shown to play a role in melanin formation. Conclusion: our data provide a valuable resource for discovering genes important in plumage melanin formation and will help further elucidate the molecular mechanisms for black and white plumage.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

Wang

Liao

et al. 2018

Cell Physiol Biochem

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“…A fragment of β-actin that spans an intron sequence was used to verify the efficiency of the reverse transcription reaction and to exclude genomic DNA contamination. The primer sequences were as follows: forward primer, 5'-AACTGGGATGACATGGAGAAGA; and reverse primer, 5'-ATGGCTGGGGTGTTGAAGGT (Li et al, 2012).…”

Section: Rna Isolation and Reverse Transcriptionmentioning

confidence: 99%

“…Then, Solexa sequencing of the pooled RNA from the LPS-treated samples and the control samples was conducted at Shanghai Hanyu Bio-Tech (Li et al, 2012;Jiang et al, 2013). The Anase Duck database (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/all.dir/) was employed for sequence analysis.…”

Section: Rna-seq Data Mining and Gene Ontology (Go) Analysismentioning

confidence: 99%

“…The sequences of the quantitative real-time PCR primers were as follows: CCL4 forward primer, 5'-ACTCTGACCCACCAACCT and reverse primer, 5'-GATTTCACGTCCCTTCCT (Tm = 54°C); STEAP3 forward primer, 5'-GTCAGTAACAACACCGAAATCA and reverse primer, 5'-TTACCATCCCTGGCACCT (Tm = 54°C); CD71 forward primer, 5'-TACTTAGCGGATGGTGATG and reverse primer, 5'-TTCTTGTTTGCCCTTTGC (Tm = 60°C); LBP forward primer, 5'-TTGCCACTGCCAAGTTCCT and reverse primer, 5'-AGCTGGCGGTGTTGAAGAA (Tm = 55°C); β-actin was used as the reference gene to normalize the quantification of each target mRNA. Primer sequences for β-actin were as follows: forward primer, 5'-AACTGGGATGACATGGAGAAGA and reverse primer, 5'-ATGGCTGGGGTGTTGAAGGT (Tm = 60°C) (Li et al, 2012). The level of relative mRNA expression of the target genes was calculated as fold changes of the threshold cycle (Ct) value relative to the reference gene using the 2 -ΔΔCt method.…”

Section: Real-time Pcr Analysismentioning

confidence: 99%

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Identification of genes and pathways related to lipopolysaccharide signaling in duckling spleens

Deng¹,

Yu²,

Liu³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Lipopolysaccharide (LPS), the major component of the outer cell wall of Gram-negative bacteria, activates the immune system and threatens the health of livestock and poultry. However, little is known about the genes and pathways involved in the immune response of ducklings to LPS. To elucidate the genes involved in the response of 7-day-old duckling spleens treated with LPS, RNA from LPS-treated and control duckling spleens was analyzed by RNA-Seq. The results showed 11,095 and 10,840 genes with >10 clean reads in the LPS-treated and control groups, respectively. Among these genes, 89 were differentially expressed (log 2 ratio ≥ 1, P ≤ 0.01, false discovery rate ≤ 0.001); 67 of these were upregulated and 22 were downregulated in the LPS-treated group compared to the control. GO and GO-rich analysis showed that differentially expressed genes were enriched in 13 functional categories (P < 0.05). Pathway analysis and pathway richness analysis showed that differentially expressed genes were enriched in six pathway categories (P < 0.05). Further analysis showed that some immune system-related signaling pathways, such as the hematopoietic cell lineage, Toll-like receptor signaling pathway, T cell receptor signaling pathway, T cell receptor signaling pathway, complement and coagulation cascades, antigen processing and presentation, and chemokine signaling pathway, are active during the immune response. To confirm the RNA-Seq results, we detected CCL4, LBP, CD71, and STEAP3 expression using real-time PCR analysis, and the results were consistent with the RNA-Seq results. Our results provide new information on the genes involved in the immune response of duckling spleens to LPS.

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“…Transcriptomics is an important post-genomic era research field that not only studies gene expression and regulation, but also investigates gene functions. It is the foundation and starting point of investigations on the function and structure of genes (Jääger et al, 2012;Li et al, 2012;Sangwan et al, 2013). Single cell RNA-Seq technology is a powerful tool that can provide information about tens of thousands of genes from a single cell.…”

Section: Introductionmentioning

confidence: 99%

Single cell transcriptome profiling revealed differences in gene expression during oocyte maturation in Haimen white goats

Yin¹,

Cheng²,

Guo³

et al. 2017

Genet. Mol. Res.

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ABSTRACT. Juvenile in vitro embryo transfer is an important animal reproductive technology that can shorten the generation interval of livestock, explore the reproductive potential of dams with excellent genetic traits, accelerate genetic progress and production efficiency of the herd, and provide a wealth of genetic resources for livestock breeding. However, oocytes from kids do not develop as well as those from female goats during in vitro maturation. To identify differences during different stages of oocyte maturation, we used single cell transcriptome sequencing to compare gene expression in mature oocytes from kids and female goats. We identified 1086 differentially expressed genes in mature oocytes from kids and female goats. Of these, we observed upregulated expression in 355 genes and downregulated expression in 435 genes. The differentially expressed genes were involved in a total of 245 different pathways; of which 30 were significant (P ≤ 0.05). We used real-time quantitative polymerase chain reaction to screen and verify the expression of five genes specifically involved in oocyte maturation (MOS, RPS6KA1, CPEB1, ANAPC13, and CDK1). Further study of these genes will be of great importance for improving the reproductive performance of Haimen white goats.

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Identification of Genes Related to White and Black Plumage Formation by RNA-Seq from White and Black Feather Bulbs in Ducks

Cited by 80 publications

References 59 publications

Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

Identification of genes and pathways related to lipopolysaccharide signaling in duckling spleens

Single cell transcriptome profiling revealed differences in gene expression during oocyte maturation in Haimen white goats

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