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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 20 February 2024 | Viewed by 8184

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Special Issue Editors

Dr. Tao Zhang

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Guest Editor

College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Interests: poultry; genetics and breeding; gene function; epigenetics; molecular-marker-assisted breeding; adipogenesis

Dr. Genxi Zhang

E-Mail Website
Guest Editor

College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Interests: poultry; quantitative genetics; myogenesis; gene function; molecular mechanisms; non-coding RNA

Special Issue Information

Dear Colleagues,

Poultry meat and eggs are among the most common animal sources of food consumed at the global level. With continuous genetic selection, modern poultry has become the most efficient domestic animal, producing cheap and high-quality protein. The rapid development of poultry genetics and genomics breeding has brought huge economic benefits to the global poultry industry. However, numerous problems in poultry genetics and genomics remain to be addressed. For example, the complex genetic basis of important economic traits is still poorly understood, and the functional genes responsible for target traits require further mining. Genomic selection technology is immature, and its application in poultry breeding is still relatively limited.

This Special Issue aims to collect high-quality original research articles and comprehensive reviews to address emerging challenges in poultry genetics and genomics. Topics welcomed include, but are not limited to, genetic diversity and evolution, genome annotation, function and molecular mechanisms, omics studies, genomic selection, gene editing, and other new progress related to poultry genetics and genomics.

Dr. Tao Zhang
Dr. Genxi Zhang
Guest Editors

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

poultry
gene function
genome annotation
omics
gene editing
genomic selection
molecular mechanisms
molecular markers

Published Papers (10 papers)

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Research

Open AccessArticle

Exploration of Potential Target Genes of miR-24-3p in Chicken Myoblasts by Transcriptome Sequencing Analysis

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Genes 2023, 14(9), 1764; https://doi.org/10.3390/genes14091764 - 05 Sep 2023

Viewed by 326

Abstract

Broiler skeletal muscle growth is significantly influenced by miRNAs. Our earlier research demonstrated that miR-24-3p significantly suppressed the proliferation of chicken myoblasts while promoting their differentiation. The purpose of this study is to investigate miR-24-3p potential target genes in chickens. We collected myoblasts of Jinghai yellow chicken and transfected four samples with mimics of miR-24-3p and another four samples with mimic NC (negative control) for RNA-seq. We obtained 54.34 Gb of raw data in total and 50.79 Gb of clean data remained after filtering. Moreover, 11,635 genes were found to be co-expressed in these two groups. The mimic vs. NC comparison group contained 189 DEGs in total, 119 of which were significantly up-regulated and 70 of which were significantly down-regulated. Important biological process (BP) terminology such as nuclear chromosomal segregation, reproduction, and nuclear division were discovered by GO enrichment analysis for DEGs in the mimic vs. NC comparison group. KEGG pathway analysis showed that focal adhesion, cytokine–cytokine receptor interaction, the TGF-β signaling pathway, and the MAPK signaling pathway were enriched in the top 20. Variation site analysis illustrated the SNP (single nucleotide polymorphisms) and INDEL (insertion–deletion) in the tested samples. By comparing the target genes predicted by miRDB (MicroRNA target prediction database) and TargetScan with the 189 DEGs found by the transcriptome sequencing, we discovered two up-regulated DEGs (NEURL1 and IQSEC3) and two down-regulated DEGs (REEP1 and ST6GAL1). Finally, we carried out qPCR experiments on eight DEGs and discovered that the qPCR results matched the sequencing outcomes. These findings will aid in identifying potential miR-24-3p target genes in chicken skeletal muscle and offer some new directions for upcoming research on broiler breeding. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Combine with RNA-seq Reveals the Effect of Melatonin in the Synthesis of Melanin in Primary Melanocytes of Silky Fowls Black-Bone Chicken

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Genes 2023, 14(8), 1648; https://doi.org/10.3390/genes14081648 - 18 Aug 2023

Viewed by 436

Abstract

(1) Background: It was found that the melanin of black-bone chicken has various effects such as scavenging DPPH free radicals and anti-oxidation, and the synthesis of melanin is affected by various factors including hormones. In addition, several studies have found that melatonin affects the melanoma cell synthesis of melanin, which has not been reported in chicken primary melanocytes; so, relevant studies were conducted. (2) Methods: In this study, chicken primary melanocytes were isolated and characterized, and then melanocytes were treated with different concentrations of melatonin to investigate the effects of melatonin on melanin synthesis in chicken melanocytes in terms of melanin synthesis-related genes, melanin content, and tyrosinase activity, and combined with RNA seq to detect the change in gene expression level of chicken melanocytes after melatonin treatment. (3) Results: We isolated and characterized primary melanocytes, and indirect immunofluorescence assay results showed positive melanocyte marker genes. RT-qPCR results showed that melatonin decreased the expression of melanin synthesis-related genes. In addition, melatonin reduced the melanin content and decreased the tyrosinase activity of melanocytes in the treated group. A total of 1703 differentially expressed genes were screened by RNA-seq, and in addition, in the KEGG results, the signaling pathway associated with melanin synthesis, and the mTOR signaling pathway were enriched. (4) Conclusions: Melatonin could decrease the synthesis of melanin in chicken primary melanocytes. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Characterization of the Effects of Host p53 and Fos on Gallid Alpha Herpesvirus 1 Replication

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Genes 2023, 14(8), 1615; https://doi.org/10.3390/genes14081615 - 12 Aug 2023

Viewed by 482

Abstract

Treatment options for herpesvirus infections that target the interactions between the virus and the host have been identified as promising. Our previous studies have shown that transcription factors p53 and Fos are essential host determinants of gallid alpha herpesvirus 1 (ILTV) infection. The impact of p53 and Fos on ILTV replication has ‘not been fully understood yet. Using the sole ILTV-permissive chicken cell line LMH as a model, we examined the effects of hosts p53 and Fos on all phases of ILTV replication, including viral gene transcription, viral genome replication, and infectious virion generation. We achieved this by manipulating the expression of p53 and Fos in LMH cells. Our results demonstrate that the overexpression of either p53 or Fos can promote viral gene transcription at all stages of the temporal cascade of ILTV gene expression, viral genome replication, and infectious virion production, as assessed through absolute quantitative real-time PCR, ILTV-specific RT-qPCR assays, and TCID₅₀ assays. These findings are consistent with our previous analyses of the effects of Fos and p53 knockdowns on virus production and also suggest that both p53 and Fos may be dispensable for ILTV replication. Based on the synergistic effect of regulating ILTV, we further found that there is an interaction between p53 and Fos. Interestingly, we found that p53 also has targeted sites upstream of ICP4, and these sites are very close to the Fos sites. In conclusion, our research offers an in-depth understanding of how hosts p53 and Fos affect ILTV replication. Understanding the processes by which p53 and Fos regulate ILTV infection will be improved by this knowledge, potentially paving the way for the development of novel therapeutics targeting virus–host interactions as a means of treating herpesvirus infections. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

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Genes 2023, 14(8), 1605; https://doi.org/10.3390/genes14081605 - 10 Aug 2023

Viewed by 429

Abstract

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima’s D and Fu’s Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima’s D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Molecular Regulation of Differential Lipid Molecule Accumulation in the Intramuscular Fat and Abdominal Fat of Chickens

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Genes 2023, 14(7), 1457; https://doi.org/10.3390/genes14071457 - 17 Jul 2023

Viewed by 459

Abstract

Reducing abdominal fat (AF) accumulation and increasing the level of intramuscular fat (IMF) simultaneously is a major breeding goal in the poultry industry. To explore the different molecular mechanisms underlying AF and IMF, gene expression profiles in the breast muscle (BM) and AF from three chicken breeds were analyzed. A total of 4737 shared DEGs were identified between BM and AF, of which 2602 DEGs were upregulated and 2135 DEGs were downregulated in the BM groups compared with the AF groups. DEGs involved in glycerophospholipid metabolism and glycerolipid metabolism were potential regulators, resulting in the difference in lipid metabolite accumulation between IMF and AF. The PPAR signaling pathway was the most important pathway involved in tissue-specific lipid deposition. Correlation analysis showed that most representative DEGs enriched in the PPAR signaling pathway, such as FABP5, PPARG, ACOX1, and GK2, were negatively correlated with PUFA-enriched glycerophospholipid molecules. Most DEGs related to glycerophospholipid metabolism, such as GPD2, GPD1, PEMT, CRLS1, and GBGT1, were positively correlated with glycerophospholipid molecules, especially DHA- and arachidonic acid (ARA)-containing glycerophospholipid molecules. This study elucidated the molecular mechanism underlying tissue-specific lipid deposition and poultry meat quality. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Circ_PIAS1 Promotes the Apoptosis of ALV-J Infected DF1 Cells by Up-Regulating miR-183

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Genes 2023, 14(6), 1260; https://doi.org/10.3390/genes14061260 - 14 Jun 2023

Viewed by 582

Abstract

(1) Background: circRNAs are closed circular molecules with covalent bonds generated by reverse shearing, which have high stability and have different manifestations in different tissues, cells, or physiological conditions and play important roles in various disease processes and physiological processes. In addition, circ_PIAS1 has been screened out and verified, and the bioinformatics analyzed in previous studies. In this study, we investigated the function of circ_PIAS1 and studied its role in ALV-J infection to provide a basis for the role of circRNA in ALV-J infection. (2) Methods: the effect of circ_PIAS1 on apoptosis during ALV-J infection was studied by flow cytometry and detection of apoptotic gene expression, and miR-183 was screened by a biotin-labeled RNA pull-down technique. After overexpression and inhibition of miR-183, the effect of miR-183 on apoptosis in the process of ALV-J infection was studied by flow cytometry and detection of apoptotic gene expression. (3) Results: after overexpression of circ_PIAS1, flow cytometry and apoptotic gene expression showed that circ_PIAS1 promoted apoptosis. The results of RNA pull-down showed that 173 miRNAs could bind to circ_PIAS1, and circ_PIAS1 up-regulated the expression of miR-183. On the other hand, the same results were obtained whether miR-183 was overexpressed or inhibited that miR-183 affected ALV-J infection by promoting cell apoptosis. (4) Conclusions: circ_PIAS1 up-regulated the expression of miR-183 and influenced ALV-J infection by promoting cell apoptosis. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Genome-Wide Association Study Reveals the Genetic Basis of Duck Plumage Colors

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Genes 2023, 14(4), 856; https://doi.org/10.3390/genes14040856 - 31 Mar 2023

Cited by 1 | Viewed by 1638

Abstract

Plumage color is an artificially and naturally selected trait in domestic ducks. Black, white, and spotty are the main feather colors in domestic ducks. Previous studies have shown that black plumage color is caused by MC1R, and white plumage color is caused by MITF. We performed a genome-wide association study (GWAS) to identify candidate genes associated with white, black, and spotty plumage in ducks. Two non-synonymous SNPs in MC1R (c.52G>A and c.376G>A) were significantly related to duck black plumage, and three SNPs in MITF (chr13:15411658A>G, chr13:15412570T>C and chr13:15412592C>G) were associated with white plumage. Additionally, we also identified the epistatic interactions between causing loci. Some ducks with white plumage carry the c.52G>A and c.376G>A in MC1R, which also compensated for black and spotty plumage color phenotypes, suggesting that MC1R and MITF have an epistatic effect. The MITF locus was supposed to be an upstream gene to MC1R underlying the white, black, and spotty colors. Although the specific mechanism remains to be further clarified, these findings support the importance of epistasis in plumage color variation in ducks. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression

Ayeh Sadat Sadr

Mohammadreza Nassiri

Mostafa Ghaderi-Zefrehei

Maryam Heidari

Jacqueline Smith

and

Mustafa Muhaghegh Dolatabady

Genes 2023, 14(4), 793; https://doi.org/10.3390/genes14040793 - 25 Mar 2023

Viewed by 1124

Abstract

The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

The Expression Patterns of Exogenous Plant miRNAs in Chickens

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Genes 2023, 14(3), 760; https://doi.org/10.3390/genes14030760 - 21 Mar 2023

Viewed by 935

Abstract

(1) Background: MicroRNAs (miRNAs) are involved in a variety of biological processes, such as cell proliferation, cell differentiation, and organ development. Recent studies have shown that plant miRNAs may enter the diet and play physiological and/or pathophysiological roles in human health and disease; however, little is known about plant miRNAs in chickens. (2) Methods: Here, we analyzed miRNA sequencing data, with the use of five Chinese native chicken breeds and six different tissues (heart, liver, spleen, lung, kidney, and leg muscle), and used Illumina sequencing to detect the expression of plant miRNAs in the pectoralis muscles at fourteen developmental stages of Tibetan chickens. (3) Results: The results showed that plant miRNAs are detectable in multiple tissues and organs in different chicken breeds. Surprisingly, we found that plant miRNAs, such as tae-miR2018, were detectable in free-range Tibetan chicken embryos at different stages. The results of gavage feeding experiments also showed that synthetic tae-miR2018 was detectable in caged Tibetan chickens after ingestion. The analysis of tae-miR2018 showed that its target genes were related to skeletal muscle organ development, regulation of mesodermal cell fate specification, growth factor activity, negative regulation of the cell cycle, and regulation of growth, indicating that exogenous miRNA may regulate the development of chicken embryos. Further cell cultures and exogenous miRNA uptake assay experiments showed that synthetic wheat miR2018 can be absorbed by chicken myoblasts. (4) Conclusions: Our study found that chickens can absorb and deposit plant miRNAs in various tissues and organs. The plant miRNAs detected in embryos may be involved in the development of chicken embryos. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Open AccessArticle

Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments

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Genes 2022, 13(12), 2317; https://doi.org/10.3390/genes13122317 - 09 Dec 2022

Cited by 1 | Viewed by 1017

Abstract

The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation. Full article

(This article belongs to the Special Issue Poultry Genetics and Genomics)

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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1. Title: Integrative ChIP-seq and RNA-seq analysis reveals universal antiviral mechanism of chicken p53

Abstract: The tumor suppressor p53, which acts primarily as a transcription factor, has been shown to have antiviral functions against many viruses, such as infectious bursal disease virus (IBDV), avian leukosis virus subgroup J (ALV-J), and avian infectious laryngotracheitis virus (ILTV), in chickens. However, whether there is any universal antiviral mechanism of chicken p53 (chp53) remains unclear. In the present study, a comprehensive comparison of the molecular networks conferring the antiviral function of chp53 against IBDV, ALV-J, and ILTV was performed by a joint analysis of ChIP-seq data and RNA-seq data from chickens infected with these viruses. The enrichment of chp53 target genes in metabolic pathways was commonly observed and validated by ChIP-qPCR, suggesting a universal regulation of the metabolism of infected cells by chp53 upon the infection by different viruses. The present study provides new insights into the antiviral function of chicken p53 and indicates that targeting virus-host metabolic interaction could be a universal strategy for antiviral therapies in chickens.

2. Title: Unveiling the Molecular Mechanisms of Muscle Development During Late Embryonic Period in Broiler

3. Title: Molecular regulation of differential lipid molecule accumulation in intramuscular fat and abdominal fat of chicken

Abstract: Reducing abdominal fat (AF) accumulation and increasing the level of intramuscular fat (IMF) simultaneously is a major breeding goal in poultry industry. To explore the different molecular mechanisms between AF and IMF, gene expression profiles in the breast muscle (BM) and AF among three chicken breeds were analyzed. A total of 4737 shared DEGs were identified between BM and AF, of which 2602 DEGs were upregulated and 2135 DEGs were downregulated in the BM groups compared with that in AF groups. DEGs involved in glycerophospholipid metabolism and glycerolipid metabolism were potential regulators resulting in the difference of lipid metabolite accumulation in IMF and AF. PPAR signaling pathway was the most important pathway involved in tissue-specific lipid deposition. Correlation analysis showed that most representative DEGs enriched in PPAR signaling pathway, such as FABP5, PPARG, ACOX1, GK2, were negatively correlated with PUFA-enriched glycerophospholipid molecules. Most DEGs related to glycerophospholipid metabolism, such as GPD2, GPD1, PEMT, CRLS1 and GBGT1, were positively correlated with glycerophospholipid molecules, especially DHA- and arachidonic acid (ARA)- containing glycerophospholipid molecules. This study elucidated the molecular mechanism of tissue-specific lipid deposition and poultry meat quality.

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