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Genes
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Poultry Genetics and Genomics—2nd Edition
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Poultry Genetics and Genomics—2nd Edition

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

Deadline for manuscript submissions: closed (25 September 2024) | Viewed by 3364

Special Issue Editors

Dr. Tao Zhang

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals
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 Issues, Collections and Topics in MDPI journals

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 of interest 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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

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 marker

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Published Papers (3 papers)

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Research

19 pages, 2810 KiB  
Article
Genome-Wide Association Study Reveals the Genetic Architecture of Growth and Meat Production Traits in a Chicken F2 Resource Population
by Natalia A. Volkova, Michael N. Romanov, Anastasia N. Vetokh, Polina V. Larionova, Ludmila A. Volkova, Alexandra S. Abdelmanova, Alexander A. Sermyagin, Darren K. Griffin and Natalia A. Zinovieva
Genes 2024, 15(10), 1246; https://doi.org/10.3390/genes15101246 - 25 Sep 2024
Viewed by 725
Abstract
Background/Objectives: For genomic selection to enhance the efficiency of broiler production, finding SNPs and candidate genes that define the manifestation of main selected traits is essential. We conducted a genome-wide association study (GWAS) for growth and meat productivity traits of roosters from a [...] Read more.
Background/Objectives: For genomic selection to enhance the efficiency of broiler production, finding SNPs and candidate genes that define the manifestation of main selected traits is essential. We conducted a genome-wide association study (GWAS) for growth and meat productivity traits of roosters from a chicken F2 resource population (n = 152). Methods: The population was obtained by crossing two breeds with contrasting phenotypes for performance indicators, i.e., Russian White (slow-growing) and Cornish White (fast-growing). The birds were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. After LD filtering of the data, 54,188 SNPs were employed for the GWAS analysis that allowed us to reveal significant specific associations for phenotypic traits of interest and economic importance. Results: At the threshold value of p < 9.2 × 10−7, 83 SNPs associated with body weight at the age of 28, 42, and 63 days were identified, as well as 171 SNPs associated with meat qualities (average daily gain, slaughter yield, and dressed carcass weight and its components). Moreover, 34 SNPs were associated with a group of three or more traits, including 15 SNPs significant for a group of growth traits and 5 SNPs for a group of meat productivity indicators. Relevant to these detected SNPs, nine prioritized candidate genes associated with the studied traits were revealed, including WNT2, DEPTOR, PPA2, UNC80, DDX51, PAPPA, SSC4D, PTPRU, and TLK2. Conclusions: The found SNPs and candidate genes can serve as genetic markers for growth and meat performance characteristics in chicken breeding in order to achieve genetic improvement in broiler production. Full article
(This article belongs to the Special Issue Poultry Genetics and Genomics—2nd Edition)
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12 pages, 1646 KiB  
Article
Identification and Characterization of the miRNA Transcriptome Controlling Green Pigmentation of Chicken Eggshells
by Kai Shi, Dongfeng Li, Xusheng Jiang, Yuesong Du and Minli Yu
Genes 2024, 15(6), 811; https://doi.org/10.3390/genes15060811 - 19 Jun 2024
Viewed by 944
Abstract
Green eggs are mainly caused by inserting an avian endogenous retrovirus (EVA-HP) fragment into the SLCO1B3 gene. Although the genotypes for this insertion allele are consistent, eggshell color (ESC) may vary after a peak laying period; light-colored eggs are undesired by consumers and [...] Read more.
Green eggs are mainly caused by inserting an avian endogenous retrovirus (EVA-HP) fragment into the SLCO1B3 gene. Although the genotypes for this insertion allele are consistent, eggshell color (ESC) may vary after a peak laying period; light-colored eggs are undesired by consumers and farmers and result in financial loss, so it is necessary to resolve this problem. miRNAs are small non-coding RNAs that exert essential functions in animal development and diseases. However, the regulatory miRNAs and detailed molecular mechanisms regulating eggshell greenness remain unclear. In the present study, we determined the genotype of green-eggshell hens through the detection of a homozygous allele insertion in the SLCO1B3 gene. The shell gland epithelium was obtained from green-eggshell hens that produced white and green shell eggs to perform transcriptome sequencing and investigate the important regulatory mechanisms that influence the ESC. Approximately 921 miRNAs were expressed in these two groups, which included 587 known miRNAs and 334 novel miRNAs, among which 44 were differentially expressed. There were 22 miRNAs that were significantly upregulated in the green and white groups, respectively, which targeted hundreds of genes, including KIT, HMOX2, and several solute carrier family genes. A Gene Ontology enrichment analysis of the target genes showed that the differentially expressed miRNA-targeted genes mainly belonged to the functional categories of homophilic cell adhesion, gland development, the Wnt signaling pathway, and epithelial tube morphogenesis. A KEGG enrichment analysis showed that the Hedgehog signaling pathway was significantly transformed in this study. The current study provides an overview of the miRNA expression profiles and the interaction between the miRNAs and their target genes. It provides valuable insights into the molecular mechanisms underlying green eggshell pigmentation, screening more effective hens to produce stable green eggs and obtaining higher economic benefits. Full article
(This article belongs to the Special Issue Poultry Genetics and Genomics—2nd Edition)
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28 pages, 2101 KiB  
Article
Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka
by Michael N. Romanov, Alexey V. Shakhin, Alexandra S. Abdelmanova, Natalia A. Volkova, Dmitry N. Efimov, Vladimir I. Fisinin, Liudmila G. Korshunova, Dmitry V. Anshakov, Arsen V. Dotsev, Darren K. Griffin and Natalia A. Zinovieva
Genes 2024, 15(4), 524; https://doi.org/10.3390/genes15040524 - 22 Apr 2024
Cited by 4 | Viewed by 1321
Abstract
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic [...] Read more.
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits. Full article
(This article belongs to the Special Issue Poultry Genetics and Genomics—2nd Edition)
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