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: 25 September 2024 | Viewed by 1091

Special Issue Editors

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

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Keywords

  • poultry
  • gene function
  • genome annotation
  • omics
  • gene editing
  • genomic selection
  • molecular mechanisms
  • molecular marker

Published Papers (2 papers)

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Research

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 188
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
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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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