Genetic Analysis of Important Traits in Poultry

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 14559

Special Issue Editors

1. Embrapa Suínos e Aves, Concórdia, SC, Brazil
2. Programa de Pós-Graduação em Zootecnia, Departamento de Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, Chapecó 89815-630, Brazil
Interests: poultry breeding and genetics; genomics; transcriptomics; metabolic disorders
Embrapa Suínos e Aves, Concórdia, SC, Brazil
Interests: animal genetics; genomics; functional genomics; poultry genetics and genomics; complex traits
Unit of Animal Genomics, University of Liège, Liège, Belgium
Interests: animal genetics; genomics; functional genomics; poultry genetics and genomics; bovine genetics and genomics

Special Issue Information

Dear Colleagues,

Chicken is one of the most efficient livestock. This has been achieved by improvements in several areas, but especially due to the genetic selection. Poultry production has had a great advance in the last few decades, but there are still many challenges to be addressed, such as dealing with metabolic problems that have occurred due to the rapid growth and the inclusion of new phenotypes in breeding programs. New technologies have allowed the discovery of genes and their functions, which opened new possibilities for improve poultry production.

This Special Issue will cover different types of analysis, from genetic parameter estimates of new phenotypes to the high-throughput analysis involving omics to unravel the genetic control of complex traits of interest in poultry. Current research integrating analysis of multi-omics for the identification of candidate genes and functional variants underlying economically important traits will also be part of this Special Issue.

Dr. Mônica Corrêa Ledur
Dr. Adriana M. G. Ibelli
Dr. Gabriel Costa Monteiro Moreira
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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • broiler chickens
  • laying hens
  • turkeys
  • quails
  • gene discovery
  • high-throughput analysis
  • GWAS
  • RNA-seq
  • functional genomics
  • epigenetics

Published Papers (8 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

13 pages, 4114 KiB  
Article
A Functional Variant Alters the Binding of Bone morphogenetic protein 2 to the Transcription Factor NF-κB to Regulate Bone morphogenetic protein 2 Gene Expression and Chicken Abdominal Fat Deposition
by Meng Yuan, Xin Liu, Mengdie Wang, Ziwei Li, Hui Li, Li Leng and Shouzhi Wang
Animals 2023, 13(21), 3401; https://doi.org/10.3390/ani13213401 - 02 Nov 2023
Viewed by 845
Abstract
In this study, we employed a dual-luciferase reporter assay and electrophoretic mobility shift analysis (EMSA) in vitro to explore whether a 12-base pair (bp) insertion/deletion (InDel) variant (namely g.14798187_14798188insTCCCTGCCCCCT) within intron 2 of the chicken BMP2 gene, which was significantly associated with chicken [...] Read more.
In this study, we employed a dual-luciferase reporter assay and electrophoretic mobility shift analysis (EMSA) in vitro to explore whether a 12-base pair (bp) insertion/deletion (InDel) variant (namely g.14798187_14798188insTCCCTGCCCCCT) within intron 2 of the chicken BMP2 gene, which was significantly associated with chicken abdominal fat weight and abdominal fat percentage, is a functional marker and its potential regulatory mechanism. The reporter analysis demonstrated that the luciferase activity of the deletion allele was extremely significantly higher than that of the insertion allele (p < 0.01). A bioinformatics analysis revealed that compared to the deletion allele, the insertion allele created a transcription factor binding site of nuclear factor-kappa B (NF-κB), which exhibited an inhibitory effect on fat deposition. A dual-luciferase reporter assay demonstrated that the inhibitory effect of NF-κB on the deletion allele was stronger than that on the insertion allele. EMSA indicated that the binding affinity of NF-κB for the insertion allele was stronger than that for the deletion allele. In conclusion, the 12-bp InDel chicken BMP2 gene variant is a functional variant affecting fat deposition in chickens, which may partially regulate BMP2 gene expression by affecting the binding of transcription factor NF-κB to the BMP2 gene. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

21 pages, 5632 KiB  
Article
Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits
by Bolívar Samuel Sosa-Madrid, Gerasimos Maniatis, Noelia Ibáñez-Escriche, Santiago Avendaño and Andreas Kranis
Animals 2023, 13(21), 3306; https://doi.org/10.3390/ani13213306 - 24 Oct 2023
Viewed by 842
Abstract
Monitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-term data from [...] Read more.
Monitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-term data from small experimental populations selected for a handful of traits. Here, we used a large dataset from a commercial breeding line spread over a period of twenty-three years. A total of 2,059,869 records and 2,062,112 animals in the pedigree were used for the estimations of variance components for the traits: body weight (BWT; 2,059,869 records) and hen-housed egg production (HHP; 45,939 records). Data were analysed with three estimation approaches: sliding overlapping windows, under frequentist (restricted maximum likelihood (REML)) and Bayesian (Gibbs sampling) methods; expected variances using coefficients of the full relationship matrix; and a “double trait covariances” analysis by computing correlations and covariances between the same trait in two distinct consecutive windows. The genetic variance showed marginal fluctuations in its estimation over time. Whereas genetic, maternal permanent environmental, and residual variances were similar for BWT in both the REML and Gibbs methods, variance components when using the Gibbs method for HHP were smaller than the variances estimated when using REML. Large data amounts were needed to estimate variance components and detect their changes. For Gibbs (REML), the changes in genetic variance from 1999–2001 to 2020–2022 were 82.29 to 93.75 (82.84 to 93.68) for BWT and 76.68 to 95.67 (98.42 to 109.04) for HHP. Heritability presented a similar pattern as the genetic variance estimation, changing from 0.32 to 0.36 (0.32 to 0.36) for BWT and 0.16 to 0.15 (0.21 to 0.18) for HHP. On the whole, genetic parameters tended slightly to increase over time. The expected variance estimates were lower than the estimates when using overlapping windows. That indicates the low effect of the drift-selection process on the genetic variance, or likely, the presence of genetic variation sources compensating for the loss. Double trait covariance analysis confirmed the maintenance of variances over time, presenting genetic correlations >0.86 for BWT and >0.82 for HHP. Monitoring genetic variance in broiler breeding programmes is important to sustain genetic progress. Although the genetic variances of both traits fluctuated over time, in some windows, particularly between 2003 and 2020, increasing trends were observed, which warrants further research on the impact of other factors, such as novel mutations, operating on the dynamics of genetic variance. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

15 pages, 12434 KiB  
Article
Transcriptomic Analysis on Pectoral Muscle of European Meat Pigeons and Shiqi Pigeons during Embryonic Development
by Fada Li, Chenyu Zhu, Yongquan Luo, Songchao Li, Qi Wang, Yuanhao Han, Zhongping Wu, Xiujin Li, Yayan Liang, Yitian Chen, Xu Shen, Yunmao Huang, Yunbo Tian and Xumeng Zhang
Animals 2023, 13(20), 3267; https://doi.org/10.3390/ani13203267 - 19 Oct 2023
Viewed by 874
Abstract
In avian muscle development, embryonic muscle development determines the number of myofibers after birth. Therefore, in this study, we investigated the phenotypic differences and the molecular mechanism of pectoral muscle development of the European meat pigeon Mimas strain (later called European meat pigeon) [...] Read more.
In avian muscle development, embryonic muscle development determines the number of myofibers after birth. Therefore, in this study, we investigated the phenotypic differences and the molecular mechanism of pectoral muscle development of the European meat pigeon Mimas strain (later called European meat pigeon) and Shiqi pigeon on embryonic day 6 (E6), day 10 (E10), day 14 (E14) and day 1 after birth (P1). The results showed that the myofiber density of the Shiqi pigeon was significantly higher than that of the European meat pigeon on E6, and myofibers with a diameter in the range of 50~100 μm of the Shiqi pigeon on P1 were significantly higher than those of European meat pigeon. A total of 204 differential expressed genes (DEGs) were obtained from RNA-seq analysis in comparison between pigeon breeds at the same stage. DEGs related to muscle development were found to significantly enrich the cellular amino acid catabolism, carboxylic acid catabolism, extracellular matrix receptor interaction, REDOX enzyme activity, calcium signaling pathway, ECM receptor interaction, PPAR signaling pathway and other pathways. Using Cytoscape software to create mutual mapping, we identified 33 candidate genes. RT-qPCR was performed to verify the 8 DEGs selected—DES, MYOD, MYF6, PTGS1, MYF5, MYH1, MSTN and PPARG—and the results were consistent with RNA-seq. This study provides basic data for revealing the distinct embryonic development mechanism of pectoral muscle between European meat pigeons and Shiqi pigeons. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

14 pages, 1847 KiB  
Article
Identification of SNPs Associated with Goose Meat Quality Traits Using a Genome-Wide Association Study Approach
by Guangliang Gao, Keshan Zhang, Ping Huang, Xianzhi Zhao, Qin Li, Youhui Xie, Chunhui Yin, Jing Li, Zhen Wang, Hang Zhong, Jiajia Xue, Zhuping Chen, Xianwen Wu and Qigui Wang
Animals 2023, 13(13), 2089; https://doi.org/10.3390/ani13132089 - 24 Jun 2023
Cited by 1 | Viewed by 1435
Abstract
(1) Background: Goose meat is highly valued for its economic significance and vast market potential due to its desirable qualities, including a rich nutritional profile, tender texture, relatively low-fat content, and high levels of beneficial unsaturated fatty acids. However, there is an urgent [...] Read more.
(1) Background: Goose meat is highly valued for its economic significance and vast market potential due to its desirable qualities, including a rich nutritional profile, tender texture, relatively low-fat content, and high levels of beneficial unsaturated fatty acids. However, there is an urgent need to improve goose breeding by identifying molecular markers associated with meat quality. (2) Methods: We evaluated meat quality traits, such as meat color, shear force (SF), cooking loss rate (CLR), and crude fat content (CFC), in a population of 215 male Sichuan white geese at 70 days of age. A GWAS was performed to identify potential molecular markers associated with goose meat quality. Furthermore, the selected SNPs linked to meat quality traits were genotyped using the MALDI-TOP MS method. (3) Results: A dataset of 2601.19 Gb of WGS data was obtained from 215 individuals, with an average sequencing depth of 10.89×. The GWAS revealed the identification of 43 potentially significant SNP markers associated with meat quality traits in the Sichuan white goose population. Additionally, 28 genes were identified as important candidate genes for meat quality. The gene enrichment analysis indicated a substantial enrichment of genes within a 1Mb vicinity of SNPs in both the protein digestion and absorption pathway and the Glycerolipid metabolism pathway. (4) Conclusion: This study provides valuable insights into the genetic and molecular mechanisms underlying goose meat quality traits, offering crucial references for molecular breeding in this field. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

14 pages, 942 KiB  
Article
Comparison of Immune-Related Gene Expression in Two Chicken Breeds Following Infectious Bronchitis Virus Vaccination
by Schwann Chuwatthanakhajorn, Chi-Sheng Chang, Kannan Ganapathy, Pin-Chi Tang and Chih-Feng Chen
Animals 2023, 13(10), 1642; https://doi.org/10.3390/ani13101642 - 15 May 2023
Cited by 1 | Viewed by 1956
Abstract
This study aims to identify the immune-related genes and the corresponding biological pathways following infectious bronchitis virus vaccination in Taiwan Country and White Leghorn chicken breeds. Transcriptomic analyses of the spleen of these two breeds were conducted by next-generation sequencing. Compared to White [...] Read more.
This study aims to identify the immune-related genes and the corresponding biological pathways following infectious bronchitis virus vaccination in Taiwan Country and White Leghorn chicken breeds. Transcriptomic analyses of the spleen of these two breeds were conducted by next-generation sequencing. Compared to White Leghorn chicken, Taiwan Country chicken showed a significantly higher level of anti-infectious bronchitis virus (IBV) antibodies at 14 and 21 days pos vaccination. At 7 days post vaccination, in the Taiwan Country chicken, higher expression of mitogen-activated protein kinase 10, Major histocompatibility complex class 1, and V-set pre-B cell surrogate light chain 3 were found. In contrast, the White Leghorn chicken had a high expression of interleukin 4 induced 1, interleukin 6, and interleukin 22 receptor subunit alpha 2. These findings have highlighted the variations in immune induction between chickens with distinct genetic background and provided biological pathways and specific genes involved in immune responses against live attenuated IBV vaccine. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

16 pages, 9748 KiB  
Article
Genome-Wide Analysis of the KLF Gene Family in Chicken: Characterization and Expression Profile
by Xuanze Ling, Qifan Wang, Jin Zhang and Genxi Zhang
Animals 2023, 13(9), 1429; https://doi.org/10.3390/ani13091429 - 22 Apr 2023
Viewed by 1804
Abstract
The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, [...] Read more.
The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, little is known about the function of the KLF gene family in chickens. In this study, we performed genome-wide studies of chicken KLF genes and analyzed their biological and expression characteristics. We identified 13 KLF genes from chickens. Our phylogenetic, motif, and conserved domain analyses indicate that the KLF gene family has remained conserved through evolution. Synteny analysis showed the collinear relationship among KLFs, which indicated that they had related biomolecular functions. Interaction network analysis revealed that KLFs worked with 20 genes in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that KLF2 was involved in Apelin and Forkhead Box O (FOXO) signaling pathways. Moreover, qPCR showed that 13 KLF genes were expressed in the nine selected tissues and displayed various gene expression patterns in chickens. RNA-seq showed that KLF3 and KLF10 genes were differentially expressed in the normal and high-fat diet fed groups, and KLF4, KLF5, KLF6, KLF7, KLF9, KLF12, and KLF13 genes were differentially expressed between undifferentiated and differentiated chicken preadipocytes. Besides, RNA-seq also showed that KLF genes displayed different expression patterns in muscle at 11 and 16 embryonic days old, and in 1-day-old chickens. These results indicated that the KLF genes were involved in the development of muscle and fat in chickens. Our findings provide some valuable reference points for the subsequent study of the function of KLF genes. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

10 pages, 4025 KiB  
Article
Identification of Duplication Genotypes of the Feathering Rate Gene in Chicken by a Multiplex PCR Following Electrophoresis and/or Sanger Sequencing
by Qingmiao Shen, Junying Li, Haigang Bao and Changxin Wu
Animals 2023, 13(6), 1091; https://doi.org/10.3390/ani13061091 - 18 Mar 2023
Cited by 2 | Viewed by 1367
Abstract
Sex-linked phenotypes of late feathering (LF) and early feathering (EF) are controlled by a pair of alleles K and k+. Autosexing based on the feathering rate is widely used in poultry production. It is reported that a tandem duplication of 176,324 [...] Read more.
Sex-linked phenotypes of late feathering (LF) and early feathering (EF) are controlled by a pair of alleles K and k+. Autosexing based on the feathering rate is widely used in poultry production. It is reported that a tandem duplication of 176,324 base pairs linked to the K locus is responsible for LF expression and could be used as a molecular marker to detect LF chicken. So far, there is no genotyping method that can accurately and stably identify the LF homozygote and heterozygote in all chicken breeds. In the present study, a multiplex PCR test was developed to identify EF, LF homozygote, and heterozygote according to electrophoretic bands and the relative height of the peaks by Sanger sequencing. We tested 413 chickens of six native Chinese breeds with this method. The identification was consistent with the sex and phenotype records of the chickens. Band density analysis was performed, and the results supported our genotyping using the new assay. In order to further verify the accuracy of this test in distinguishing homozygote and heterozygote males, 152 LF males were mated with EF females, and the results of the offspring’s phenotypes were consistent with our expectations. Our results support tandem duplication as molecular markers of LF, and this new test is applicable to all LF chickens associated with tandem duplication. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

Review

Jump to: Research

33 pages, 8098 KiB  
Review
Evolutions in Commercial Meat Poultry Breeding
by Anne-Marie Neeteson, Santiago Avendaño, Alfons Koerhuis, Brendan Duggan, Eduardo Souza, James Mason, John Ralph, Paige Rohlf, Tim Burnside, Andreas Kranis and Richard Bailey
Animals 2023, 13(19), 3150; https://doi.org/10.3390/ani13193150 - 09 Oct 2023
Cited by 1 | Viewed by 4030
Abstract
This paper provides a comprehensive overview of the history of commercial poultry breeding, from domestication to the development of science and commercial breeding structures. The development of breeding goals over time, from mainly focusing on production to broad goals, including bird welfare and [...] Read more.
This paper provides a comprehensive overview of the history of commercial poultry breeding, from domestication to the development of science and commercial breeding structures. The development of breeding goals over time, from mainly focusing on production to broad goals, including bird welfare and health, robustness, environmental impact, biological efficiency and reproduction, is detailed. The paper outlines current breeding goals, including traits (e.g., on foot and leg health, contact dermatitis, gait, cardiovascular health, robustness and livability), recording techniques, their genetic basis and how trait these antagonisms, for example, between welfare and production, are managed. Novel areas like genomic selection and gut health research and their current and potential impact on breeding are highlighted. The environmental impact differences of various genotypes are explained. A future outlook shows that balanced, holistic breeding will continue to enable affordable lean animal protein to feed the world, with a focus on the welfare of the birds and a diversity of choice for the various preferences and cultures across the world. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Poultry)
Show Figures

Figure 1

Back to TopTop