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Poultry Breeding and Genetics
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Poultry Breeding and Genetics

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

Deadline for manuscript submissions: closed (20 April 2024) | Viewed by 7727

Special Issue Editor

Dr. Hong Li

E-Mail Website
Guest Editor
College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
Interests: chicken; gene expression regulation; meat quality traits; growth traits; reproductive traits; lipid metabolism; cell biology; molecular biology

Special Issue Information

Dear Colleagues,

As a major source of protein in our daily diet, chicken meat and eggs are widely consumed due to their high quality and low cost. Poultry breeding and genetics have experienced rapid advancement since the completion of the chicken genome sequence in 2004, and they have been extensively used to understand the genetic determinants of complex traits. With the development of high-throughput sequencing technology, molecular biology, bioinformatics and genetics, the genetic basis and regulation mechanism of important economic traits in poultry including reproductive traits, meat quality, growth traits, disease resistance, and other important traits have attracted attention and witnessed remarkable progress through the use of multi-omics (genome, epigenome, transcriptome, proteome, and metabolome), 3D genomics, Hi-C and so on.  However, much of their detailed regulatory mechanism is unknown. Genes is now inviting submissions for a Special Issue on the topic of “Poultry Breeding and Genetics”. The contents cover genetic variation detection, selection methods for breeding, transgenesis and genome editing, the genetic basis of disease resistance, control of gene expression and regulation, reproduction and meat quality, etc. Research articles, reviews, short communications, brief reports, and other forms of original articles on this topic are all welcome. The hope is that this Special Issue will open new avenues to discover the theoretical and practical aspects of poultry phenotype traits and provide valuable information for poultry breeding projects.

Dr. Hong Li
Guest Editor

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 expression regulation
  • RNA-seq
  • genomics
  • growth traits
  • reproductive traits
  • meat quality traits
  • cell biology
  • molecular biology

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Published Papers (5 papers)

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Research

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15 pages, 2425 KiB  
Article
A Network of Circular RNA and MicroRNA Sequencing Provides Insights into Pigment Deposition of Changshun Blue Eggshell Chickens
by Siyu Chen, Mengqiao Zhao, Kecheng Chen, Jiaming Xu and Hua Li
Genes 2024, 15(6), 812; https://doi.org/10.3390/genes15060812 - 19 Jun 2024
Viewed by 873
Abstract
Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was used to analyse the uterine gland [...] Read more.
Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was used to analyse the uterine gland transcriptome (CircRNA and miRNA) of Changshun chicken blue-shell hens producing four different eggshell color eggs including dark blue PK(DB) and light blue (LB), dark brown and greenish (between blue and pink, DP) and pink (p). We found that miR-192-x, targeting SLC16a7, was expressed in DB, DP, and LB groups compared with the PK group, which indicates that miR-192-x may play a role in the blue eggshell color. KEGG and GO analyses showed that the “metabolic pathways” with targeted genes such BLVRA and HMOX1 were detected in dark and light blue color eggshell chickens, which confirms the different ratios of biliverdin and HO-1 involved in the deposition of blue color. As annotated by connectivity analysis, RASGRF1 and RASGRF2, belonging to the RASGRF family, are involved in the Ras signaling pathway, which plays an important role in cell growth, differentiation, metastasis and apoptosis. Our findings enrich the database of circRNA, miRNAs and genes for chicken uterine tissue, which will be useful in accelerating molecular selection for blue eggshell color layers. Full article
(This article belongs to the Special Issue Poultry Breeding and Genetics)
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15 pages, 8402 KiB  
Article
Genetic Analysis of Egg Production Traits in Luhua Chickens: Insights from a Multi-Trait Animal Model and a Genome-Wide Association Study
by Qianwen Yang, Xubin Lu, Guohui Li, Huiyong Zhang, Chenghao Zhou, Jianmei Yin, Wei Han and Haiming Yang
Genes 2024, 15(6), 796; https://doi.org/10.3390/genes15060796 - 17 Jun 2024
Viewed by 1173
Abstract
Egg production plays a pivotal role in the economic viability of hens. To analyze the genetic rules of egg production, a total of 3151 Luhua chickens were selected, the egg production traits including egg weight at first laying (Start-EW), egg weight at 43 [...] Read more.
Egg production plays a pivotal role in the economic viability of hens. To analyze the genetic rules of egg production, a total of 3151 Luhua chickens were selected, the egg production traits including egg weight at first laying (Start-EW), egg weight at 43 weeks (EW-43), egg number at 43 weeks (EN-43), and total egg number (EN-All) were recorded. Then, the effects of related factors on egg production traits were explored, using a multi-trait animal model for genetic parameter estimation and a genome-wide association study (GWAS). The results showed that body weight at first egg (BWFE), body weight at 43 weeks (BW-43), age at first egg (AFE), and seasons had significant effects on the egg production traits. Start-EW and EW-43 had moderate heritability of 0.30 and 0.21, while EN-43 and EN-All had low heritability of 0.13 and 0.16, respectively. Start-EW exhibited a robust positive correlation with EW-43, while Start-EW was negatively correlated with EN-43 and EN-All. Furthermore, gene ontology (GO) results indicated that Annexin A2 (ANXA2) and Frizzled family receptor 7 (FZD7) related to EW-43, Cyclin D1 (CCND1) and A2B adenosine receptor (ADORA2B) related to EN-All, and have been found to be mainly involved in metabolism and growth processes, and deserve more attention and further study. This study contributes to accelerating genetic progress in improving low heritability egg production traits in layers, especially in Luhua chickens. Full article
(This article belongs to the Special Issue Poultry Breeding and Genetics)
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16 pages, 6833 KiB  
Article
Integrating Bioinformatics and Machine Learning for Genomic Prediction in Chickens
by Xiaochang Li, Xiaoman Chen, Qiulian Wang, Ning Yang and Congjiao Sun
Genes 2024, 15(6), 690; https://doi.org/10.3390/genes15060690 - 26 May 2024
Viewed by 1551
Abstract
Genomic prediction plays an increasingly important role in modern animal breeding, with predictive accuracy being a crucial aspect. The classical linear mixed model is gradually unable to accommodate the growing number of target traits and the increasingly intricate genetic regulatory patterns. Hence, novel [...] Read more.
Genomic prediction plays an increasingly important role in modern animal breeding, with predictive accuracy being a crucial aspect. The classical linear mixed model is gradually unable to accommodate the growing number of target traits and the increasingly intricate genetic regulatory patterns. Hence, novel approaches are necessary for future genomic prediction. In this study, we used an illumina 50K SNP chip to genotype 4190 egg-type female Rhode Island Red chickens. Machine learning (ML) and classical bioinformatics methods were integrated to fit genotypes with 10 economic traits in chickens. We evaluated the effectiveness of ML methods using Pearson correlation coefficients and the RMSE between predicted and actual phenotypic values and compared them with rrBLUP and BayesA. Our results indicated that ML algorithms exhibit significantly superior performance to rrBLUP and BayesA in predicting body weight and eggshell strength traits. Conversely, rrBLUP and BayesA demonstrated 2–58% higher predictive accuracy in predicting egg numbers. Additionally, the incorporation of suggestively significant SNPs obtained through the GWAS into the ML models resulted in an increase in the predictive accuracy of 0.1–27% across nearly all traits. These findings suggest the potential of combining classical bioinformatics methods with ML techniques to improve genomic prediction in the future. Full article
(This article belongs to the Special Issue Poultry Breeding and Genetics)
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12 pages, 2048 KiB  
Article
Genetic Architecture of Abdominal Fat Deposition Revealed by a Genome-Wide Association Study in the Laying Chicken
by Jun Guo, Liang Qu, Dan Shao, Qiang Wang, Yongfeng Li, Taocun Dou, Xingguo Wang, Yuping Hu and Haibing Tong
Genes 2024, 15(1), 10; https://doi.org/10.3390/genes15010010 - 20 Dec 2023
Viewed by 1159
Abstract
Fat has a high energy density, and excessive fatness has been recognized as a problem for egg production and the welfare of chickens. The identification of a genetic polymorphism controlling fat deposition would be helpful to select against excessive fatness in the laying [...] Read more.
Fat has a high energy density, and excessive fatness has been recognized as a problem for egg production and the welfare of chickens. The identification of a genetic polymorphism controlling fat deposition would be helpful to select against excessive fatness in the laying hen. This study aimed to estimate genomic heritability and identify the genetic architecture of abdominal fat deposition in a population of chickens from a Dongxiang blue-shelled local breed crossbred with the White Leghorn. A genome-wide association study was conducted on abdominal fat percentage, egg production and body weights using a sample of 1534 hens genotyped with a 600 K Chicken Genotyping Array. The analysis yielded a heritability estimate of 0.19 ± 0.04 for abdominal fat percentage; 0.56 ± 0.04 for body weight at 72 weeks; 0.11 ± 0.03 for egg production; and 0.24 ± 0.04 for body weight gain. The genetic correlation of abdominal fat percentage with egg production between 60 and 72 weeks of age was −0.35 ± 0.18. This implies a potential trade-off between these two traits related to the allocation of resources. Strong positive genetic correlations were found between fat deposition and weight traits. A promising locus close to COL12A1 on chromosome 3, associated with abdominal fat percent, was found in the present study. Another region located around HTR2A on chromosome 1, where allele substitution was predicted to be associated with body weight gain, accounted for 2.9% of phenotypic variance. Another region located on chromosome 1, but close to SOX5, was associated with egg production. These results may be used to influence the balanced genetic selection for laying hens. Full article
(This article belongs to the Special Issue Poultry Breeding and Genetics)
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Review

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13 pages, 2155 KiB  
Review
Genomic Insights into Molecular Regulation Mechanisms of Intramuscular Fat Deposition in Chicken
by Yuzhu Cao, Yuxin Xing, Hongbo Guan, Chenglin Ma, Qihui Jia, Weihua Tian, Guoxi Li, Yadong Tian, Xiangtao Kang, Xiaojun Liu and Hong Li
Genes 2023, 14(12), 2197; https://doi.org/10.3390/genes14122197 - 10 Dec 2023
Cited by 3 | Viewed by 2309
Abstract
Intramuscular fat (IMF) plays an important role in the tenderness, water-holding capacity, and flavor of chicken meat, which directly affect meat quality. In recent years, regulatory mechanisms underlying IMF deposition and the development of effective molecular markers have been hot topics in poultry [...] Read more.
Intramuscular fat (IMF) plays an important role in the tenderness, water-holding capacity, and flavor of chicken meat, which directly affect meat quality. In recent years, regulatory mechanisms underlying IMF deposition and the development of effective molecular markers have been hot topics in poultry genetic breeding. Therefore, this review focuses on the current understanding of regulatory mechanisms underlying IMF deposition in chickens, which were identified by multiple genomic approaches, including genome-wide association studies, whole transcriptome sequencing, proteome sequencing, single-cell RNA sequencing (scRNA-seq), high-throughput chromosome conformation capture (HiC), DNA methylation sequencing, and m6A methylation sequencing. This review comprehensively and systematically describes genetic and epigenetic factors associated with IMF deposition, which provides a fundamental resource for biomarkers of IMF deposition and provides promising applications for genetic improvement of meat quality in chicken. Full article
(This article belongs to the Special Issue Poultry Breeding and Genetics)
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