Genetics and Breeding Advances in Poultry Health and Production

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

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 5717

Special Issue Editors


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Guest Editor
Department of Anatomic Pathology, Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA
Interests: poultry; molecular genetics; immunogenetics; bioinformatics

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Guest Editor
Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
Interests: poultry; molecular biology; functional genomics; growth biology; muscle development; muscle growth

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Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Interests: poultry breeding and genetics; disease resistance; poultry production

Special Issue Information

Dear Colleagues,

The past few decades have seen remarkable improvements of poultry production, such as faster growth and more egg production, driven largely by genetic selection and breeding. However, there are still concerning issues for the modern poultry industry, such as compromised meat quality and poultry health due to rapid growth, reduced tolerance to heat stress, and great loss due to infectious diseases, which are exacerbated by irreconcilable phenotype traits, noticeable global climate changes, and emerging and evolving pathogen strains. The complex genetic regulation networks consisting of alternative splicing, transcriptional factor binding, gene rearrangement, mutations and copy number changes, chromatin conformation and interactions, epigenetic changes, and diverse cellular interactions (e.g., host–pathogen interactions) pose a great challenge to improve these quantitative traits. Fortunately, with advanced techniques such as gene editing, CRISPR screening, high-throughput sequencing and machine learning, we can now solve these complex issues with improved precision and find core information among the big data with enhanced accuracy. With the aim of presenting current advances and enlightening thoughts on future prospects, this Special Issue will present a collection of papers illustrating the application of these techniques in understanding molecular mechanisms underlying critical phenotypes such as muscle growth, stress tolerance and disease resistance.

Dr. Jibin Zhang
Prof. Dr. Kichoon Lee
Dr. Hongyan Sun
Guest Editors

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Keywords

  • genetics and breeding
  • gene editing
  • bioinformatics
  • immunology
  • muscle growth
  • disease resistance
  • stress tolerance

Published Papers (6 papers)

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Research

13 pages, 2510 KiB  
Article
A 16S RNA Analysis of Yangzhou Geese with Varying Body Weights: Gut Microbial Difference and Its Correlation with Body Weight Parameters
by Xinlei Xu, Suyu Fan, Hao Wu, Haoyu Li, Xiaoyu Shan, Mingfeng Wang, Yang Zhang, Qi Xu and Guohong Chen
Animals 2024, 14(14), 2042; https://doi.org/10.3390/ani14142042 - 12 Jul 2024
Viewed by 282
Abstract
China is a major goose-raising country, and the geese industry plays a significant role in animal husbandry. Therefore, goose growth performance (body weight) is a critical topic. Goose gut microbiota influences weight gain by regulating its energy metabolism and digestion. Additionally, the impact [...] Read more.
China is a major goose-raising country, and the geese industry plays a significant role in animal husbandry. Therefore, goose growth performance (body weight) is a critical topic. Goose gut microbiota influences weight gain by regulating its energy metabolism and digestion. Additionally, the impact of cecal microbial community structure on goose growth and development, energy metabolism, and immunity has been examined. However, most studies have used different additives or feeds as variables. Improving the understanding of the dynamic changes in gut microbial communities in geese of different body weights during their growth and development and their correlation with the host’s body weight is necessary. In this study, the cecal microbiota of healthy Yangzhou geese with large (L) and small (S) body weights, all at the same age (70 days old) and under the same feeding conditions, were sequenced using 16S rRNA. The sequencing results were annotated using QIIME2 (classify-sklearn algorithm) software, and the linkET package was used to explore the correlation between intestinal microorganisms and the body weight of the Yangzhou goose (Spearman). At the phylum level, the Firmicutes/Bacteroidetes ratio in the large body weight group was approximately 20% higher than that in the small body weight group, with Bacteroidetes and Firmicutes exhibiting a highly significant negative correlation. At the genus level, Bacteroides constituted the most abundant microbial group in both groups, although the Prevotellaceae_Ga6A1_group exhibited a higher abundance in the large than the small weight group. Spearman correlation analysis and the linkET package were used to analyze the correlation between cecal microflora and production performance indicators that showed significant differences between the two groups and showed that birth weight was significantly positively correlated with Deferribacterota at the phylum level. At the genus level, leg and chest muscle weights exhibited significant positive correlations with Prevotellace-ae_Ga6A1_group, suggesting its critical role in promoting the growth and development of goose leg and chest muscles. A significant negative correlation was observed between [Ruminococ-cus]_torque and Prevotellaceae_Ga6A1_group. These findings offer a crucial theoretical foundation for the study of gastrointestinal microorganisms and provide insights into the development and formulation of poultry probiotics. Full article
(This article belongs to the Special Issue Genetics and Breeding Advances in Poultry Health and Production)
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25 pages, 4149 KiB  
Article
Genetic Variation in Natural and Induced Antibody Responses in Layer Chickens
by Jesus Arango, Anna Wolc, Jeb Owen, Kendra Weston and Janet E. Fulton
Animals 2024, 14(11), 1623; https://doi.org/10.3390/ani14111623 - 30 May 2024
Viewed by 451
Abstract
Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. [...] Read more.
Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. As a result, antibodies have been used as a trait in selection for immune defense. The goal of this study was to identify genomic regions associated with natural and induced antibodies in chickens using low-pass sequencing. Enzyme-linked immunosorbent assays were used to quantify innate (natural) antibodies binding KLH, OVA, and PHA and induced (adaptive) antibodies binding IBD, IBV, NDV, and REO. We collected plasma from four White Leghorn (WL), two White Plymouth Rock (WPR), and two Rhode Island Red (RIR) lines. Samples numbers ranged between 198 and 785 per breed. GWAS was performed within breed on data pre-adjusted for Line-Hatch-Sex effects using GCTA. A threshold of p = 10−6 was used to select genes for downstream annotation and enrichment analysis with SNPEff and Panther. Significant enrichment was found for the defense/immunity protein, immunoglobulin receptor superfamily, and the antimicrobial response protein in RIR; and the immunoglobulin receptor superfamily, defense/immunity protein, and protein modifying enzyme in WL. However, none were present in WPR, but some of the selected SNP were annotated in immune pathways. This study provides new insights regarding the genetics of the antibody response in layer chickens. Full article
(This article belongs to the Special Issue Genetics and Breeding Advances in Poultry Health and Production)
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8 pages, 762 KiB  
Article
Growth of White Leghorn Chicken Immune Organs after Long-Term Divergent Selection for High or Low Antibody Response to Sheep Red Blood Cells
by Christa F. Honaker, Robert L. Taylor, Jr., Frank W. Edens and Paul B. Siegel
Animals 2024, 14(10), 1487; https://doi.org/10.3390/ani14101487 - 17 May 2024
Viewed by 588
Abstract
Long-term divergent selection from a common founder population for a single trait—antibody response to sheep erythrocytes 5 days post-injection—has resulted in two distinct lines of White Leghorn chickens with a well-documented difference in antibody titers: high (HAS)- and low (LAS)-antibody selected lines. Subpopulations—high [...] Read more.
Long-term divergent selection from a common founder population for a single trait—antibody response to sheep erythrocytes 5 days post-injection—has resulted in two distinct lines of White Leghorn chickens with a well-documented difference in antibody titers: high (HAS)- and low (LAS)-antibody selected lines. Subpopulations—high (HAR)- and low (LAR)-antibody relaxed—were developed from generation 24 of the selected lines to relax selection. The objective of the current experiment was to determine if this long-term selection and relaxation of selection impacted the growth of two organs important to chicken immunity: the spleen and the bursa of Fabricius. Spleens and bursae were obtained from ten chickens per line at nine timepoints (E18, D0, D6, D13, D20, D35, D49, D63, and D91) throughout their rapid growth phase and presented as a percent of body weight. Significance was set at p ≤ 0.05. For the spleen, all lines consistently increased in size relative to body weight to D49, followed by a consistent decline. All lines had a similar growth pattern, but HAS spleens grew faster than LAS spleens. For the bursa, LAS was smaller than the other three lines as an embryo and also smaller than HAS through D63. In the selected lines, bursa weight peaked at D35, whereas the relaxed lines peaked at D49. By D91, there was no difference between lines. Artificial and natural selection, represented by the long-term selected and relaxed antibody lines, resulted in differences in the growth patterns and relative weights of the spleen and bursa of Fabricius. Full article
(This article belongs to the Special Issue Genetics and Breeding Advances in Poultry Health and Production)
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19 pages, 6160 KiB  
Article
Molecular Mechanisms of circRNA–miRNA–mRNA Interactions in the Regulation of Goose Liver Development
by Shuibing Liu, Chuan Li, Xiaolong Hu, Huirong Mao, Sanfeng Liu and Biao Chen
Animals 2024, 14(6), 839; https://doi.org/10.3390/ani14060839 - 8 Mar 2024
Viewed by 1028
Abstract
The liver, a crucial metabolic organ in animals, is responsible for the synthesis, breakdown, and transport of lipids. However, the regulatory mechanisms involving both coding and noncoding RNAs that oversee the development of the goose liver remain elusive. This study aimed to fill [...] Read more.
The liver, a crucial metabolic organ in animals, is responsible for the synthesis, breakdown, and transport of lipids. However, the regulatory mechanisms involving both coding and noncoding RNAs that oversee the development of the goose liver remain elusive. This study aimed to fill this knowledge gap by conducting RNA-seq to profile the expression of circular RNAs (circRNAs) and microRNAs (miRNAs) during goose liver development. We analyzed circRNAs in liver samples from Sichuan white geese at three developmental stages: posthatching day 0, 10 weeks (fast growth stage), and 30 weeks (sexual maturation stage). Our findings revealed 11,079 circRNAs and 994 miRNAs, among which the differentially expressed circRNAs and miRNAs were significantly enriched in pathways such as fatty acid biosynthesis, degradation, and metabolism. Further analysis of the target genes of the differentially expressed miRNAs revealed enrichment in pathways related to fatty acid biosynthesis, metabolism, PPAR signaling, DNA replication, and the cell cycle. We also established circRNA–miRNA–mRNA regulatory networks, identifying key regulatory factors and miRNAs. In conclusion, our study offers valuable insights into the complex interplay of circRNA–miRNA–mRNA interactions during goose liver development, and illuminates the molecular pathways that regulate this vital life function. Full article
(This article belongs to the Special Issue Genetics and Breeding Advances in Poultry Health and Production)
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11 pages, 1224 KiB  
Communication
Effects of Heat Stress and Lipopolysaccharides on Gene Expression in Chicken Immune Cells
by Guang Yang, Xinyi Zhou, Shutao Chen, Anfang Liu, Lingbin Liu, Haiwei Wang, Qigui Wang and Xi Lan
Animals 2024, 14(4), 532; https://doi.org/10.3390/ani14040532 - 6 Feb 2024
Viewed by 837
Abstract
Prolonged exposure to high temperatures and humidity can trigger heat stress in animals, leading to subsequent immune suppression. Lipopolysaccharides (LPSs) act as upstream regulators closely linked to heat stress, contributing to their immunosuppressive effects. After an initial examination of transcriptome sequencing data from [...] Read more.
Prolonged exposure to high temperatures and humidity can trigger heat stress in animals, leading to subsequent immune suppression. Lipopolysaccharides (LPSs) act as upstream regulators closely linked to heat stress, contributing to their immunosuppressive effects. After an initial examination of transcriptome sequencing data from individual samples, 48 genes displaying interactions were found to potentially be associated with heat stress. Subsequently, to delve deeper into this association, we gathered chicken bone marrow dendritic cells (BMDCs). We combined heat stress with lipopolysaccharides and utilized a 48 × 48 Fluidigm IFC quantitative microarray to analyze the patterns of gene changes under various treatment conditions. The results of the study revealed that the combination of heat stress and LPSs in a coinfection led to reduced expressions of CRHR1, MEOX1, and MOV10L1. These differentially expressed genes triggered a pro-inflammatory response within cells via the MAPK and IL-17 signaling pathways. This response, in turn, affected the intensity and duration of inflammation when experiencing synergistic stimulation. Therefore, LPSs exacerbate the immunosuppressive effects of heat stress and prolong cellular adaptation to stress. The combination of heat stress and LPS stimulation induced a cellular inflammatory response through pathways involving cAMP, IL-17, MAPK, and others, consequently leading to decreased expression levels of CRHR1, MEOX1, and MOV10L1. Full article
(This article belongs to the Special Issue Genetics and Breeding Advances in Poultry Health and Production)
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13 pages, 2134 KiB  
Article
Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken
by Shuaishuai Tian, Wendan Tang, Ziqi Zhong, Ziyi Wang, Xinfeng Xie, Hong Liu, Fuwen Chen, Jiaxin Liu, Yuxin Han, Yao Qin, Zhen Tan and Qian Xiao
Animals 2023, 13(10), 1645; https://doi.org/10.3390/ani13101645 - 15 May 2023
Cited by 5 | Viewed by 1608
Abstract
Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity [...] Read more.
Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity (ROH) along the genome using re-sequenced whole-genome sequencing data from 235 Wenchang chickens. A total of 16,511,769 single nucleotide polymorphisms (SNPs) and 53,506 ROH segments were identified in all individuals, and the ROH of Wenchang chicken were mainly composed of short segments (0–1 megabases (Mb)). On average, 5.664% of the genome was located in ROH segments across the Wenchang chicken samples. According to several parameters, the genetic diversity of the Wenchang chicken was relatively high. The average inbreeding coefficient of Wenchang chickens based on FHOM, FGRM, and FROH was 0.060 ± 0.014, 0.561 ± 0.020, and 0.0566 ± 0.01, respectively. A total of 19 ROH islands containing 393 genes were detected on 9 different autosomes. Some of these genes were putatively associated with growth performance (AMY1a), stress resistance (THEMIS2, PIK3C2B), meat traits (MBTPS1, DLK1, and EPS8L2), and fat deposition (LANCL2, PPARγ). These findings provide a better understanding of the degree of inbreeding in Wenchang chickens and the hereditary basis of the characteristics shaped under selection. These results are valuable for the future breeding, conservation, and utilization of Wenchang and other chicken breeds. Full article
(This article belongs to the Special Issue Genetics and Breeding Advances in Poultry Health and Production)
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