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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 May 2024) | Viewed by 18655

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Dr. Zhuanjian Li

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College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
Interests: structural variation; molecular biology; transcriptional regulation; myoblast proliferation and differentiation; noncoding RNA
Special Issues, Collections and Topics in MDPI journals

Dr. Tuanhui Ren

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College of Veterinary Medicine, Jilin University, Changchun, China
Interests: transcriptome; metabolome; molecular biology; gut microbiome

Dr. Li Zhang

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Guest Editor

College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
Interests: poultry; meat science; genes; regulation

Special Issue Information

Dear Colleagues,

This Special Issue, entitled “Poultry Breeding: Genetics and Genomics”, aims to collect high-quality research articles, review articles, and communications on advances in the molecular genetics and genomics of poultry. Improving poultry egg and meat production plays an important role in reducing hunger and maintaining food security around the world. Developments in poultry genetics and breeding have come in part from genetic selection for improved feed efficiency and a better understanding of poultry nutrition. A growing body of research indicates that genetics and genomes have a strong influence on the growth, development and egg-laying performance of poultry. With the development and popularization of sequencing technology, we look forward to witnessing more cutting-edge research in molecular genetics and functional genomes related to chickens, ducks, geese and other species.

Topics of interest for this Special Issue include, but are not limited to:

Epigenetics in poultry;
Gene regulation in poultry;
Multi-omics data analysis, including the transcriptome and metabolome；
Genome-wide association analysis;
Variations such as SNPs and Indels in genes.

Dr. Zhuanjian Li
Dr. Tuanhui Ren
Dr. Li Zhang
Guest Editors

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Keywords

poultry
epigenetics
gene regulation
multi-omics data analysis

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Published Papers (9 papers)

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13 pages, 3567 KiB

Open AccessArticle

The Effect of Short- and Long-Term Cryopreservation on Chicken Primordial Germ Cells

by Mariam Ibrahim, Ewa Grochowska, Bence Lázár, Eszter Várkonyi, Marek Bednarczyk and Katarzyna Stadnicka

Genes 2024, 15(5), 624; https://doi.org/10.3390/genes15050624 - 14 May 2024

Viewed by 1169

Abstract

Primordial germ cells (PGCs) are the precursors of functional gametes and the only cell type capable of transmitting genetic and epigenetic information from generation to generation. These cells offer valuable starting material for cell-based genetic engineering and genetic preservation, as well as epigenetic studies. While chicken PGCs have demonstrated resilience in maintaining their germness characteristics during both culturing and cryopreservation, their handling remains a complex challenge requiring further refinement. Herein, the study aimed to compare the effects of different conditions (freezing-thawing and in vitro cultivation) on the expression of PGC-specific marker genes. Embryonic blood containing circulating PGCs was isolated from purebred Green-legged Partridgelike chicken embryos at 14–16 Hamburger–Hamilton (HH) embryonic development stage. The blood was pooled separately for males and females following sex determination. The conditions applied to the blood containing PGCs were as follows: (1) fresh isolation; (2) cryopreservation for a short term (2 days); and (3) in vitro culture (3 months) with long-term cryopreservation of purified PGCs (~2 years). To characterize PGCs, RNA isolation was carried out, followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to assess the expression levels of specific germ cell markers (SSEA1, CVH, and DAZL), as well as pluripotency markers (OCT4 and NANOG). The investigated genes exhibited consistent expression among PGCs maintained under diverse conditions, with no discernible differences observed between males and females. Notably, the analyzed markers demonstrated higher expression levels in PGCs when subjected to freezing than in their freshly isolated counterparts. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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16 pages, 3680 KiB

Open AccessArticle

Dynamic Expression Profile of Follicles at Different Stages in High- and Low-Production Laying Hens

by Lan Yang, Xuewei Fan, Kaiyuan Tian, Sensen Yan, Chunhong Xu, Yixiang Tian, Chengpeng Xiao, Xintao Jia, Junlai Shi, Ying Bai and Wenting Li

Genes 2024, 15(1), 40; https://doi.org/10.3390/genes15010040 - 26 Dec 2023

Cited by 1 | Viewed by 1732

Abstract

Improving the efficiency of hens and extending the egg-laying cycle require maintaining high egg production in the later stages. The ovarian follicles, as the primary functional units for ovarian development and oocyte maturation, play a crucial role in regulating the continuous ovulation of hens. The egg production rate of laying hens is mostly affected by proper follicle growth and ovulation in the ovaries. The objective of this study was to identify the key genes and signaling pathways involved in the development of ovarian follicles in Taihang hens through transcriptome screening. In this study, RNA sequencing was used to compare and analyze the transcriptomes of ovarian follicles at four developmental stages: small white follicles (SWF), small yellow follicles (SYF), F5 follicles, and F2 follicles, from two groups: the high continual production group (H-Group) and the low continual production group (L-Group). A total of 24 cDNA libraries were constructed, and significant differential expression of 96, 199, 591, and 314 mRNAs was detected in the SWF, SYF, F5, and F2 follicles of the H and L groups, respectively. Based on the results of GO and KEGG enrichment analyses, each stage of follicle growth possesses distinct molecular genetic features, which have important effects on follicle development and significantly promote the formation of continuous production traits through the biosynthesis of steroid hormones, cytokine–cytokine receptor interaction, and neuroactive ligand–receptor interaction. Additionally, through STEM analysis, we identified 59 DEGs, including ZP4, KCNH1, IGFs, HMGA2, and CDH1, potentially associated with follicular development within four significant modules. This study represents the first transcriptome investigation of follicles in hens with high and low egg-producing characteristics at four crucial developmental stages. These findings provide important molecular evidence for understanding the regulation of follicular development and its variations. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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15 pages, 2065 KiB

Open AccessArticle

Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing

by Jing Feng, Wei Zhu, Hairen Shi, Da Peng, Lei Zang, Yan Wang, Luobu ZhaXi, Jiancai BaiMa, Felix Kwame Amevor, Xiaoqi Wang, Xueying Ma and Xiaoling Zhao

Genes 2023, 14(9), 1672; https://doi.org/10.3390/genes14091672 - 24 Aug 2023

Cited by 1 | Viewed by 1998

Abstract

Background: The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm. Methods: Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and Pi selections were used to identify genes under positive selection in the Tibetan black chicken genome. Results: A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (ADCY1, GNG7 and PER3), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen (CD86) was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as TRIT1, HPCAL4, NT5C1A and HEYL were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens. Conclusions: In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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15 pages, 4153 KiB

Open AccessArticle

Comparative Transcriptome Analyses of Leg Muscle during Early Growth between Geese (Anser cygnoides) Breeds Differing in Body Size Characteristics

by Jun Tang, Hongjia Ouyang, Xiaomei Chen, Danli Jiang, Yunbo Tian, Yunmao Huang and Xu Shen

Genes 2023, 14(5), 1048; https://doi.org/10.3390/genes14051048 - 7 May 2023

Cited by 8 | Viewed by 1861

Abstract

Goose is an important poultry commonly raised for meat. The early growth performance of geese significantly influences their market weight and slaughter weight, affecting the poultry industry’s economic benefits. To identify the growth surge between the Shitou goose and the Wuzong goose, we collected the early growth body traits from 0 to 12 weeks. In addition, we investigated the transcriptomic changes in leg muscles at the high growth speed period to reveal the difference between the two geese breeds. We also estimated the growth curve parameters under three models, including the logistic, von Bertalanffy, and Gompertz models. The results showed that except for body length and keel length, the best-fitting model between the body weight and body size of the Shitou and Wuzong was the logistic model. The growth turning points of Shitou and Wuzong were 5.954 and 4.944 weeks, respectively, and the turning point of their body weight was 1459.01 g and 478.54 g, respectively. Growth surge occurred at 2–9 weeks in Shitou goose and at 1–7 weeks in Wuzong goose. The body size traits of the Shitou goose and Wuzong goose showed a trend of rapid growth in the early stage and slow growth in the later stage, and the Shitou goose growth was higher than the Wuzong goose. For transcriptome sequencing, a total of 87 differentially expressed genes (DEGs) were identified with a fold change ≥ 2 and a false discovery rate < 0.05. Many DEGs have a potential function for growth, such as CXCL12, SSTR4, FABP5, SLC2A1, MYLK4, and EIF4E3. KEGG pathway analysis identified that some DEGs were significantly enriched in the calcium signaling pathway, which may promote muscle growth. The gene–gene interaction network of DEGs was mainly related to the transmission of cell signals and substances, hematological system development, and functions. This study can provide theoretical guidance for the production and breeding management of the Shitou goose and Wuzong goose and help reveal the genetic mechanisms underlying diverse body sizes between two goose breeds. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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19 pages, 2954 KiB

Open AccessArticle

Transcriptomic and Chromatin Landscape Analysis Reveals That Involvement of Pituitary Level Transcription Factors Modulate Incubation Behaviors of Magang Geese

by Jianye Chang, Di Fan, Jiaxin Liu, Yanglong Xu, Xuefei Huang, Yunbo Tian, Jin Xu, Yunmao Huang, Jue Ruan and Xu Shen

Genes 2023, 14(4), 815; https://doi.org/10.3390/genes14040815 - 28 Mar 2023

Cited by 1 | Viewed by 2193

Abstract

The incubation behavior of geese seriously affects their egg production performance. Studies on incubation behavior have identified functional genes, but the regulatory architecture relationship between functional genes and chromatin accessibility remains poorly understood. Here, we present an integrated analysis of open chromatin profiles and transcriptome to identify the cis-regulatory element and their potential transcription factors involved in regulating incubation behavior in goose pituitary. Assay for transposase-accessible chromatin sequencing (ATAC-seq) revealed that open chromatin regions increased in the pituitary during the transition from incubation behavior to laying. We identified 920 significant differential accessible regions (DARs) in the pituitary. Compared to the laying stage, most DARs had higher chromatin accessibility in the brooding stage. Motif analysis of open DARs showed that the most significant transcription factor (TF) occupied sites predominantly enriched in motifs binding to the RFX family (RFX5, RFX2, and RFX1). While the majority of TF motifs enriched under sites of the nuclear receptor (NR) family (ARE, GRE, and PGR) in closed DARs at the incubation behavior stage. Footprint analysis indicated that the transcription factor RFX family exhibited higher binding on chromatin at the brooding stage. To further elucidate the effect of changes in chromatin accessibility on gene expression levels, a comparison of the transcriptome revealed 279 differentially expressed genes (DEGs). The transcriptome changes were associated with processes of steroid biosynthesis. By integrating ATAC-seq and RNA-seq, few DARs directly affect incubation behavior by regulating the transcription levels of genes. Five DAR-related DEGs were found to be closely related to maintaining the incubation behavior in geese. Footprinting analysis revealed a set of transcription factors (RFX1, RFX2, RFX3, RFX5, BHLHA15, SIX1, and DUX) which displayed the highest activity at the brooding stage. SREBF2 was predicted to be the unique differentially expressed transcription factor whose mRNA level was down-regulated and enriched in hyper-accessible regions of PRL in the broody stage. In the present study, we comprehensively profiled the transcriptome and chromatin accessibility in the pituitary related to incubation behavior. Our findings provided insight into the identification and analysis of regulatory elements in goose incubation behavior. The epigenetic alterations profiled here can help decipher the epigenetic mechanisms that contribute to the regulation of incubation behavior in birds. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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14 pages, 4533 KiB

Open AccessArticle

Integration Analysis of circRNA–miRNA–mRNA and Identification of Critical Networks in Valgus-Varus Deformity (Gallus gallus)

by Jianzeng Li, Yanchao Ma, Chunxia Cai, Lujie Zhang, Xinxin Liu, Ruirui Jiang, Donghua Li, Zhuanjian Li, Xiangtao Kang, Yadong Tian and Ruili Han

Genes 2023, 14(3), 622; https://doi.org/10.3390/genes14030622 - 1 Mar 2023

Cited by 2 | Viewed by 1726

Abstract

Valgus-valgus deformity (VVD) is a common leg deformity in broilers with inward or outward deviation of the tibiotarsus and tarsometatarsus. The competing endogenous RNA (ceRNA) network plays an essential role in the study of leg disease. However, its role in the etiology and pathogenesis of VVD remains unclear. Here, based on case (VVD) and control (normal) group design, we performed analyses of differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed mRNAs (DEmRNAs). Transcriptome data derived 86 DEcircRNAs, 13 DEmiRNAs and 410 DEmRNAs. Functional analysis showed that DEmRNAs were significantly enriched in cell cycle, apoptosis, ECM-receptor interaction, FoxO signaling pathway and protein processing synthesis. DEcirc/miRNA-associated DEmRNAs were associated with skeletal and muscle growth and development pathways, including mTOR, Wnt, and VEGF signaling pathways. Subsequently, a circRNA–miRNA–mRNA regulatory network was constructed based on the ceRNA hypothesis, including 8 circRNAs, 6 miRNAs, and 31 mRNAs, which were significantly enriched in the skeletal developmental pathway. Finally, two key mRNAs (CDC20 and CTNNB1) and their regulatory axes were screened by the PPI network and cytohubba. The expression levels of CDC20 and CTNNB1 in cartilage and seven other tissues were also quantified by qPCR. In conclusion, we analyzed the functions of DEmRNA, DEcircRNA and DEmiRNA and constructed the hub ceRNA regulatory axis, and obtained two hub genes, CDC20 and CTNNB1. The study more deeply explored the etiology and pathogenesis of VVD and lays the foundation for further study of the role of the ceRNA network on skeletal development. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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18 pages, 3113 KiB

Open AccessArticle

Molecular Characterization, Expression Profile, and A 21-bp Indel within the ASB9 Gene and Its Associations with Chicken Production Traits

by Panpan Qin, Yang Liu, Xinran Niu, Yixuan Liu, Yushi Zhang, Yufang Niu, Yanxing Wang, Bingjie Chen, Ruili Han, Yadong Tian, Xiaojun Liu, Xiangtao Kang, Ruirui Jiang and Zhuanjian Li

Genes 2023, 14(2), 339; https://doi.org/10.3390/genes14020339 - 28 Jan 2023

Cited by 2 | Viewed by 1811

Abstract

A growing number of studies have shown that members of the ankyrin repeat and suppressors of cytokine signaling (SOCS) box-containing protein (ASB) family are extensively involved in biological processes such as cell growth, tissue development, insulin signaling, ubiquitination, protein degradation, and skeletal muscle membrane protein formation, while the specific biological role of ankyrin-repeat and SOCS box protein 9 (ASB9) remains unclear. In this study, a 21 bp indel in the intron of ASB9 was identified for the first time in 2641 individuals from 11 different breeds and an F₂ resource population, and differences were observed among individuals with different genotypes (II, ID, and DD). An association study of a cross-designed F₂ resource population revealed that the 21-bp indel was significantly related to growth and carcass traits. The significantly associated growth traits were body weight (BW) at 4, 6, 8, 10, and 12 weeks of age; sternal length (SL) at 4, 8, and 12 weeks of age; body slope length (BSL) at 4, 8, and 12 weeks of age; shank girth (SG) at 4 and 12 weeks of age; tibia length (TL) at 12 weeks of age; and pelvic width (PW) at 4 weeks of age (p < 0.05). This indel was also significantly correlated with carcass traits including semievisceration weight (SEW), evisceration weight (EW), claw weight (CLW), breast muscle weight (BMW), leg weight (LeW), leg muscle weight (LMW), claw rate (CLR), and shedding weight (ShW) (p < 0.05). In commercial broilers, the II genotype was the dominant genotype and underwent extensive selection. Interestingly, the ASB9 gene was expressed at significantly higher levels in the leg muscles of Arbor Acres broilers than those of Lushi chickens, while the opposite was true for the breast muscles. In summary, the 21-bp indel in the ASB9 gene significantly influenced the expression of the ASB9 gene in muscle tissue and was associated with multiple growth and carcass traits in the F₂ resource population. These findings suggested that the 21-bp indel within the ASB9 gene could be used in marker-assisted selection breeding for traits related to chicken growth. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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15 pages, 4176 KiB

Open AccessArticle

Revealing the Regulatory Mechanism of lncRNA-LMEP on Melanin Deposition Based on High-Throughput Sequencing in Xichuan Chicken Skin

by Pengwei Zhang, Yanfang Cao, Yawei Fu, Huiyuan Zhu, Shuohui Xu, Yanhua Zhang, Wenting Li, Guirong Sun, Ruirui Jiang, Ruili Han, Hong Li, Guoxi Li, Yadong Tian, Xiaojun Liu, Xiangtao Kang and Donghua Li

Genes 2022, 13(11), 2143; https://doi.org/10.3390/genes13112143 - 17 Nov 2022

Cited by 6 | Viewed by 2000

Abstract

The therapeutic, medicinal, and nourishing properties of black-bone chickens are highly regarded by consumers in China. However, some birds may have yellow skin (YS) or light skin rather than black skin (BS), which causes economic losses every year. Long noncoding RNAs (lncRNAs) are widely present in living organisms, and they perform various biological functions. Many genes associated with BS pigmentation have been discovered, but the lncRNAs involved and their detailed mechanisms have remained untested. We detected 56 differentially expressed lncRNAs from the RNA-seq of dorsal skin (BS versus YS) and found that TCONS_00054154 plays a vital role in melanogenesis by the combined analysis of lncRNAs and mRNAs. We found that the full length of the TCONS_00054154 sequence was 3093 bp by RACE PCR, and we named it LMEP. Moreover, a subcellular localization analysis identified that LMEP is mainly present in the cytoplasm. After the overexpression and the interference with LMEP, the tyrosinase content significantly increased and decreased, respectively (p < 0.05). In summary, we identified the important lncRNAs of chicken skin pigmentation and initially determined the effect of LMEP on melanin deposition. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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Review

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11 pages, 250 KiB

Open AccessReview

Unraveling the Genetic Foundations of Broiler Meat Quality: Advancements in Research and Their Impact

by Tian Lu, Bahareldin Ali Abdalla Gibril, Jiguo Xu and Xinwei Xiong

Genes 2024, 15(6), 746; https://doi.org/10.3390/genes15060746 - 6 Jun 2024

Viewed by 2657

Abstract

As societal progress elevates living standards, the focus on meat consumption has shifted from quantity to quality. In broiler production, optimizing meat quality has become paramount, prompting efforts to refine various meat attributes. Recent advancements in sequencing technologies have revealed the genome’s complexity, surpassing previous conceptions. Through experimentation, numerous genetic elements have been linked to crucial meat quality traits in broiler chickens. This review synthesizes the current understanding of genetic determinants associated with meat quality attributes in broilers. Researchers have unveiled the pivotal insights detailed herein by employing diverse genomic methodologies such as QTL-based investigations, candidate gene studies, single-nucleotide polymorphism screening, genome-wide association studies, and RNA sequencing. These studies have identified numerous genes involved in broiler meat quality traits, including meat lightness (COL1A2 and ACAA2), meat yellowness (BCMO1 and GDPD5), fiber diameter (myostatin and LncIRS1), meat pH (PRDX4), tenderness (CAPN1), and intramuscular fat content (miR-24-3p and ANXA6). Consequently, a comprehensive exploration of these genetic elements is imperative to devise novel molecular markers and potential targets, promising to revolutionize strategies for enhancing broiler meat quality. Full article

(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)

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