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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 January 2023) | Viewed by 20259

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Prof. Dr. Chungang Feng

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Guest Editor

College of Animal Science &Technology, Nanjing Agricultural University, Nanjing, China
Interests: poultry; genetics; genomics; functional genomics; breeding; genomic selection

Prof. Dr. Diyan Li

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Guest Editor

College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
Interests: chicken genetics and breeding; animal genetics and evolution; three-dimensional genomics

Special Issue Information

Dear Colleagues,

Poultry genetics and breeding is a rapidly changing field, and quantitative, population, and molecular genetic approaches have been utilized to elucidate the biological mechanisms of economically important traits in poultry over the past few decades. Many functional genes and mutations of morphological and pigmentation phenotypes in poultry have been identified through genetic mapping and functional genomics. However, there are a number of challenges in studying the mechanisms of complex traits. In recent years, cutting-edge genetic and genomic technologies, such as next-generation sequencing and omics applications, have facilitated our understanding of the mechanism of complex traits in poultry, including feed efficiency, meat and egg quality, and disease resistance. Genomic selection has been widely studied and applied in breeding improved layers and broilers. Gene editing is valuable for characterizing gene function and will be a future challenge in poultry breeding.

This Special Issue aims to highlight recent advances in poultry genetics and breeding in various fields. Broad topic areas include phenomics, genetics, genomics, functional genomics, metabolomics, omics data application, gene editing, genomic selection, genetic evaluation, and genomic prediction in poultry. Contributions by experts in the field in the form of research papers and critical reviews are invited.

Prof. Dr. Chungang Feng
Prof. Dr. Diyan Li
Guest Editors

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Keywords

poultry
genetics
breeding
genomics
functional genomics
epigenomics
omics data
genomic selection
gene editing

Published Papers (10 papers)

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Research

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18 pages, 3866 KiB

Open AccessArticle

Identification of New Genes and Genetic Variant Loci Associated with Breast Muscle Development in the Mini-Cobb F2 Chicken Population Using a Genome-Wide Association Study

by Yang He, Hongmei Shi, Zijian Li, Jiajia Kang, Mengyuan Li, Mengqian Liu, Yong Liu, Jinbo Zhao, Tengfei Dou, Junjing Jia, Yong Duan, Kun Wang and Changrong Ge

Genes 2022, 13(11), 2153; https://doi.org/10.3390/genes13112153 - 18 Nov 2022

Cited by 4 | Viewed by 1768

Abstract

Native chicken has become a favorite choice for consumers in many Asian countries recently, not only for its potential nutritional value but also for its deep ties to local food culture. However, low growth performance and limited meat production restrict their economic potential. Conducting a genome-wide association study (GWAS) for chicken-breast muscle development will help identify loci or candidate genes for different traits and potentially provide new insight into this phenotype in chickens and other species. To improve native chicken growth performance, especially breast muscle development, we performed a GWAS to explore the potential genetic mechanisms of breast muscle development in an F2 population constructed by reciprocal crosses between a fast-growing broiler chicken (Cobb500) and a slow-growing native chicken (Daweishan mini chicken). The results showed that 11 SNPs, which exceeded the 10% genome significance level (p = 1.79 × 10⁻⁸) were considered associated with breast muscle development traits, where six SNPS, NC_006126.5: g.3138376T>G, NC_006126.5: g.3138452A>G, NC_006088.5: g.73837197A>G, NC_006088.5: g.159574275A>G, NC_006089.5: g.80832197A>G, and NC_006127.5: g.48759869G>T was first identified in this study. In total, 13 genes near the SNPs were chosen as candidate genes, and none of them had previously been studied for their role in breast muscle development. After grouping the F2 population according to partial SNPs, significant differences in breast muscle weight were found among different genotypes (p < 0.05), and the expression levels of ALOX5AP, USPL1, CHRNA9, and EFNA5 among candidate genes were also significantly different (p < 0.05). The results of this study will contribute to the future exploration of the potential genetic mechanisms of breast muscle development in domestic chickens and also support the expansion of the market for native chicken in the world. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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15 pages, 3375 KiB

Open AccessArticle

by Pengtao Yuan, Yinli Zhao, Hongtai Li, Shuaihao Li, Shengxin Fan, Bin Zhai, Yuanfang Li, Ruili Han, Xiaojun Liu, Yadong Tian, Xiangtao Kang, Yanhua Zhang and Guoxi Li

Genes 2022, 13(11), 1974; https://doi.org/10.3390/genes13111974 - 29 Oct 2022

Cited by 4 | Viewed by 1422

Abstract

Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1–9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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17 pages, 3282 KiB

Open AccessArticle

Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds

by Natalia V. Dementieva, Yuri S. Shcherbakov, Valentina I. Tyshchenko, Valeriy P. Terletsky, Anatoly B. Vakhrameev, Olga A. Nikolaeva, Anna E. Ryabova, Anastasiia I. Azovtseva, Olga V. Mitrofanova, Grigoriy K. Peglivanyan, Natalia R. Reinbah, Darren K. Griffin and Michael N. Romanov

Genes 2022, 13(10), 1876; https://doi.org/10.3390/genes13101876 - 16 Oct 2022

Cited by 3 | Viewed by 2127

Abstract

Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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11 pages, 1592 KiB

Open AccessArticle

A Novel Single-Nucleotide Polymorphism in WNT4 Promoter Affects Its Transcription and Response to FSH in Chicken Follicles

by Conghao Zhong, Yiya Wang, Cuiping Liu, Yunliang Jiang and Li Kang

Genes 2022, 13(10), 1774; https://doi.org/10.3390/genes13101774 - 01 Oct 2022

Cited by 4 | Viewed by 1318

Abstract

The signaling pathway of the wingless-type mouse mammary tumor virus integration site (Wnt) plays an important role in ovarian and follicular development. In our previous study, WNT4 was shown to be involved in the selection and development of chicken follicles by upregulating the expression of follicle-stimulating hormone receptors (FSHR), stimulating the proliferation of follicular granulosa cells, and increasing the secretion of steroidal hormones. FSH also stimulates the expression of WNT4. To further explore the molecular mechanism by which FSH upregulates WNT4 and characterize the cis-elements regulating WNT4 transcription, in this study, we determined the critical regulatory regions affecting chicken WNT4 transcription. We then identified a single-nucleotide polymorphism (SNP) in this region, and finally analyzed the associations of the SNP with chicken production traits. The results showed that the 5′ regulatory region from −3354 to −2689 of WNT4 had the strongest activity and greatest response to FSH stimulation, and we identified one SNP site in this segment, −3015 (G > C), as affecting the binding of NFAT5 (nuclear factor of activated T cells 5) and respones to FSH stimulation. When G was replaced with C at this site, it eliminated the NFAT5 binding. The mRNA level of WNT4 in small yellow follicles of chickens with genotype GG was significantly higher than that of the other two genotypes. Moreover, this locus was found to be significantly associated with comb length in hens. Individuals with the genotype CC had longer combs. Collectively, these data suggested that SNP−3015 (G > C) is involved in the regulation of WNT4 gene expression by responding FSH and affecting the binding of NFAT5 and that it is associated with chicken comb length. The current results provide a reference for further revealing the response mechanism between WNT and FSH. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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19 pages, 3975 KiB

Open AccessArticle

Characterization of CRH-Binding Protein (CRHBP) in Chickens: Molecular Cloning, Tissue Distribution and Investigation of Its Role as a Negative Feedback Regulator within the Hypothalamus–Pituitary–Adrenal Axis

by Yiping Wan, Zheng Zhang, Dongliang Lin, Xinglong Wang, Tianjiao Huang, Jiancheng Su, Jiannan Zhang, Juan Li and Yajun Wang

Genes 2022, 13(10), 1680; https://doi.org/10.3390/genes13101680 - 20 Sep 2022

Cited by 4 | Viewed by 2381

Abstract

Corticotropin (ACTH) is a pituitary hormone playing important roles in stress response within the hypothalamus–pituitary–adrenal (HPA) axis. The biosynthesis and secretion of ACTH are controlled by multiple factors, including corticotropin-releasing hormone (CRH). As a key hypothalamus-derived regulator, CRH binds to corticotropin-releasing hormone receptor 1 (CRHR1) in the anterior pituitary gland to regulate ACTH synthesis and release. Thus, CRH-binding protein (CRHBP), which binds CRH with high affinity to inhibit CRH-induced ACTH secretion from pituitary cells, draws wide attention. In contrast to the extensive investigation of CRHBP in mammals and other lower vertebrates, the gene structure, tissue expression and physiological functions of CRHBP in birds remain largely unknown. In the present study, using chicken (c-) as our animal model, we examined the gene structure, tissue expression and functionality of CRHBP. Our results showed that: (1) cCRHBP cDNA encodes a 345 amino acid precursor, which shares high sequence identity with that of mammals, reptiles, frogs and fish; (2) cCRHBP is abundantly expressed in the brain (cerebrum and hypothalamus), pituitary and ovary; (3) cCRHBP inhibits the signaling of cCRHRs induced by cCRH, thus reducing the cCRH-induced ACTH secretion from cultured chick pituitary cells; (4) stress mediators (e.g., glucocorticoids) and stress significantly upregulate CRHBP mRNA expression in chickens, supporting its role as a negative feedback regulator in the HPA axis. The present study enriches our understanding of the conserved roles of CRHBP across vertebrates. In addition, chicken is an important poultry animal with multiple economic traits which are tightly controlled by the HPA axis. The characterization of the chicken CRHBP gene helps to reveal the molecular basis of the chicken HPA axis and is thus beneficial to the poultry industry. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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13 pages, 1344 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Local Chicken Ecotypes in Burkina Faso Using Microsatellite Markers

by Zare Yacouba, Houaga Isidore, Kere Michel, Gnanda B. Isidore, Traore Boureima, Millogo Vinsoun, Konkobo Maurice, Bandaogo Ousseni, Zongo Moussa, Bougouma-Yameogo M. C. Valerie, Rekaya Romdhane and Nianogo A. Joseph

Genes 2022, 13(9), 1523; https://doi.org/10.3390/genes13091523 - 24 Aug 2022

Cited by 2 | Viewed by 2239

Abstract

The objective of this study was to investigate the genetic diversity and population structure of local chicken ecotypes from Burkina Faso using microsatellite markers. A total of 71 individuals representing local chicken populations from the Centre-East (18), Centre-North (17), Sahel (18) and South-West (18) were used to estimate genetic diversity indices, population structure and phylogenetic relationships using 20 selected polymorphic microsatellite markers. The number of alleles, mean number of alleles, mean of observed and expected heterozygosity and polymorphic information content were 127, 6.35, 0.391, 0.521, 0.539 and 0.541, respectively. The estimated overall fixation index between loci (F), among populations (F_IS) and inbreeding coefficient within chicken ecotypes were 0.239, 0.267 and 0.243, respectively. Analysis of the molecular variance revealed that 77% of the total genetic diversity was attributed to within-population variation and the remaining 1% and 22% were attributed to among-regions differentiation (F_ST) and among-individual differentiation (F_IT), respectively. The highest pairwise genetic distance (0.026) was found between the local Konde ecotype and those from the Centre-North region while the lowest distance was observed between local chickens from the Sahel and the Centre-North regions (0.003). Neighbour-joining phylogenetic tree and principal component discriminant analyses confirmed the observed genetic distances between populations. The results show that local chickens in Burkina Faso have a rich genetic diversity with little differentiation between the studied populations. This study provides important information on measures of genetic diversity that could help in the design and implementation of future genetic improvement and conservation programs for local chickens in Burkina Faso. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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9 pages, 12370 KiB

Open AccessArticle

Mechanism of SCD Participation in Lipid Droplet-Mediated Steroidogenesis in Goose Granulosa Cells

by Xin Yuan, Ibn Iddriss Abdul-Rahman, Shenqiang Hu, Liang Li, Hua He, Lu Xia, Jiwei Hu, Mingxia Ran, Yali Liu, Mariama Abdulai and Jiwen Wang

Genes 2022, 13(9), 1516; https://doi.org/10.3390/genes13091516 - 24 Aug 2022

Cited by 3 | Viewed by 1734

Abstract

Stearoyl-CoA desaturase (SCD) is a key enzyme catalyzing the rate-limiting step in monounsaturated fatty acids (MUFAs) production. There may be a mechanism by which SCD is involved in lipid metabolism, which is assumed to be essential for goose follicular development. For this reason, a cellular model of SCD function in goose granulosa cells (GCs) via SCD overexpression and knockdown was used to determine the role of SCD in GC proliferation using flow cytometry. We found that SCD overexpression induced and SCD knockdown inhibited GCs proliferation. Furthermore, ELISA analysis showed that SCD overexpression increased the total cholesterol (TC), progesterone, and estrogen levels in GCs, while SCD knockdown decreased TC, progesterone, and estrogen levels (p < 0.05). Combining these results with those of related multi-omics reports, we proposed a mechanism of SCD regulating the key lipids and differentially expressed gene (DEGs) in glycerophospholipid and glycerolipid metabolism, which participate in steroidogenesis mediated by the lipid droplet deposition in goose GCs. These results add further insights into understanding the lipid metabolism mechanism of goose GCs. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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22 pages, 3750 KiB

Open AccessArticle

Physicochemical, Nutritional Properties and Metabolomics Analysis Fat Deposition Mechanism of Chahua Chicken No. 2 and Yao Chicken

by Yong Liu, Shuangmin Liang, Kun Wang, Xiannian Zi, Ru Zhang, Guangzheng Wang, Jiajia Kang, Zijian Li, Tengfei Dou and Changrong Ge

Genes 2022, 13(8), 1358; https://doi.org/10.3390/genes13081358 - 28 Jul 2022

Cited by 2 | Viewed by 1597

Abstract

Poultry is an important dietary source of animal protein, accounting for approximately 30% of global meat consumption. Because of its low price, low fat and cholesterol content, and no religious restrictions, chicken is considered a widely available healthy meat. Chahua chicken No. 2 is a synthetic breed of Chahua chicken derived from five generations of specialized strain breeding. In this study, Chahua chicken No. 2 (CH) and Yao chicken (Y) were used as the research objects to compare the differences in physicochemical and nutritional indicators of meat quality between the two chicken breeds, and metabolomics was used to analyze the differences in metabolites and lipid metabolism pathways and to explore the expression of genes involved in adipogenesis. The physical index and nutritional value of CH are better than that of Y, and the chemical index of Y is better than that of CH. However, the chemical index results of CH are also within the normal theoretical value range. Comprehensive comparison shows that the meat quality of CH is relatively good. Metabolomics analysis showed that CH and Y had 85 different metabolites, and the differential metabolites were mainly classified into eight categories. KEGG pathway enrichment analysis revealed 13 different metabolic pathways. The screened PPARG, FABP3, ACSL5, FASN, UCP3 and SC5D were negatively correlated with muscle fat deposition, while PPARα, ACACA and ACOX1 were positively correlated with muscle fat deposition. The meat quality of CH was better than Y. The metabolites and metabolic pathways obtained by metabonomics analysis mainly involved the metabolism of amino acids and fatty acids, which were consistent with the differences in meat quality between the two breeds and the contents of precursors affecting flavor. The screened genes were associated with fatty deposition in poultry. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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11 pages, 1627 KiB

Open AccessArticle

Identification of the Core Promoter and Variants Regulating Chicken CCKAR Expression

by Zhepeng Wang, Angus M. A. Reid, Peter W. Wilson and Ian C. Dunn

Genes 2022, 13(6), 1083; https://doi.org/10.3390/genes13061083 - 18 Jun 2022

Cited by 2 | Viewed by 1521

Abstract

Decreased expression of chicken cholecystokinin A receptor (CCKAR) attenuates satiety, which contributes to increased food intake and growth for modern broilers. The study aims to define the core promoter of CCKAR, and to identify variants associated with expression activity. A 21 kb region around the CCKAR was re-sequenced to detect sequence variants. A series of 5′-deleted promoter plasmids were constructed to define the core promoter of CCKAR. The effects of sequence variants located in promoter (PSNP) and conserved (CSNP) regions on promoter activity were analyzed by comparing luciferase activity between haplotypes. A total of 182 variants were found in the 21 kb region. There were no large structural variants around CCKAR. pNL−328/+183, the one with the shortest insertion, showed the highest activity among the six promoter constructs, implying that the key cis elements regulating CCKAR expression are mainly distributed 328 bp upstream. We detected significant activity differences between high- and low-growth associated haplotypes in four of the six promoter constructs. The high-growth haplotypes of constructs pNL−1646/+183, pNL−799/+183 and pNL−528/+183 showed lower activities than the low-growth haplotypes, which is consistent with decreased expression of CCKAR in high-growth chickens. Lower expression of the high-growth allele was also detected for the CSNP5-containing construct. The data suggest that the core promoter of CCKAR is located the 328 bp region upstream from the transcription start site. Lower expression activities shown by the high-growth haplotypes in the reporter assay suggest that CSNP5 and variants located between 328 bp and 1646 bp upstream form a promising molecular basis for decreased expression of CCKAR and increased growth in chickens. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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Review

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14 pages, 1002 KiB

Open AccessReview

Molecular Regulatory Mechanisms in Chicken Feather Follicle Morphogenesis

by Gaige Ji, Ming Zhang, Yunjie Tu, Yifan Liu, Yanju Shan, Xiaojun Ju, Jianmin Zou, Jingting Shu, Zhongwei Sheng and Hua Li

Genes 2023, 14(8), 1646; https://doi.org/10.3390/genes14081646 - 18 Aug 2023

Cited by 3 | Viewed by 1839

Abstract

In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The feather follicle originates from the interaction between the epidermis and dermis in the early embryonic stage. Feather follicle morphogenesis is regulated by the Wnt, ectodysplasin (Eda), epidermal growth factor (EGF), fibroblast growth factor (FGF), bone morphogenetic protein (BMP), sonic hedgehog (Shh), Notch, and other signaling pathways that exist in epithelial and mesenchymal cells. The Wnt pathway is essential for feather follicle and feather morphogenesis. Eda interacts with Wnt to induce FGF expression, which attracts mesenchymal cell movement and aggregates to form feather follicle primordia. BMP acts as an inhibitor of the above signaling pathways to limit the size of the feather tract and distance between neighboring feather primordia in a dose-dependent manner. The Notch/Delta pathway can interact with the FGF pathway to promote feather bud formation. While not a part of the early morphogenesis of feather follicles, Shh and BMP signaling are involved in late feather branching. This review summarizes the roles of miRNAs/lncRNA in the regulation of feather follicle and feather growth and development and suggests topics that need to be solved in a future study. This review focuses on the regulatory mechanisms involved in feather follicle morphogenesis and analyzes the impact of SNP sites on feather follicle traits in poultry. This work may help us to understand the molecular regulatory networks influencing feather follicle growth and provide basic data for poultry carcass quality. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)

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