Genes

Editorial

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4 pages, 191 KiB

Open AccessEditorial

Special Issue: Poultry Genetics, Breeding and Biotechnology

by Jun Heon Lee

Genes 2021, 12(11), 1744; https://doi.org/10.3390/genes12111744 - 29 Oct 2021

Cited by 6 | Viewed by 3020

Abstract

Poultry products, meat and eggs, are important sources of protein in the human diet worldwide [...] Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

Research

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12 pages, 2705 KiB

Open AccessArticle

Genetic Diversity of Microneme Protein 2 and Surface Antigen 1 of Eimeria tenella

by Tuấn Cường Võ, Haung Naw, Rochelle A. Flores, Hương Giang Lê, Jung-Mi Kang, Won Gi Yoo, Woo-Hyun Kim, Wongi Min and Byoung-Kuk Na

Genes 2021, 12(9), 1418; https://doi.org/10.3390/genes12091418 - 15 Sep 2021

Cited by 9 | Viewed by 2210

Abstract

Avian coccidiosis is a disease caused by members of the genus Eimeria. Huge economic losses incurred by the global poultry industry due to coccidiosis have increased the need for cost-effective and easily available recombinant vaccines. Microneme protein 2 (MIC2) and surface antigen [...] Read more.

Avian coccidiosis is a disease caused by members of the genus Eimeria. Huge economic losses incurred by the global poultry industry due to coccidiosis have increased the need for cost-effective and easily available recombinant vaccines. Microneme protein 2 (MIC2) and surface antigen 1 (SAG1) of E. tenella have been recognised as potential vaccine candidates. However, the genetic diversity of the antigens in field isolates, which affects vaccine efficacy, has yet to be largely investigated. Here, we analysed genetic diversity and natural selection of etmic2 and etsag1 in Korean E. tenella isolates. Both genes exhibited low levels of genetic diversity in Korean isolates. However, the two genes showed different patterns of nucleotide diversity and amino acid polymorphism involving the E. tenella isolates obtained from different countries including China and India. These results underscore the need to investigate the genetic diversity of the vaccine candidate antigens and warrant monitoring of genetic heterogeneity and evolutionary aspects of the genes in larger numbers of E. tenella field isolates from different geographical areas to design effective coccidial vaccines. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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18 pages, 12165 KiB

Open AccessArticle

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

by Francesca Bernini, Alessandro Bagnato, Stefano Paolo Marelli, Luisa Zaniboni, Silvia Cerolini and Maria Giuseppina Strillacci

Genes 2021, 12(9), 1342; https://doi.org/10.3390/genes12091342 - 28 Aug 2021

Cited by 9 | Viewed by 2926

Abstract

Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others [...] Read more.

Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others statistical approaches (e.g., Wright’s F-statistics, principal component analysis, ADMIXTURE analysis), to investigate the genomic diversity in several heritage turkey breeds. We performed a genome-wide characterization of ROH-rich regions in seven autochthonous turkey breeds, i.e., Brianzolo (Brzl), Bronzato Comune Italiano (BrCI), Bronzato dei Colli Euganei (CoEu), Parma e Piacenza (PrPc), Nero d’Italia (NeIt), Ermellinato di Rovigo (ErRo) and Romagnolo (Roma). ROHs were detected based on a 650K SNP genotyping. ROH_islands were identified as homozygous ROH regions shared by at least 75% of birds (within breed). Annotation of genes was performed with DAVID. The admixture analyses revealed that six breeds are unique populations while the Roma breed consists in an admixture of founder populations. Effective population size estimated on genomic data shows a numeric contraction. ROH_islands harbour genes that may be interesting for target selection in commercial populations also. Among them the PTGS2 and PLA2G4A genes on chr10 were related to reproduction efficiency. This is the first study mapping genetic variation in autochthonous turkey populations. Breeds were genetically different among them, with the Roma breed proving to be a mixture of the other breeds. The ROH_islands identified harboured genes peculiar to the selection that occurred in heritage breeds. Finally, this study releases previously undisclosed information on existing genetic variation in the turkey species. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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22 pages, 7196 KiB

Open AccessArticle

Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese

by Sherif Melak, Qin Wang, Ye Tian, Wei Wei, Lifan Zhang, Ahmed Elbeltagy and Jie Chen

Genes 2021, 12(8), 1203; https://doi.org/10.3390/genes12081203 - 3 Aug 2021

Cited by 12 | Viewed by 2356

Abstract

Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese [...] Read more.

Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs’ filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs—which had different allelic frequencies—were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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13 pages, 1068 KiB

Open AccessArticle

Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

by Jihye Cha, Hyojun Choo, Krishnamoorthy Srikanth, Seung-Hwan Lee, Ju-Whan Son, Mi-Rim Park, Nayeon Kim, Gul Won Jang and Jong-Eun Park

Genes 2021, 12(8), 1170; https://doi.org/10.3390/genes12081170 - 29 Jul 2021

Cited by 17 | Viewed by 3137

Abstract

Meat from Korean native chickens (KNCs) has high consumer demand; however, slow growth performance and high variation in body weight (BW) of KNCs remain an issue. Genome-wide association study (GWAS) is a powerful method to identify quantitative trait-associated genomic loci. A GWAS, based [...] Read more.

Meat from Korean native chickens (KNCs) has high consumer demand; however, slow growth performance and high variation in body weight (BW) of KNCs remain an issue. Genome-wide association study (GWAS) is a powerful method to identify quantitative trait-associated genomic loci. A GWAS, based on a large-scale KNC population, is needed to identify underlying genetic mechanisms related to its growth traits. To identify BW-associated genomic regions, we performed a GWAS using the chicken 60K single nucleotide polymorphism (SNP) panel for 1328 KNCs. BW was measured at 8 weeks of age, from 2018 to 2020. Twelve SNPs were associated with BW at the suggestive significance level (p < 2.95 × 10⁻⁵) and located near or within 11 candidate genes, including WDR37, KCNIP4, SLIT2, PPARGC1A, MYOCD and ADGRA3. Gene set enrichment analysis based on the GWAS results at p < 0.05 (1680 SNPs) showed that 32 Gene Ontology terms and two Kyoto Encyclopedia of Genes and Genomes pathways, including regulation of transcription, motor activity, the mitogen-activated protein kinase signaling pathway, and tight junction, were significantly enriched (p < 0.05) for BW-associated genes. These pathways are involved in cell growth and development, related to BW gain. The identified SNPs are potential biomarkers in KNC breeding. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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12 pages, 1266 KiB

Open AccessArticle

Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

by Joanna Grzegorczyk, Artur Gurgul, Maria Oczkowicz, Tomasz Szmatoła, Agnieszka Fornal and Monika Bugno-Poniewierska

Genes 2021, 12(7), 1074; https://doi.org/10.3390/genes12071074 - 14 Jul 2021

Cited by 7 | Viewed by 3275

Abstract

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda^® breed, constituting 95% of the country’s population, whereas geese of [...] Read more.

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda^® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda^® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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18 pages, 779 KiB

Open AccessArticle

Molecular Cloning and Functional Characterization of Three 5-HT Receptor Genes (HTR1B, HTR1E, and HTR1F) in Chickens

by Caiyun Sun, Yang Qiu, Qin Ren, Xiao Zhang, Baolong Cao, Yi Zou, Juan Li, Jiannan Zhang and Yajun Wang

Genes 2021, 12(6), 891; https://doi.org/10.3390/genes12060891 - 9 Jun 2021

Cited by 13 | Viewed by 3292

Abstract

The serotonin (5-hydroxytryptamine, 5-HT) signaling system is involved in a variety of physiological functions, including the control of cognition, reward, learning, memory, and vasoconstriction in vertebrates. Contrary to the extensive studies in the mammalian system, little is known about the molecular characteristics of [...] Read more.

The serotonin (5-hydroxytryptamine, 5-HT) signaling system is involved in a variety of physiological functions, including the control of cognition, reward, learning, memory, and vasoconstriction in vertebrates. Contrary to the extensive studies in the mammalian system, little is known about the molecular characteristics of the avian serotonin signaling network. In this study, we cloned and characterized the full-length cDNA of three serotonin receptor genes (HTR1B, HTR1E and HTR1F) in chicken pituitaries. Synteny analyses indicated that HTR1B, HTR1E and HTR1F were highly conserved across vertebrates. Cell-based luciferase reporter assays showed that the three chicken HTRs were functional, capable of binding their natural ligands (5-HT) or selective agonists (CP94253, BRL54443, and LY344864) and inhibiting intracellular cAMP production in a dose-dependent manner. Moreover, activation of these receptors could stimulate the MAPK/ERK signaling cascade. Quantitative real-time PCR analyses revealed that HTR1B, HTR1E and HTR1F were primarily expressed in various brain regions and the pituitary. In cultured chicken pituitary cells, we found that LY344864 could significantly inhibit the secretion of PRL stimulated by vasoactive intestinal peptide (VIP) or forskolin, revealing that HTR1F might be involved in the release of prolactin in chicken. Our findings provide insights into the molecular mechanism and facilitate a better understanding of the serotonergic modulation via HTR1B, HTR1E and HTR1F in avian species. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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17 pages, 3040 KiB

Open AccessArticle

Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data

by Sunghyun Cho, Prabuddha Manjula, Minjun Kim, Eunjin Cho, Dooho Lee, Seung Hwan Lee, Jun Heon Lee and Dongwon Seo

Genes 2021, 12(6), 824; https://doi.org/10.3390/genes12060824 - 27 May 2021

Cited by 7 | Viewed by 3406

Abstract

Korean native chickens (KNCs) comprise an indigenous chicken breed of South Korea that was restored through a government project in the 1990s. The KNC population has not been developed well and has mostly been used to maintain purebred populations in the government research [...] Read more.

Korean native chickens (KNCs) comprise an indigenous chicken breed of South Korea that was restored through a government project in the 1990s. The KNC population has not been developed well and has mostly been used to maintain purebred populations in the government research institution. We investigated the genetic features of the KNC population in a selection signal study for the efficient improvement of this breed. We used 600K single nucleotide polymorphism data sampled from 191 KNCs (NG, 38; NL, 29; NR, 52; NW, 39; and NY, 33) and 54 commercial chickens (Hy-line Brown, 10; Lohmann Brown, 10; Arbor Acres, 10; Cobb, 12; and Ross, 12). Haplotype phasing was performed using EAGLE software as the initial step for the primary data analysis. Pre-processed data were analyzed to detect selection signals using the ‘rehh’ package in R software. A few common signatures of selection were identified in KNCs. Most quantitative trait locus regions identified as candidate regions were associated with traits related to reproductive organs, eggshell characteristics, immunity, and organ development. Block patterns with high linkage disequilibrium values were observed for LPP, IGF11, LMNB2, ERBB4, GABRB2, NTM, APOO, PLOA1, CNTN1, NTSR1, DEF3, CELF1, and MEF2D genes, among regions with confirmed selection signals. NL and NW lines contained a considerable number of selective sweep regions related to broilers and layers, respectively. We recommend focusing on improving the egg and meat traits of KNC NL and NW lines, respectively, while improving multiple traits for the other lines. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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17 pages, 6425 KiB

Open AccessArticle

miR-21-5p Regulates the Proliferation and Differentiation of Skeletal Muscle Satellite Cells by Targeting KLF3 in Chicken

by Donghao Zhang, Jinshan Ran, Jingjing Li, Chunlin Yu, Zhifu Cui, Felix Kwame Amevor, Yan Wang, Xiaosong Jiang, Mohan Qiu, Huarui Du, Qing Zhu, Chaowu Yang and Yiping Liu

Genes 2021, 12(6), 814; https://doi.org/10.3390/genes12060814 - 26 May 2021

Cited by 28 | Viewed by 3320

Abstract

The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) play an important role in the development of skeletal muscle. Our previous sequencing data showed that miR-21-5p is one of the most abundant miRNAs in chicken skeletal muscle. Therefore, in this study, the [...] Read more.

The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) play an important role in the development of skeletal muscle. Our previous sequencing data showed that miR-21-5p is one of the most abundant miRNAs in chicken skeletal muscle. Therefore, in this study, the spatiotemporal expression of miR-21-5p and its effects on skeletal muscle development of chickens were explored using in vitro cultured SMSCs as a model. The results in this study showed that miR-21-5p was highly expressed in the skeletal muscle of chickens. The overexpression of miR-21-5p promoted the proliferation of SMSCs as evidenced by increased cell viability, increased cell number in the proliferative phase, and increased mRNA and protein expression of proliferation markers including PCNA, CDK2, and CCND1. Moreover, it was revealed that miR-21-5p promotes the formation of myotubes by modulating the expression of myogenic markers including MyoG, MyoD, and MyHC, whereas knockdown of miR-21-5p showed the opposite result. Gene prediction and dual fluorescence analysis confirmed that KLF3 was one of the direct target genes of miR-21-5p. We confirmed that, contrary to the function of miR-21-5p, KLF3 plays a negative role in the proliferation and differentiation of SMSCs. Si-KLF3 promotes cell number and proliferation activity, as well as the cell differentiation processes. Our results demonstrated that miR-21-5p promotes the proliferation and differentiation of SMSCs by targeting KLF3. Collectively, the results obtained in this study laid a foundation for exploring the mechanism through which miR-21-5p regulates SMSCs. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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18 pages, 1301 KiB

Open AccessArticle

Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests

by Simon Jansen, Ulrich Baulain, Christin Habig, Faisal Ramzan, Jens Schauer, Armin Otto Schmitt, Armin Manfred Scholz, Ahmad Reza Sharifi, Annett Weigend and Steffen Weigend

Genes 2021, 12(5), 702; https://doi.org/10.3390/genes12050702 - 8 May 2021

Cited by 6 | Viewed by 2888

Abstract

Skeletal disorders, including fractures and osteoporosis, in laying hens cause major welfare and economic problems. Although genetics have been shown to play a key role in bone integrity, little is yet known about the underlying genetic architecture of the traits. This study aimed [...] Read more.

Skeletal disorders, including fractures and osteoporosis, in laying hens cause major welfare and economic problems. Although genetics have been shown to play a key role in bone integrity, little is yet known about the underlying genetic architecture of the traits. This study aimed to identify genes associated with bone breaking strength and bone mineral density of the tibiotarsus and the humerus in laying hens. Potentially informative single nucleotide polymorphisms (SNP) were identified using Random Forests classification. We then searched for genes known to be related to bone stability in close proximity to the SNPs and identified 16 potential candidates. Some of them had human orthologues. Based on our findings, we can support the assumption that multiple genes determine bone strength, with each of them having a rather small effect, as illustrated by our SNP effect estimates. Furthermore, the enrichment analysis showed that some of these candidates are involved in metabolic pathways critical for bone integrity. In conclusion, the identified candidates represent genes that may play a role in the bone integrity of chickens. Although further studies are needed to determine causality, the genes reported here are promising in terms of alleviating bone disorders in laying hens. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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19 pages, 3566 KiB

Open AccessArticle

Characterization of Four Orphan Receptors (GPR3, GPR6, GPR12 and GPR12L) in Chickens and Ducks and Regulation of GPR12 Expression in Ovarian Granulosa Cells by Progesterone

by Zejiao Li, Biying Jiang, Baolong Cao, Zheng Zhang, Jiannan Zhang, Juan Li, Yan Huang and Yajun Wang

Genes 2021, 12(4), 489; https://doi.org/10.3390/genes12040489 - 27 Mar 2021

Cited by 6 | Viewed by 3367

Abstract

The three structurally related orphan G protein-coupled receptors, GRP3, GPR6, and GPR12, are reported to be constitutively active and likely involved in the regulation of many physiological/pathological processes, such as neuronal outgrowth and oocyte meiotic arrest in mammals. However, the information regarding these [...] Read more.

The three structurally related orphan G protein-coupled receptors, GRP3, GPR6, and GPR12, are reported to be constitutively active and likely involved in the regulation of many physiological/pathological processes, such as neuronal outgrowth and oocyte meiotic arrest in mammals. However, the information regarding these orphan receptors in nonmammalian vertebrates is extremely limited. Here, we reported the structure, constitutive activity, and tissue expression of these receptors in two representative avian models: chickens and ducks. The cloned duck GPR3 and duck/chicken GPR6 and GPR12 are intron-less and encode receptors that show high amino acid (a.a.) sequence identities (66–88%) with their respective mammalian orthologs. Interestingly, a novel GPR12-like receptor (named GPR12L) sharing 66% a.a. identity to that in vertebrates was reported in the present study. Using dual-luciferase reporter assay and Western blot, we demonstrated that GPR3, GPR6, GPR12, and GPR12L are constitutively active and capable of stimulating the cAMP/PKA signaling pathway without ligand stimulation in birds (and zebrafish), indicating their conserved signaling property across vertebrates. RNA-seq data/qRT-PCR assays revealed that GPR6 and GPR12L expression is mainly restricted to the chicken brain, while GPR12 is highly expressed in chicken ovarian granulosa cells (GCs) and oocytes of 6 mm growing follicles and its expression in cultured GCs is upregulated by progesterone. Taken together, our data reveal the structure, function, and expression of GPR3, GPR6, GPR12, and GPR12L in birds, thus providing the first piece of evidence that GPR12 expression is upregulated by gonadal steroid (i.e., progesterone) in vertebrates. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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14 pages, 2602 KiB

Open AccessArticle

Identification of SNPs Associated with Stress Response Traits within High Stress and Low Stress Lines of Japanese Quail

by Steven Shumaker, Bhuwan Khatri, Stephanie Shouse, Dongwon Seo, Seong Kang, Wayne Kuenzel and Byungwhi Kong

Genes 2021, 12(3), 405; https://doi.org/10.3390/genes12030405 - 12 Mar 2021

Cited by 2 | Viewed by 2144

Abstract

Mitigation of stress is of great importance in poultry production, as chronic stress can affect the efficiency of production traits. Selective breeding with a focus on stress responses can be used to combat the effects of stress. To better understand the genetic mechanisms [...] Read more.

Mitigation of stress is of great importance in poultry production, as chronic stress can affect the efficiency of production traits. Selective breeding with a focus on stress responses can be used to combat the effects of stress. To better understand the genetic mechanisms driving differences in stress responses of a selectively bred population of Japanese quail, we performed genomic resequencing on 24 birds from High Stress (HS) and Low Stress (LS) lines of Japanese quail using Illumina HiSeq 2 × 150 bp paired end read technology in order to analyze Single Nucleotide Polymorphisms (SNPs) within the genome of each line. SNPs are common mutations that can lead to genotypic and phenotypic variations in animals. Following alignment of the sequencing data to the quail genome, 6,364,907 SNPs were found across both lines of quail. 10,364 of these SNPs occurred in coding regions, from which 2886 unique, non-synonymous SNPs with a SNP% ≥ 0.90 and a read depth ≥ 10 were identified. Using Ingenuity Pathway Analysis, we identified genes affected by SNPs in pathways tied to immune responses, DNA repair, and neurological signaling. Our findings support the idea that the SNPs found within HS and LS lines of quail could direct the observed changes in phenotype. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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18 pages, 1181 KiB

Open AccessArticle

High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds

by Prabuddha Manjula, Minjun Kim, Sunghyun Cho, Dongwon Seo and Jun Heon Lee

Genes 2021, 12(2), 240; https://doi.org/10.3390/genes12020240 - 8 Feb 2021

Cited by 9 | Viewed by 2939

Abstract

The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, [...] Read more.

The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) < 0.5) than the Set 2 markers (PIC = 0.4–0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (H_e) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, H_e = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, H_e = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the D_A distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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19 pages, 3362 KiB

Open AccessArticle

Identification of microRNA-Associated-ceRNA Networks Regulating Crop Milk Production in Pigeon (Columba livia)

by Pingzhuang Ge, Hui Ma, Yunlei Li, Aixin Ni, Adamu Mani Isa, Panlin Wang, Shixiong Bian, Lei Shi, Yunhe Zong, Yuanmei Wang, Linlin Jiang, Hailai Hagos, Jingwei Yuan, Yanyan Sun and Jilan Chen

Genes 2021, 12(1), 39; https://doi.org/10.3390/genes12010039 - 30 Dec 2020

Cited by 12 | Viewed by 3086

Abstract

Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate many biological events. However, the roles of miRNA and ceRNA in regulating crop milk production are still unknown. [...] Read more.

Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate many biological events. However, the roles of miRNA and ceRNA in regulating crop milk production are still unknown. In this study, we investigated the miRNAs expression profile of female pigeon crop, explored the potential key genes, and found the regulatory mechanisms of crop milk production. A total of 71 miRNAs were identified differentially expressed significantly. Meanwhile, miR-20b-5p, miR-146b-5p, miR-21-5p, and miR-26b-5p were found to be the key miRNAs regulating lactation. Target genes of these miRNAs participated mainly in cell development; protein and lipid synthesis; and ion signaling processes, such as cell-cell adhesion, epithelial cell morphogenesis, calcium signaling pathway, protein digestion, and absorption. In the ceRNA network, miR-193-5p was located in the central position, and miR-193-5p/CREBRF/LOC110355588, miR-460b-5p/GRHL2/MSTRG.132954, and miR-193-5p/PIK3CD/LOC110355588 regulatory axes were believed to affect lactation. Collectively, our findings enriched the miRNA expression profile of pigeon and provided novel insights into the microRNA-associated-ceRNA networks regulating crop milk production in pigeon. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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11 pages, 4457 KiB

Open AccessArticle

Production of Recombinant Monoclonal Antibodies in the Egg White of Gene-Targeted Transgenic Chickens

by Takehiro Mukae, Sho Okumura, Takuma Watanobe, Kyoko Yoshii, Takahiro Tagami and Isao Oishi

Genes 2021, 12(1), 38; https://doi.org/10.3390/genes12010038 - 30 Dec 2020

Cited by 21 | Viewed by 5380

Abstract

Increased commercial demand for monoclonal antibodies (mAbs) has resulted in the urgent need to establish efficient production systems. We previously developed a transgenic chicken bioreactor system that effectively produced human cytokines in egg whites using genome-edited transgenic chickens. Here, we describe the application [...] Read more.

Increased commercial demand for monoclonal antibodies (mAbs) has resulted in the urgent need to establish efficient production systems. We previously developed a transgenic chicken bioreactor system that effectively produced human cytokines in egg whites using genome-edited transgenic chickens. Here, we describe the application of this system to mAb production. The genes encoding the heavy and light chains of humanized anti-HER2 mAb, linked by a 2A peptide sequence, were integrated into the chicken ovalbumin gene locus using a CRISPR/Cas9 protocol. The knock-in hens produced a fully assembled humanized mAb in their eggs. The mAb expression level in the egg white was 1.4–1.9 mg/mL, as determined by ELISA. Furthermore, the antigen binding affinity of the anti-HER2 mAb obtained was estimated to be equal to that of the therapeutic anti-HER2 mAb (trastuzumab). In addition, antigen-specific binding by the egg white mAb was demonstrated by immunofluorescence against HER2-positive and -negative cells. These results indicate that the chicken bioreactor system can efficiently produce mAbs with antigen binding capacity and can serve as an alternative production system for commercial mAbs. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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26 pages, 5388 KiB

Open AccessArticle

Effect of 20(S)-Hydroxycholesterol on Multilineage Differentiation of Mesenchymal Stem Cells Isolated from Compact Bones in Chicken

by Roshan Adhikari, Chongxiao Chen and Woo Kyun Kim

Genes 2020, 11(11), 1360; https://doi.org/10.3390/genes11111360 - 17 Nov 2020

Cited by 11 | Viewed by 2742

Abstract

Bone health and body weight gain have significant economic and welfare importance in the poultry industry. Mesenchymal stem cells (MSCs) are common progenitors of different cell lineages such as osteoblasts, adipocytes, and myocytes. Specific oxysterols have shown to be pro-osteogenic and anti-adipogenic in [...] Read more.

Bone health and body weight gain have significant economic and welfare importance in the poultry industry. Mesenchymal stem cells (MSCs) are common progenitors of different cell lineages such as osteoblasts, adipocytes, and myocytes. Specific oxysterols have shown to be pro-osteogenic and anti-adipogenic in mouse and human MSCs. To determine the effect of 20(S)-hydroxycholesterol (20S) on osteogenic, adipogenic, and myogenic differentiation in chicken, mesenchymal stem cells isolated from compact bones of broiler chickens (cBMSCs) were subjected to various doses of 20S, and markers of lineage-specific mRNA were analyzed using real-time PCR and cell cytochemistry. Further studies were conducted to evaluate the molecular mechanisms involved in lineage-specific differentiation pathways. Like human and mouse MSCs, 20S oxysterol expressed pro-osteogenic, pro-myogenic, and anti-adipogenic differentiation potential in cBMSCs. Moreover, 20(S)-Hydroxycholesterol induced markers of osteogenic genes and myogenic regulatory factors when exposed to cBMSCs treated with their specific medium. In contrast, 20S oxysterol suppressed expression of adipogenic marker genes when exposed to cBMSCs treated with OA, an adipogenic precursor of cBMSCs. To elucidate the molecular mechanism by which 20S exerts its differentiation potential in all three lineages, we focused on the hedgehog signaling pathway. The hedgehog inhibitor, cyclopamine, completely reversed the effect of 20S induced expression of osteogenic and anti-adipogenic mRNA. However, there was no change in the mRNA expression of myogenic genes. The results showed that 20S oxysterol promotes osteogenic and myogenic differentiation and decreases adipocyte differentiation of cBMSCs. This study also showed that the induction of osteogenesis and adipogenesis inhibition in cBMSCs by 20S is mediated through the hedgehog signaling mechanism. The results indicated that 20(S) could play an important role in the differentiation of chicken-derived MSCs and provided the theory basis on developing an intervention strategy to regulate skeletal, myogenic, and adipogenic differentiation in chicken, which will contribute to improving chicken bone health and meat quality. The current results provide the rationale for the further study of regulatory mechanisms of bioactive molecules on the differentiation of MSCs in chicken, which can help to address skeletal health problems in poultry. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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14 pages, 1208 KiB

Open AccessArticle

Induction of Chicken Host Defense Peptides within Disease-Resistant and -Susceptible Lines

by Hyun-Jun Jang, Melissa Monson, Michael Kaiser and Susan J Lamont

Genes 2020, 11(10), 1195; https://doi.org/10.3390/genes11101195 - 14 Oct 2020

Cited by 8 | Viewed by 2615

Abstract

Host defense peptides (HDPs) are multifunctional immune molecules that respond to bacterial and viral pathogens. In the present study, bone marrow-derived cells (BMCs) and chicken embryonic fibroblasts (CEFs) were cultured from a Leghorn line (Ghs6) and Fayoumi line (M15.2), which are inbred chicken [...] Read more.

Host defense peptides (HDPs) are multifunctional immune molecules that respond to bacterial and viral pathogens. In the present study, bone marrow-derived cells (BMCs) and chicken embryonic fibroblasts (CEFs) were cultured from a Leghorn line (Ghs6) and Fayoumi line (M15.2), which are inbred chicken lines relatively susceptible and resistant to various diseases, respectively. The cells were treated by lipopolysaccharide (LPS) or polyinosinic-polycytidylic acid (poly(I:C)) and, subsequently, mRNA expression of 20 chicken HDPs was analyzed before and after the stimulation. At homeostasis, many genes differed between the chicken lines, with the Fayoumi line having significantly higher expression (p < 0.05) than the Leghorn line: AvBD1, 2, 3, 4, 6, and 7 in BMCs; CATH1, CATH3, and GNLY in CEFs; and AvDB5, 8, 9, 10, 11, 12, 13 in both BMCs and CEFs. After LPS treatment, the expression of AvBD1, 2, 3, 4, 5, 9, 12, CATH1, and CATHB1 was significantly upregulated in BMCs, but no genes changed expression in CEFs. After poly(I:C) treatment, AvBD2, 11, 12, 13, CATHB1 and LEAP2 increased in both cell types; CATH2 only increased in BMCs; and AvBD3, 6, 9, 14, CATH1, CATH3, and GNLY only increased in CEFs. In addition, AvBD7, AvBD14, CATH1, CATH2, GNLY, and LEAP2 showed line-specific expression dependent upon cell type (BMC and CEF) and stimulant (LPS and poly(I:C)). The characterization of mRNA expression patterns of chicken HDPs in the present study suggests that their functions may be associated with multiple types of disease resistance in chickens. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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21 pages, 6924 KiB

Open AccessArticle

Metabolomic Analysis of SCD during Goose Follicular Development: Implications for Lipid Metabolism

by Xin Yuan, Shenqiang Hu, Liang Li, Hehe Liu, Hua He and Jiwen Wang

Genes 2020, 11(9), 1001; https://doi.org/10.3390/genes11091001 - 26 Aug 2020

Cited by 11 | Viewed by 4844

Abstract

Stearoyl-CoA desaturase (SCD) is known to be an important rate-limiting enzyme in the production of monounsaturated fatty acids (MUFAs). However, the role of this enzyme in goose follicular development is poorly understood. To investigate the metabolic mechanism of SCD during goose follicular development, [...] Read more.

Stearoyl-CoA desaturase (SCD) is known to be an important rate-limiting enzyme in the production of monounsaturated fatty acids (MUFAs). However, the role of this enzyme in goose follicular development is poorly understood. To investigate the metabolic mechanism of SCD during goose follicular development, we observed its expression patterns in vivo and in vitro using quantitative reverse-transcription (qRT)-PCR. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine a cellular model of SCD function in granulosa cells (GCs) via SCD overexpression and knockdown. qRT-PCR analysis showed that SCD was abundantly expressed in the GC layer, and was upregulated in preovulatory follicles. Peak expression was found in F1 and prehierarchal follicles with diameters of 4–6 mm and 8–10 mm, respectively. We further found that mRNA expression and corresponding enzyme activity occur in a time-dependent oscillation pattern in vitro, beginning on the first day of GC culture. By LC-MS/MS, we identified numerous changes in metabolite activation and developed an overview of multiple metabolic pathways, 10 of which were associated with lipid metabolism and enriched in both the overexpressed and knockdown groups. Finally, we confirmed cholesterol and pantothenol or pantothenate as potential metabolite biomarkers to study SCD-related lipid metabolism in goose GCs. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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Review

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29 pages, 3524 KiB

Open AccessReview

Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken

by Sara Nematbakhsh, Chong Pei Pei, Jinap Selamat, Noordiana Nordin, Lokman Hakim Idris and Ahmad Faizal Abdull Razis

Genes 2021, 12(3), 414; https://doi.org/10.3390/genes12030414 - 13 Mar 2021

Cited by 62 | Viewed by 7549

Abstract

In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer’s health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic [...] Read more.

In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer’s health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic selection, feeding strategies, housing, and environmental strategies, as well as hormone supplementation. Recent investigations at the molecular level have revealed the significant role of the transcriptional and post-transcriptional regulatory networks and their interaction on modulating fat metabolism in chickens. At the transcriptional level, different transcription factors are known to regulate the expression of lipogenic and adipogenic genes through various signaling pathways, affecting chicken fat metabolism. Alternatively, at the post-transcriptional level, the regulatory mechanism of microRNAs (miRNAs) on lipid metabolism and deposition has added a promising dimension to understand the structural and functional regulatory mechanism of lipid metabolism in chicken. Therefore, this review focuses on the progress made in unraveling the molecular function of genes, transcription factors, and more notably significant miRNAs responsible for regulating adipogenesis, lipogenesis, and fat deposition in chicken. Moreover, a better understanding of the molecular regulation of lipid metabolism will give researchers novel insights to use functional molecular markers, such as miRNAs, for selection against excessive fat deposition to improve chicken production efficiency and meat quality. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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14 pages, 1583 KiB

Open AccessFeature PaperReview

Precise Genome Editing in Poultry and Its Application to Industries

by Jin Se Park, Kyung Youn Lee and Jae Yong Han

Genes 2020, 11(10), 1182; https://doi.org/10.3390/genes11101182 - 12 Oct 2020

Cited by 19 | Viewed by 5465

Abstract

Poultry such as chickens are valuable model animals not only in the food industry, but also in developmental biology and biomedicine. Recently, precise genome-editing technologies mediated by the CRISPR/Cas9 system have developed rapidly, enabling the production of genome-edited poultry models with novel traits [...] Read more.

Poultry such as chickens are valuable model animals not only in the food industry, but also in developmental biology and biomedicine. Recently, precise genome-editing technologies mediated by the CRISPR/Cas9 system have developed rapidly, enabling the production of genome-edited poultry models with novel traits that are applicable to basic sciences, agriculture, and biomedical industry. In particular, these techniques have been combined with cultured primordial germ cells (PGCs) and viral vector systems to generate a valuable genome-edited avian model for a variety of purposes. Here, we summarize recent progress in CRISPR/Cas9-based genome-editing technology and its applications to avian species. In addition, we describe further applications of genome-edited poultry in various industries. Full article

(This article belongs to the Special Issue Poultry Genetics, Breeding and Biotechnology)

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