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1.
BMC Genomics ; 20(1): 771, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31646968

RESUMO

BACKGROUND: The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms. RESULTS: We performed an exhaustive genome-wide search for significant SNP-SNP interactions associated with male birds' body weight (BW) (n = 475) at multiple time points (day of hatch (BW0) and 1, 3, 5, and 7 weeks (BW1, BW3, BW5, and BW7)). Statistical analysis detected 67, four, and two significant SNP pairs associated with BW0, BW1, and BW3, respectively, with a significance threshold at 8.67 × 10- 12 (Bonferroni-adjusted: 1%). Meanwhile, no significant SNP pairs associated with BW5 and BW7 were found. The SNP-SNP interaction networks of BW0, BW1, and BW3 were built and annotated. CONCLUSIONS: With strong annotated information and a strict significant threshold, SNP-SNP interactions underpinned the gene-gene interactions that might occur between chromosomes or within the same chromosome. Comparing and combing the networks, the results indicated that the genetic network for chicken body weight was dynamic and time-dependent.


Assuntos
Peso Corporal/genética , Galinhas/genética , Epistasia Genética , Polimorfismo de Nucleotídeo Único , Animais , Estudos de Associação Genética , Masculino , Fenótipo
2.
J Agric Food Chem ; 67(40): 11230-11235, 2019 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-31523955

RESUMO

Ochratoxin A (OTA) is a mycotoxin which could cause strong immunosuppressive toxicological effects in animals and humans. Heterophil extracellular traps (HETs) as a novel defense of chicken heterophils play an important role against pathogen infection. It has been reported that OTA can weaken the phagocytosis function of neutrophils. However, whether or not OTA shows immunosuppressive effects on HET release remains unclear. In the present study, we aim to first investigate the effects of OTA on HET release and then try to clarify the mechanisms in this process. OTA-induced HET structures were observed and analyzed by fluorescence confocal microscopy. The quantitative determination of OTA-induced HETs was measured by PicoGreen and a fluorescence microplate. The results clearly showed that OTA obviously induced the release of HET-like structures in heterophils, and these extracellular networks were composed by chromatin decorated with histones and neutrophil elastase. Reactive oxygen species (ROS) production was also increased in the process of OTA-induced HET formation. Furthermore, the inhibitors of NADPH oxidase, ERK [Formula: see text], and p38 MAPK signaling pathways significantly decreased OTA-induced HET formation. The abovementioned results suggest that OTA-induced HET formation is related to ROS production dependent on the activation of NADPH oxidase, ERK [Formula: see text], and p38 MAPK signaling pathways. Taken together, this study first shows that OTA possesses the ability to trigger HET formation, which provides our understanding of the host that continuously suffered OTA exposure leading to the hyporeactivity of the immune system against infection.


Assuntos
Galinhas/imunologia , MAP Quinases Reguladas por Sinal Extracelular/imunologia , Armadilhas Extracelulares/imunologia , NADPH Oxidases/imunologia , Neutrófilos/efeitos dos fármacos , Ocratoxinas/toxicidade , Espécies Reativas de Oxigênio/imunologia , Proteínas Quinases p38 Ativadas por Mitógeno/imunologia , Animais , Galinhas/genética , MAP Quinases Reguladas por Sinal Extracelular/genética , Armadilhas Extracelulares/genética , Sistema de Sinalização das MAP Quinases/efeitos dos fármacos , Masculino , NADPH Oxidases/genética , Neutrófilos/enzimologia , Neutrófilos/imunologia , Fagocitose , Proteínas Quinases p38 Ativadas por Mitógeno/genética
3.
Genet Sel Evol ; 51(1): 44, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31412777

RESUMO

BACKGROUND: Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens. RESULTS: We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb. CONCLUSIONS: A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes .


Assuntos
Galinhas/genética , Técnicas de Genotipagem , Sequenciamento Completo do Genoma , Animais , Cruzamento , Custos e Análise de Custo , Cruzamentos Genéticos , Conjuntos de Dados como Assunto , Feminino , Efeito Fundador , Técnicas de Genotipagem/economia , Masculino , Linhagem , Polimorfismo de Nucleotídeo Único , Software , Sequenciamento Completo do Genoma/economia
4.
J Agric Food Chem ; 67(35): 9727-9737, 2019 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-31398034

RESUMO

The present study aimed to search for chicken abdominal fat deposition-related polymorphisms within RB1 and to provide functional evidence for significantly associated genetic variants. Association analyses showed that 11 single nucleotide polymorphisms (SNPs) in intron 17 of RB1, were significantly associated with both abdominal fat weight (P < 0.05) and abdominal fat percentage (P < 0.05). Functional analysis revealed that the A allele of g.32828A>G repressed the transcriptional efficiency of RB1 in vitro, through binding nuclear factor-kappa B (NF-KB) and SRY-related HMG box protein 2 (SOX2). Furthermore, RB1 mRNA expression levels in the abdominal fat tissue of individuals with the A/A genotype of g.32828A>G were lower than those of individuals with the G/G genotype. Collectively, we propose that the intronic SNP g.32828A>G of RB1 is an obesity-associated variant that directly affects binding with NF-KB and SOX2, leading to changes in RB1 expression which in turn may influence chicken abdominal fat deposition.


Assuntos
Adiposidade , Proteínas Aviárias/metabolismo , Galinhas/metabolismo , NF-kappa B/metabolismo , Proteína do Retinoblastoma/genética , Proteína do Retinoblastoma/metabolismo , Fatores de Transcrição SOX/metabolismo , Gordura Abdominal/metabolismo , Alelos , Animais , Proteínas Aviárias/genética , Sítios de Ligação , Galinhas/genética , Galinhas/crescimento & desenvolvimento , Íntrons , NF-kappa B/genética , Polimorfismo de Nucleotídeo Único , Ligação Proteica , Fatores de Transcrição SOX/genética
5.
J Agric Food Chem ; 67(35): 9950-9957, 2019 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-31403788

RESUMO

Protein glycosylation is a ubiquitous posttranslational modification that modulates protein properties, thereby influencing bioactivities within a system. Duck egg white (DEW) proteins exhibit diverse biological properties compared with their chicken egg white (CEW) counterparts, which might be related to glycosylation. N-Glycoproteome analysis of DEW was conducted, and a total of 231 N-glycosites from 68 N-glycoproteins were identified. Gene ontology analysis was used to elucidate the biofunctions of DEW N-glycoproteins and compare them with those of CEW, which showed that the differences mostly involved molecular functions and biological processes. The biological functions of DEW N-glycoproteins were illuminated through bioinformatics analysis and comparison with CEW orthologues, which showed different allergenicities and antibacterial abilities. These divergences might be initiated by specific alterations in glycosylation, which can enhance the proteolysis resistance and protein steric hindrance. These results provide new insights for discovering the effects of N-glycosylation on biofunctions during the divergence of homologous proteins.


Assuntos
Galinhas/genética , Patos/genética , Proteínas do Ovo/química , Glicoproteínas/química , Animais , Evolução Biológica , Galinhas/metabolismo , Patos/metabolismo , Proteínas do Ovo/genética , Proteínas do Ovo/metabolismo , Clara de Ovo/química , Glicoproteínas/genética , Glicoproteínas/metabolismo , Glicosilação , Proteômica
6.
BMC Evol Biol ; 19(1): 137, 2019 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-31269894

RESUMO

BACKGROUND: Previously, we have demonstrated that genes involved in ovarian function are highly conserved throughout evolution. In this study, we aimed to document the conservation of genes involved in spermatogenesis from flies to vertebrates and their expression profiles in vertebrates. RESULTS: We retrieved 379 Drosophila melanogaster genes that are functionally involved in male reproduction according to their mutant phenotypes and listed their vertebrate orthologs. 83% of the fly genes have at least one vertebrate ortholog for a total of 625 mouse orthologs. This conservation percentage is almost twice as high as the 42% rate for the whole fly genome and is similar to that previously found for genes preferentially expressed in ovaries. Of the 625 mouse orthologs, we selected 68 mouse genes of interest, 42 of which exhibited a predominant relative expression in testes and 26 were their paralogs. These 68 mouse genes exhibited 144 and 60 orthologs in chicken and zebrafish, respectively, gathered in 28 groups of paralogs. Almost two thirds of the chicken orthologs and half of the zebrafish orthologs exhibited a relative expression ≥50% in testis. Finally, our focus on functional in silico data demonstrated that most of these genes were involved in the germ cell process, primarily in structure elaboration/maintenance and in acid nucleic metabolism. CONCLUSION: Our work confirms that the genes involved in germ cell development are highly conserved across evolution in vertebrates and invertebrates and display a high rate of conservation of preferential testicular expression among vertebrates. Among the genes highlighted in this study, three mouse genes (Lrrc46, Pabpc6 and Pkd2l1) have not previously been described in the testes, neither their zebrafish nor chicken orthologs. The phylogenetic approach developed in this study finally allows considering new testicular genes for further fundamental studies in vertebrates, including model species (mouse and zebrafish).


Assuntos
Galinhas/genética , Evolução Molecular , Testículo/metabolismo , Peixe-Zebra/genética , Animais , Drosophila melanogaster/genética , Masculino , Camundongos , Filogenia , Espermatogênese/genética , Testículo/citologia
7.
J Agric Food Chem ; 67(29): 8268-8278, 2019 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-31283221

RESUMO

Species authentication of meat and fish products is crucial to safeguard public health, economic investment, and religious sanctity. We developed a heptaplex polymerase chain reaction assay targeting short amplicon length (73-198 bp) for the simultaneous detection and differentiation of cow, buffalo, chicken, cat, dog, pig, and fish species in raw and processed food using species-specific primers targeting mitochondrial cytb, ND5, and 16s rRNA genes. Assay validation of adulterated and various heat-treated meatball matrices showed excellent stability and sensitivity under all processing conditions. The detection limit was 0.01-0.001 ng of DNA under pure states and 0.5% meat in meatball products. Buffalo was detected in 86.7% (13 out of 15) of tested commercial beef products, while chicken, pork, and fish products were found to be pure. The developed assay was efficient enough to detect target species simultaneously, even in highly degraded and processed food products at reduced time.


Assuntos
Contaminação de Alimentos/análise , Produtos da Carne/análise , Reação em Cadeia da Polimerase/métodos , Animais , Búfalos/genética , Gatos/genética , Bovinos/genética , Galinhas/genética , Cães/genética , Peixes/genética , Suínos/genética
8.
Anim Genet ; 50(5): 475-483, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31305959

RESUMO

Ten indigenous chicken breeds were originally distributed in Jiangxi Province, China, and they define a critical component of Chinese chicken genetic resources. We have investigated the population genetics of seven Jiangxi chicken breeds using 600K chicken BeadChip SNP data. To provide a genome-wide perspective for the population structure of all 10 Jiangxi chicken breeds, we herein genotyped 78 additional individuals from the seven breeds and 63 chickens from three uninvestigated breeds-Yugan Black (YG), Nancheng Black (NC) and Wanzai Yellow using 55K chicken SNP arrays. We then explored merged data of 17 101 SNPs from 235 individuals to infer the population structure of the 10 breeds. We showed that NC and YG are two regional populations of the same breed, as individuals from the two populations clustered together to form a branch separate from the other breeds in the neighbor-joining tree, they always grouped together in multidimensional principal component analyses and they displayed an identical pattern of ancestral lineage composition. Hence, NC and YG should be considered a single breed in the state-supported conservation scheme. Moreover, we conducted a genome scan for signatures of selection for black plumage. bayescan and hapflk analyses of two contrasting groups (three black-feathered breeds vs. six non-black-feathered breeds) consistently detected 25 putative regions under selection. Nine pigmentation- associated genes (DCT, SLC24A5, SLC30A4, MYO5A, CYP19A1, NADK2, SLC45A2, GNAQ and DCP2) reside within these regions, and these genes are interesting candidates for black plumage and provide a starting point for further identification of causative mutations for black feathers in chicken.


Assuntos
Galinhas/classificação , Galinhas/genética , Plumas/fisiologia , Animais , Galinhas/fisiologia , China , Variação Genética , Estudo de Associação Genômica Ampla , Pigmentação , Polimorfismo de Nucleotídeo Único
9.
Anim Genet ; 50(5): 460-474, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31355950

RESUMO

RNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to transcriptome diversity. Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species. Although this mechanism is well described in mammals, only a few studies have been performed in chicken. Here, candidate or potential RNA editing sites were identified in eight different tissues of chicken (brain, spleen, colon, lung, kidney, heart, testes and liver). We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-T sites, attesting to the lack of this type of editing mechanism in chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in a change in amino acids, showed a critical role in the nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site. Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the number and editing ratio of non-synonymous sites were higher than for those of synonymous sites. Interestingly, we found several tissue-specific edited genes, including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart, that were associated with functional processes relevant to the corresponding tissue. This finding highlights the importance of RNA editing in several chicken tissues, especially the brain, and establishes a foundation for further exploration of this process.


Assuntos
Galinhas/genética , Especificidade de Órgãos , Edição de RNA , Animais , Transcriptoma
10.
J Sci Food Agric ; 99(14): 6582-6588, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31328268

RESUMO

BACKGROUND: This study was conducted to investigate effects of dietary zinc methionine (Zn-Met) supplementation on laying performance, zinc (Zn) status, intestinal morphology, and Zn transporters in laying hens compared with zinc sulfate (ZnSO4 ). A total of 384 Hyline Grey laying hens (38 weeks old) with similar performance (1.42 ± 0.07 kg) were randomly allotted to four dietary treatments and fed with a basal diet (control) or the basal diet supplemented with Zn, either as Zn-Met at 40 and 80 mg Zn/kilogram diet or as ZnSO4 at 80 mg Zn/kilogram diet, for 10 weeks. RESULTS: There was no difference in egg weight, egg production, feed intake, and feed conversation ratio among all groups (P > 0.05). Compared with the control, Zn contents were increased (P < 0.05) in the liver, duodenum, and jejunum of laying hens fed diets supplemented with different Zn sources. There was no difference (P > 0.05) in Zn contents in liver, duodenum, and jejunum between diets supplemented with Zn-Met or ZnSO4 at 80 mg Zn/kilogram diet. Compared with the control and the ZnSO4 group (80 mg Zn/kilogram diet), supplementation with Zn-Met of 80 mg Zn/kilogram diet increased (P < 0.05) villus height, villus area, and villus height/crypt depth ratio but reduced (P < 0.05) crypt depth in jejunum. Expression of metallothionein messenger RNA of jejunum in the group fed a diet containing Zn-Met (80 mg Zn/kilogram diet) was higher (P < 0.05) than that in the control. CONCLUSION: These results indicated that Zn-Met has positive effects on the Zn status of liver, duodenum, and jejunum, intestinal morphology, and metallothionein messenger RNA expression in jejunum of laying hens compared with ZnSO4 . © 2019 Society of Chemical Industry.


Assuntos
Proteínas de Transporte/genética , Galinhas/crescimento & desenvolvimento , Galinhas/metabolismo , Intestinos/crescimento & desenvolvimento , Metionina/análogos & derivados , Compostos Organometálicos/administração & dosagem , Zinco/metabolismo , Ração Animal/análise , Animais , Proteínas de Transporte/metabolismo , Galinhas/genética , Suplementos Nutricionais/análise , Ovos/análise , Feminino , Intestinos/efeitos dos fármacos , Metionina/administração & dosagem , Metionina/metabolismo , Compostos Organometálicos/metabolismo , Zinco/análise
11.
Genet Sel Evol ; 51(1): 38, 2019 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-31286857

RESUMO

BACKGROUND: Pig and poultry breeding programs aim at improving crossbred (CB) performance. Selection response may be suboptimal if only purebred (PB) performance is used to compute genomic estimated breeding values (GEBV) because the genetic correlation between PB and CB performance ([Formula: see text]) is often lower than 1. Thus, it may be beneficial to use information on both PB and CB performance. In addition, the accuracy of GEBV of PB animals for CB performance may improve when the breed-of-origin of alleles (BOA) is considered in the genomic relationship matrix (GRM). Thus, our aim was to compare scenarios where GEBV are computed and validated by using (1) either CB offspring averages or individual CB records for validation, (2) either a PB or CB reference population, and (3) a GRM that either accounts for or ignores BOA in the CB individuals. For this purpose, we used data on body weight measured at around 7 (BW7) or 35 (BW35) days in PB and CB broiler chickens and evaluated the accuracy of GEBV based on the correlation GEBV with phenotypes in the validation population (validation correlation). RESULTS: With validation on CB offspring averages, the validation correlation of GEBV of PB animals for CB performance was lower with a CB reference population than with a PB reference population for BW35 ([Formula: see text] = 0.96), and about equal for BW7 ([Formula: see text] = 0.80) when BOA was ignored. However, with validation on individual CB records, the validation correlation was higher with a CB reference population for both traits. The use of a GRM that took BOA into account increased the validation correlation for BW7 but reduced it for BW35. CONCLUSIONS: We argue that the benefit of using a CB reference population for genomic prediction of PB animals for CB performance should be assessed either by validation on CB offspring averages, or by validation on individual CB records while using a GRM that accounts for BOA in the CB individuals. With this recommendation in mind, our results show that the accuracy of GEBV of PB animals for CB performance was equal to or higher with a CB reference population than with a PB reference population for a trait with an [Formula: see text] of 0.8, but lower for a trait with an [Formula: see text] of 0.96. In addition, taking BOA into account was beneficial for a trait with an [Formula: see text] of 0.8 but not for a trait with an [Formula: see text] of 0.96.


Assuntos
Peso Corporal/genética , Cruzamento , Galinhas/genética , Genômica/métodos , Alelos , Animais , Feminino , Genótipo , Masculino , Fenótipo , Valores de Referência
12.
J Sci Food Agric ; 99(13): 5890-5898, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31206714

RESUMO

BACKGROUND: Eggs are important foods in the daily diet of humans and have great biological activity and a high digestibility. Egg yolk is a good source of biologically active substances such as fatty acids, phospholipids, sterols and tocopherols. The eggs of seven chicken genotypes were analyzed for their chemical composition, and a detailed study of the lipids in egg yolk was conducted. RESULTS: Energy composition of the egg yolk and egg albumen was 29.06-30.51 MJ kg-1 and 19.77-20.93 MJ kg-1 respectively. Regarding their chemical composition: water ranged from 471.7 to 515.4 g kg-1 and 878.3-885.9 g kg-1 ; fat content in dry matter ranged from 607 to 647 g kg-1 and 6.7-11.6 g kg-1 ; protein varied from 302 to 331.7 g kg-1 and 823.6-892.5 g kg-1 ; ash ranged from 33.7 to 37.7 g kg-1 and 63.8-74.0 g kg-1 ; and nitrogen-free extracts ranged from 12.7 to 36.5 g kg-1 and 35.0-96.2 g kg-1 . The sterols and phospholipids in the yolk lipids were 16-26 g kg-1 and 59-127 g kg-1 . The main fatty acids in the lipids were oleic (39.1-47.3%) and palmitic (26.0-35.5%) acids. Cholesterol in the yolk lipids ranged from 15.9 to 25.9 g kg-1 . Phosphatidylcholine (389-573 g kg-1 ), phosphatidylethanolamine (219-355 g kg-1 ) and phosphatidylinositol (112-284 g kg-1 ) were the main phospholipids. The content of saturated fatty acids in the phospholipids was significantly higher than that in triacylglycerols. CONCLUSION: Small variations in the chemical composition of eggs from seven different genotypes were observed. Significant differences in the fatty acid compositions of the main classes of phospholipids and the triacylglycerol fraction were established. © 2019 Society of Chemical Industry.


Assuntos
Galinhas/genética , Ovos/análise , Animais , Colesterol/análise , Gema de Ovo/química , Ácidos Graxos/análise , Genótipo , Nutrientes/análise , Fosfolipídeos/análise , Triglicerídeos/análise
13.
Food Chem ; 295: 395-402, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31174774

RESUMO

A simple and rapid method for animal species identification to prevent food adulteration based on mitochondrial DNA using two independent multiplex polymerase chain reactions (PCRs) and microchip electrophoresis was developed. This method was designed to identify fourteen domestic animals (Group I: cattle, donkey, dog, fox, raccoon-dog, deer and horse; Group II: pig, sheep, goat, chicken, duck, cat and mouse) simultaneously using ten pairs of primers and three of which were degenerate primers. Sequences for species-specific primers were generated based on mitochondrial genes, including 12S rRNA, 16S rRNA, ND2 and CO I. This method was validated in terms of the specificity, sensitivity and practicability, and the developed multiplex PCR method was able to correctly identify animal species of raw meats and processed meat products. The detection limits of two multiplex PCRs were 0.02 ng DNA for animal species in Group I and 0.2 ng DNA for Group II, respectively.


Assuntos
Análise de Alimentos/métodos , Contaminação de Alimentos/análise , Carne/análise , Reação em Cadeia da Polimerase Multiplex/métodos , Animais , Bovinos/genética , Galinhas/genética , Primers do DNA , DNA Mitocondrial/genética , Cervos/genética , Patos/genética , Equidae/genética , Análise de Alimentos/instrumentação , Genes Mitocondriais , Cabras/genética , Cavalos/genética , Camundongos/genética , Reação em Cadeia da Polimerase Multiplex/instrumentação , RNA Ribossômico , RNA Ribossômico 16S , Ovinos/genética , Especificidade da Espécie , Suínos/genética
14.
Genet Sel Evol ; 51(1): 25, 2019 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-31164080

RESUMO

BACKGROUND: The cuticle is an invisible glycosylated protein layer that covers the outside of the eggshell and forms a barrier to the transmission of microorganisms. Cuticle-specific staining and in situ absorbance measurements have been used to quantify cuticle deposition in several pure breeds of chicken. For brown eggs, a pre-stain and a post-stain absorbance measurement is required to correct for intrinsic absorption by the natural pigment. For white eggs, a post-stain absorbance measurement alone is sufficient to estimate cuticle deposition. The objective of the research was to estimate genetic parameters and provide data to promote adoption of the technique to increase cuticle deposition and reduce vertical transmission of microorganisms. RESULTS: For all pure breeds examined here, i.e. Rhode Island Red, two White Leghorns, White Rock and a broiler breed, the estimate of heritability for cuticle deposition from a meta-analysis was moderately high (0.38 ± 0.04). In the Rhode Island Red breed, the estimate of the genetic correlation between measurements recorded at early and late times during the egg-laying period was ~ 1. There was no negative genetic correlation between cuticle deposition and production traits. Estimates of the genetic correlation of cuticle deposition with shell color ranged from negative values or 0 in brown-egg layers to positive values in white- or tinted-egg layers. Using the intrinsic fluorescence of tryptophan in the cuticle proteins to quantify the amount of cuticle deposition failed because of complex quenching processes. Tryptophan fluorescence intensity at 330 nm was moderately heritable, but there was no evidence of a non-zero genetic correlation with cuticle deposition. This was complicated furthermore by a negative genetic correlation of fluorescence with color in brown eggs, due to the quenching of tryptophan fluorescence by energy transfer to protoporphyrin pigment. We also confirmed that removal of the cuticle increased reflection of ultraviolet wavelengths from the egg. CONCLUSIONS: These results provide additional evidence for the need to incorporate cuticle deposition into breeding programs of egg- and meat-type birds in order to reduce vertical and horizontal transmission of potentially pathogenic organisms and to help improve biosecurity in poultry.


Assuntos
Cruzamento/métodos , Galinhas/genética , Casca de Ovo/metabolismo , Polimorfismo Genético , Animais , Resistência à Doença/genética , Casca de Ovo/microbiologia , Feminino , Masculino , Doenças das Aves Domésticas/genética
15.
Nature ; 571(7766): 505-509, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31243369

RESUMO

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento , Organogênese/genética , Transcriptoma/genética , Animais , Evolução Biológica , Galinhas/genética , Feminino , Humanos , Macaca mulatta/genética , Masculino , Camundongos , Gambás/genética , Coelhos , Ratos
16.
Nature ; 571(7766): 510-514, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31243368

RESUMO

Although many long noncoding RNAs (lncRNAs) have been identified in human and other mammalian genomes, there has been limited systematic functional characterization of these elements. In particular, the contribution of lncRNAs to organ development remains largely unexplored. Here we analyse the expression patterns of lncRNAs across developmental time points in seven major organs, from early organogenesis to adulthood, in seven species (human, rhesus macaque, mouse, rat, rabbit, opossum and chicken). Our analyses identified approximately 15,000 to 35,000 candidate lncRNAs in each species, most of which show species specificity. We characterized the expression patterns of lncRNAs across developmental stages, and found many with dynamic expression patterns across time that show signatures of enrichment for functionality. During development, there is a transition from broadly expressed and conserved lncRNAs towards an increasing number of lineage- and organ-specific lncRNAs. Our study provides a resource of candidate lncRNAs and their patterns of expression and evolutionary conservation across mammalian organ development.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento , Especificidade de Órgãos/genética , Organogênese/genética , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Especificidade da Espécie , Animais , Atlas como Assunto , Galinhas/genética , Evolução Molecular , Feminino , Humanos , Macaca mulatta/genética , Masculino , Camundongos , Gambás/genética , Proteínas/genética , RNA Longo não Codificante/análise , Coelhos , Ratos
17.
Genet Sel Evol ; 51(1): 31, 2019 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-31238874

RESUMO

BACKGROUND: Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In this study, we recorded several production traits, feed intake, body weight, digestibility, and egg quality of 400 commercial white egg-laying hens before and during a 4-week heat treatment. For the phenotypes that had estimated heritabilities (using 600k SNP chip data) higher than 0, SNP associations were tested using the same 600k genotype data. RESULTS: Seventeen phenotypes had heritability estimates higher than 0, including measurements at various time points for feed intake, feed efficiency, body weight, albumen weight, egg quality expressed in Haugh units, egg mass, and also for change in egg mass from prior to heat exposure to various time points during the 4-week heat treatment. Quantitative trait loci (QTL) were identified for 10 of these 17 phenotypes. Some of the phenotypes shared QTL including Haugh units before heat exposure and after 4 weeks of heat treatment. CONCLUSIONS: Estimated heritabilities differed from 0 for 17 traits, which indicates that they are under genetic control and that there is potential for improving these traits through selective breeding. The association of different QTL with the same phenotypes before heat exposure and during heat treatment indicates that genomic control of traits under heat stress is distinct from that under thermoneutral conditions. This study contributes to the knowledge on the genomic control of response to heat stress in laying hens.


Assuntos
Galinhas/genética , Resposta ao Choque Térmico/genética , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável , Agricultura , Criação de Animais Domésticos , Animais , Galinhas/fisiologia , Ovos , Feminino , Temperatura Alta , Oviposição , Fenótipo
18.
Poult Sci ; 98(8): 3114-3118, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31115461

RESUMO

The blue-eggshell and dwarf traits have an important economic value in poultry production. Using a genetic aggregation-based strategy, the molecular marker-assisted selection technology was jointly used to provide a rapid breeding method for pure strain chickens simultaneously with hens exhibiting the blue-eggshell and dwarf traits. Overall, 80 male dwarf chickens and 1,000 hybrid blue-eggshell hens (F0) were used for the hybridization experiment. Subsequently, the crossing of F1 or F2 chicks was performed in succession. The F1 and F2 chicks were respectively detected by the joint molecular markers of the solute carrier organic anion transporter family, namely, 1B3 (SLCO1B3) and the growth hormone receptor (GHR) genes, which relate to blue-eggshell and dwarf traits. Meanwhile, the selection of blue-eggshell and dwarf phenotypes was used to validate the data obtained by the molecular markers. The results showed that F1 chicks included the heterozygous and wild-type of SLCO1B3, as well as the homozygous (hens) and heterozygous (roosters) of GHR. However, F2 chicks included 3 different genotypes of both SLCO1B3 and GHR. Ultimately, 196 F1 roosters (concurrently with heterozygous genotype of SLCO1B3 and GHR) and 1,073 F1 hens (concurrently with heterozygous genotype of SLCO1B3 and homozygous genotype of GHR) were obtained from the initial 10,040 F1 chicks. Further, 27 F2 roosters and 345 F2 hens, which simultaneously carried the homozygous genotype of SLCO1B3 and GHR, were screened from the initial 6,000 F2 chicks. Data obtained on the blue-eggshell and dwarf phenotypes were consistent with the results by molecular markers. Similarly, the purity verification of the strain obtained through 2 crossing experiments (F0♂ × F2♀ and F2♂ × F2♀) revealed that all chickens had the blue-eggshell and dwarf traits, supporting that the obtained F2 strain was pure. In summary, for the first time, we successfully bred a pure strain chicken with blue-eggshell and dwarf traits by jointly using the molecular markers of the SLCO1B3 and GHR genes. Our study provides a new method for the rapid cultivation of new chicken strains.


Assuntos
Galinhas/genética , Nanismo/genética , Casca de Ovo , Hibridização Genética , Animais , Cruzamento/métodos , Cor , Feminino , Masculino , Receptores da Somatotropina/genética , Membro 1B3 da Família de Transportadores de Ânion Orgânico Carreador de Soluto/genética
19.
BMC Genomics ; 20(1): 345, 2019 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-31064348

RESUMO

BACKGROUND: Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been formed and those represent the diversity of the species. However, other than the natural evolutionary forces, management practices (including those that threaten the persistence of genetic diversity) following domestication have shaped the genetic make-up of and diversity between today's chicken breeds. As part of the SYNBREED project, samples from a wide variety of chicken populations have been collected across the globe and were genotyped with a high density SNP array. The panel consists of the wild type, commercial layers and broilers, indigenous village/local type and fancy chicken breeds. The SYNBREED chicken diversity panel (SCDP) is made available to serve as a public basis to study the genetic structure of chicken diversity. In the current study we analyzed the genetic diversity between and within the populations in the SCDP, which is important for making informed decisions for effective management of farm animal genetic resources. RESULTS: Many of the fancy breeds cover a wide spectrum and clustered with other breeds of similar supposed origin as shown by the phylogenetic tree and principal component analysis. However, the fancy breeds as well as the highly selected commercial layer lines have reduced genetic diversity within the population, with the average observed heterozygosity estimates lower than 0.205 across their breeds' categories and the average proportion of polymorphic loci lower than 0.680. We show that there is still a lot of genetic diversity preserved within the wild and less selected African, South American and some local Asian and European breeds with the average observed heterozygosity greater than 0.225 and the average proportion of polymorphic loci larger than 0.720 within their breeds' categories. CONCLUSIONS: It is important that such highly diverse breeds are maintained for the sustainability and flexibility of future chicken breeding. This diversity panel provides opportunities for exploitation for further chicken molecular genetic studies. With the possibility to further expand, it constitutes a very useful community resource for chicken genetic diversity research.


Assuntos
Cruzamento , Galinhas/genética , Biologia Computacional/métodos , Marcadores Genéticos , Genética Populacional , Polimorfismo de Nucleotídeo Único , Animais , Galinhas/classificação , Feminino , Genótipo , Masculino , Filogenia
20.
Br Poult Sci ; 60(4): 366-372, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31046426

RESUMO

1. In current breeding programmes, uniformity of end products and producing animals that are robust to environmental challenges are desirable. Several studies have provided evidence of the presence of genetic heterogeneity of residual variance and proposed that it could be possible to increase uniformity of livestock productions by selection. The present study aimed to define the micro environmental sensitivity of dual-purpose chickens for body weight at hatch. 2. The data set consisted of 24,321 female and 21,547 male chickens' records of hatch weight from 19 consecutive generations of Mazandaran fowl. The statistical analysis was carried out in a two-step approach: first, an animal model was fitted to the data and then, the impact of additive genetic effects on the residual variance of the studied trait was investigated. 3. The estimate of heritability for body weight at hatch was in the range of 0.23-0.25 for female and 0.14-0.16 for male offspring, respectively. The proportion of maternal environmental variance to phenotypic variance ranged from 0.24 to 0.27 for female and 0.17 to 0.24 for male offspring. Heritabilities in females were higher than males. Estimates of the heritability of residual variance ranged between 0.067 and 0.090. The genetic coefficients of variation were high ranging between 0.83 and 0.86. Genetic correlations between hatch weight and its residual variance estimates from bivariate analysis were -0.39 and -0.44 in females and males, respectively. 4. The results suggest that there is an opportunity to simultaneously improve body weight and the uniformity of body weight by selecting for lower residual variance in native chickens.


Assuntos
Animais Recém-Nascidos/fisiologia , Peso Corporal/genética , Galinhas/fisiologia , Heterogeneidade Genética , Animais , Animais Recém-Nascidos/genética , Galinhas/genética , Feminino , Irã (Geográfico) , Masculino
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