Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers

Growth performance is an important economic trait in chicken. MicroRNAs (miRNAs) have been shown to play important roles in various biological processes, but their functions in chicken growth are not yet clear. To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two-tail samples (highest and lowest body weight) from Recessive White Rock (WRR) and Xinghua Chickens (XH) were performed on high throughput small RNA deep sequencing. In this study, a total of 921 miRNAs were identified, including 733 known mature miRNAs and 188 novel miRNAs. There were 200, 279, 257 and 297 differentially expressed miRNAs in the comparisons of WRRh vs. WRRl, WRRh vs. XHh, WRRl vs. XHl, and XHh vs. XHl group, respectively. A total of 22 highly differentially expressed miRNAs (fold change > 2 or < 0.5; p-value < 0.05; q-value < 0.01), which also have abundant expression (read counts > 1000) were found in our comparisons. As far as two analyses (WRRh vs. WRRl, and XHh vs. XHl) are concerned, we found 80 common differentially expressed miRNAs, while 110 miRNAs were found in WRRh vs. XHh and WRRl vs. XHl. Furthermore, 26 common miRNAs were identified among all four comparisons. Four differentially expressed miRNAs (miR-223, miR-16, miR-205a and miR-222b-5p) were validated by quantitative real-time RT-PCR (qRT-PCR). Regulatory networks of interactions among miRNAs and their targets were constructed using integrative miRNA target-prediction and network-analysis. Growth hormone receptor (GHR) was confirmed as a target of miR-146b-3p by dual-luciferase assay and qPCR, indicating that miR-34c, miR-223, miR-146b-3p, miR-21 and miR-205a are key growth-related target genes in the network. These miRNAs are proposed as candidate miRNAs for future studies concerning miRNA-target function on regulation of chicken growth.

MicroRNA-23b Promotes Avian Leukosis Virus Subgroup J (ALV-J) Replication by Targeting IRF1

Avian leukosis virus subgroup J (ALV-J) can cause several different leukemia-like proliferative diseases in the hemopoietic system of chickens. Here, we investigated the transcriptome profiles and miRNA expression profiles of ALV-J-infected and uninfected chicken spleens to identify the genes and miRNAs related to ALV-J invasion. In total, 252 genes and 167 miRNAs were differentially expressed in ALV-J-infected spleens compared to control uninfected spleens. miR-23b expression was up-regulated in ALV-J-infected spleens compared with the control spleens, and transcriptome analysis revealed that the expression of interferon regulatory factor 1 (IRF1) was down-regulated in ALV-J-infected spleens compared to uninfected spleens. A dual-luciferase reporter assay showed that IRF1 was a direct target of miR-23b. miR-23b overexpression significantly (P = 0.0022) decreased IRF1 mRNA levels and repressed IRF1-3′-UTR reporter activity. In vitro experiments revealed that miR-23b overexpression strengthened ALV-J replication, whereas miR-23b loss of function inhibited ALV-J replication. IRF1 overexpression inhibited ALV-J replication, and IRF1 knockdown enhanced ALV-J replication. Moreover, IRF1 overexpression significantly (P = 0.0014) increased IFN-β expression. In conclusion, these results suggested that miR-23b may play an important role in ALV-J replication by targeting IRF1.

Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome

Amino acids are utilized with different frequencies both among species and among genes within the same genome. Up to date, no study on the amino acid usage pattern of chicken has been performed. In the present study, we carried out a systematic examination of the amino acid usage in the chicken proteome. Our data indicated that the relative amino acid usage is positively correlated with the tRNA gene copy number. GC contents, including GC1, GC2, GC3, GC content of CDS and GC content of the introns, were correlated with the most of the amino acid usage, especially for GC rich and GC poor amino acids, however, multiple linear regression analyses indicated that only approximately 10–40% variation of amino acid usage can be explained by GC content for GC rich and GC poor amino acids. For other intermediate GC content amino acids, only approximately 10% variation can be explained. Correspondence analyses demonstrated that the main factors responsible for the variation of amino acid usage in chicken are hydrophobicity, aromaticity and genomic GC content. Gene expression level also influenced the amino acid usage significantly. We argued that the amino acid usage of chicken proteome likely reflects a balance or near balance between the action of selection, mutation, and genetic drift.

The transient expression of miR-203 and its inhibiting effects on skeletal muscle cell proliferation and differentiation

Previous studies have shown that miR-203 is a skin-specific microRNA (miRNA) with a profound role in skin cell differentiation. However, emerging microarray and deep sequencing data revealed that miR-203 is also expressed in embryonic skeletal muscle and myoblasts. In this study, we found that miR-203 was transiently upregulated in chicken embryos on days 10 to 16 (E10-E16) and was sharply downregulated and even not expressed after E16 in chicken embryonic skeletal muscle. Histological profiles and weight variations of embryo skeletal muscle revealed that miR-203 expression is correlated with muscle development. In vitro experiments showed that miR-203 exhibited downregulated expression during myoblast differentiation into myotubes. miR-203 overexpression inhibited myoblast proliferation and differentiation, whereas its loss-of-function increased myoblast proliferation and differentiation. During myogenesis, miR-203 can target and inhibit the expression of c-JUN and MEF2C, which were important for cell proliferation and muscle development, respectively. The overexpression of c-JUN significantly promoted myoblast proliferation. Conversely, knockdown of c-JUN by siRNA suppressed myoblast proliferation. In addition, the knockdown of MEF2C by siRNA significantly inhibited myoblast differentiation. Altogether, these data not only suggested that the expression of miR-203 is transitory during chicken skeletal muscle development but also showed a novel role of miR-203 in inhibiting skeletal muscle cell proliferation and differentiation by repressing c-JUN and MEF2C, respectively.

NHE1 gene associated with avian leukosis virus subgroup J infection in chicken

As a kind of binding protein, the type 1 Na(+)/H(+) exchanger (NHE1) is a receptor for the highly pathogenic Avian leukosis viruses-J subgroup (ALV-J) in chicken. In order to investigate the potential effect of chicken NHE1 gene on leukosis, we compared its expression between ALV-J-affected and -unaffected chicken, screened variations across the whole gene, and then performed association analysis with ALV-J affected/unaffected trait in three un-related chicken populations. We found that the NHE1 gene expressed in four immune tissues including spleen, bursa fabricius, liver, and thymus, and its expression was significantly up-regulated in liver and thymus of ALV-J-affected chickens (with leukosis phenotype) compared to -unaffected ones (ALV-J-negative controls). Thirty-six single nucleotide polymorphisms (SNP) were identified in a 6,105 bp region of the chicken NHE1 gene, giving rise to every 170 bp per SNP. Two SNP of g.4405A>G and g.5886C>G were genotyped with PCR-RFLP method. Results showed that g.4405A>G was significantly associated (P < 0.05) with ALV-J infection in all of the three chicken populations, including White Recessive Rock (WRR), Dwarf Yellow (DY) and Shiki Yellow (SY), while g.5886C>G was significantly associated (P < 0.05) with ALV-J infection in SY. These results indicated that the NHE1 gene was related to ALV-J infection in chicken.

DNA methylome in spleen of avian pathogenic Escherichia coli-challenged broilers and integration with mRNA expression

Avian pathogenic Escherichia coli (APEC) are responsible for heavy economic losses in poultry industry. Here we investigate DNA methylome of spleen and identify functional DNA methylation changes related to host response to APEC among groups of non-challenged chickens (NC), challenged with mild (MD) and severe pathology (SV). DNA methylation was enriched in the gene bodies and repeats. Promoter and CGIs are hypomethylated. Integration analysis revealed 22, 87, and 9 genes exhibiting inversely changed DNA methylation and gene expression in NC vs. MD, NC vs. SV, and MD vs. SV, respectively. IL8, IL2RB, and IL1RAPL1 were included. Gene network analysis suggested that besides inflammatory response, other networks and pathways such as organismal injury and abnormalities, cell signaling and molecular transport, are probably related to host response to APEC infection. Moreover, methylation changes in cell cycle processes might contribute to the lesion phenotype differences between MD and SV.

Overview of Genomic Insights into Chicken Growth Traits Based on Genome-Wide Association Study and microRNA Regulation

Over the two past decades, a significant number of studies have observed animal growth traits to examine animal genetic mechanisms due to their ease of measurement and high heritability. Chicken which has a significant impact on fundamental biology is a major source of protein worldwide, making it an ideal model for examining animal growth trait development. The genetic mechanisms of chicken growth traits have been studied using quantitative trait loci mapping through genome-scan and candidate gene approaches, genome-wide association studies (GWAS), comparative genomic strategies, microRNA (miRNA) regulation of growth development analysis, and epigenomic analysis. This review focuses on chicken GWAS and miRNA regulation of growth traits. Several recently published GWAS reports showed that most genome-wide significant single nucleotide polymorphisms are located on chromosomes 1 and 4 in chickens. Chicken growth, particularly skeletal muscle growth and development, is greatly regulated by miRNA. Using dwarf and normal chickens, let-7b was found to be involved in determining chicken dwarf phenotypes by regulating growth hormone receptor gene expression.

Overexpression of TDRP1 gene in swine testis cell and its global transcriptome analysis

The testis development-related protein-1 (TDRP1) gene was first isolated in spermatogenic cells of testis, and was related to the spermatogenesis and reproduction traits in mammals. This study was performed to further analyze the function of the pig TDRP1 gene by microarray screening of the TDRP1-overexpressed swine testis (ST) cell. After transfection of the recombinant pcDNA3.1-TDRP1 vector into the ST cell, the expression of the TDRP1 gene continued to increase at 12, 24, and 36 h post-transfection, and then decreased at 48 h, as indicated by both the fluorescence signal and quantitative PCR. Microarray screening revealed 529 upregulated and 1086 downregulated genes in TDRP1-overexpressed ST cells at 24 h post-transfection (TD-24) versus untransfected control (TD-blank), and 764 upregulated and 858 downregulated genes at 36 h post-transfection (TD-36) versus TD-blank, as well as 720 upregulated and 375 downregulated genes in TD-36 versus TD-24. As far as three contrasts were totally considered, 29 common genes were identified, including 17 upregulated genes and 12 downregulated ones. Further, Kyoto encyclopedia of genes and genomes prediction analysis indicated that some of these 29 differently expressed genes were involved in a number of biological pathways. Among the 17 upregulated genes, the PMAIP1 gene was significantly enriched in the p53 signaling pathway, and the others were the DDIT3 gene in the mitogen-activated protein kinases (MAPK) signaling pathway, the PPP1R3C gene in the insulin signaling pathway, as well as the GADD45A gene in the p53 signaling pathway, MAPK signaling pathway, and the cell cycle. Among the 12 downregulated genes, the SFRP4 gene was significantly enriched in the Wnt signaling pathway. This study indicated that the TDRP1 gene regulated PMAIP1, GADD45A, DDIT3, and PPP1R3C expression, and these genes involving p53, MAPK, insulin, and Wnt signaling pathways are related to spermatogenesis or reproduction in pig.

Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers

INTRODUCTION

Growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, in this study, we aim to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes for chicken growth. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation pattern in high and low tails of Recessive White Rock (WRR(h); WRR(l)) and that of Xinhua Chickens (XH(h); XH(l)) at 7 weeks of age. The results showed that the average methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than that of UTRs and exons. Moreover, different methylation levels were observed in different repeat types with the highest in LINE/CR1. Methylated CGIs were prominently distributed in the intergenic regions and were enriched in the size ranging 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes of WRR(h) Vs. WRR(l), 5,599 of XH(h) Vs. XH(l), 4,204 of WRR(h) Vs. XH(h), as well as 7,301 of WRR(l) Vs. XH(l). Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRR(h) Vs. WRR(l) and XH(h) Vs. XH(l)), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRR(h) Vs. XH(h) and WRR(l) Vs. XH(l)). Further analysis showed that overall 75 genes exhibited altered DNA methylation in all four contrasts, which included some well-known growth factors of IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3. In addition, we validate the MeDIP-seq results by bisulfite sequencing in some regions.

CONCLUSIONS

This study revealed the global DNA methylation pattern of chicken muscle, and identified candidate genes that potentially regulate muscle development at 7 weeks of age at methylation level.

MicroRNA profile analysis on duck feather follicle and skin with high-throughput sequencing technology

Skin acts an important protection role in animal survival and it evolves with the animal divergence. We identified the conserved miRNA families of skin among duck and other species. Cluster analysis showed that the species with similar skin characteristics were clustered into the same group, indicating miRNAs are important in skin function and skin evolution. The miRNA profiles demonstrated that different miRNA regulation mechanism may exist in contour feather follicles (with the surrounding skin) and down feather follicles (with the surrounding skin). Comparing the highly abundant miRNAs with those of mammalian hair follicles and skins, different miRNAs and miRNA families were found, suggesting the different ways in feather follicles and mammalian hair follicles. Bioinformatics prediction indicated that seven miRNAs probably targeted the genes of Wnt/β-catenin, Shh/BMP and Notch pathways which were important in feather morphogenesis. Further analysis should be conducted to experimentally validate the relationships between miRNAs and their predicted target genes because the target genes were based exclusively upon the bioinformatics.

Deep sequencing-based transcriptome analysis of chicken spleen in response to avian pathogenic Escherichia coli (APEC) infection

Avian pathogenic Escherichia coli (APEC) leads to economic losses in poultry production and is also a threat to human health. The goal of this study was to characterize the chicken spleen transcriptome and to identify candidate genes for response and resistance to APEC infection using Solexa sequencing. We obtained 14422935, 14104324, and 14954692 Solexa read pairs for non-challenged (NC), challenged-mild pathology (MD), and challenged-severe pathology (SV), respectively. A total of 148197 contigs and 98461 unigenes were assembled, of which 134949 contigs and 91890 unigenes match the chicken genome. In total, 12272 annotated unigenes take part in biological processes (11664), cellular components (11927), and molecular functions (11963). Summing three specific contrasts, 13650 significantly differentially expressed unigenes were found in NC Vs. MD (6844), NC Vs. SV (7764), and MD Vs. SV (2320). Some unigenes (e.g. CD148, CD45 and LCK) were involved in crucial pathways, such as the T cell receptor (TCR) signaling pathway and microbial metabolism in diverse environments. This study facilitates understanding of the genetic architecture of the chicken spleen transcriptome, and has identified candidate genes for host response to APEC infection.

Let-7b regulates the expression of the growth hormone receptor gene in deletion-type dwarf chickens

BACKGROUND

A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. We used microarray techniques to determine microRNA (miRNA) and mRNA expression profiles of GHR in the skeletal muscles of 14-day-old embryos as well as 7-week-old deletion-type dwarf and normal-type chickens. Our aim was to elucidate the miRNA regulation of GHR expression with respect to growth inhibition and fat deposition.

RESULTS

At the same developmental stages, different expression profiles in skeletal muscles of dwarf and normal chickens occurred for four miRNAs (miR-1623, miR-181b, let-7b, and miR-128). At different developmental stages, there was a significant difference in the expression profiles of a greater number of miRNAs. Eleven miRNAs were up-regulated and 18 down-regulated in the 7-week-old dwarf chickens when compared with profiles in 14-day-old embryos. In 7-week-old normal chickens, seven miRNAs were up-regulated and nine down-regulated compared with those in 14-day-old embryos. In skeletal muscles, 22 genes were up-regulated and 33 down-regulated in 14-day-old embryos compared with 7-week-old dwarf chickens. Sixty-five mRNAs were up-regulated and 108 down-regulated in 14-day-old embryos as compared with 7-week-old normal chickens. Thirty-four differentially expressed miRNAs were grouped into 18 categories based on overlapping seed and target sequences. Only let-7b was found to be complementary to its target in the 3' untranslated region of GHR, and was able to inhibit its expression. Kyoto Encyclopedia of Genes and Genomes pathway analysis and quantitative polymerase chain reactions indicated there were three main signaling pathways regulating skeletal muscle growth and fat deposition of chickens. These were influenced by let-7b-regulated GHR. Suppression of the cytokine signaling 3 (SOCS3) gene was found to be involved in the signaling pathway of adipocytokines.

CONCLUSIONS

There is a critical miRNA, let-7b, involved in the regulation of GHR. SOCS3 plays a critical role in regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR expression.

The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits

Background

Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits.

Methodology/Principal Finding

Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner.

Conclusions/Significance

Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.

Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits

Chicken growth traits are important economic traits in broilers. A large number of studies are available on finding genetic factors affecting chicken growth. However, most of these studies identified chromosome regions containing putative quantitative trait loci and finding causal mutations is still a challenge. In this genome-wide association study (GWAS), we identified a narrow 1.5 Mb region (173.5-175 Mb) of chicken (Gallus gallus) chromosome (GGA) 1 to be strongly associated with chicken growth using 47,678 SNPs and 489 F2 chickens. The growth traits included aggregate body weight (BW) at 0-90 d of age measured weekly, biweekly average daily gains (ADG) derived from weekly body weight, and breast muscle weight (BMW), leg muscle weight (LMW) and wing weight (WW) at 90 d of age. Five SNPs in the 1.5 Mb KPNA3-FOXO1A region at GGA1 had the highest significant effects for all growth traits in this study, including a SNP at 8.9 Kb upstream of FOXO1A for BW at 22-48 d and 70 d, a SNP at 1.9 Kb downstream of FOXO1A for WW, a SNP at 20.9 Kb downstream of ENSGALG00000022732 for ADG at 29-42 d, a SNP in INTS6 for BW at 90 d, and a SNP in KPNA3 for BMW and LMW. The 1.5 Mb KPNA3-FOXO1A region contained two microRNA genes that could bind to messenger ribonucleic acid (mRNA) of IGF1, FOXO1A and KPNA3. It was further indicated that the 1.5 Mb GGA1 region had the strongest effects on chicken growth during 22-42 d.

Variation in sequence and expression of the avian FTO, and association with glucose metabolism, body weight, fatness and body composition in chickens

OBJECTIVE

The fat mass and obesity-associated gene (FTO), a crucial gene that affects human obesity and metabolism, has been widely studied in mammals but remains poorly characterized in birds. We aimed to identify variant FTO transcripts in domestic avian species, and to characterize the expression and biological functions of FTO in chickens.

METHODS

Variant FTO transcripts and their expression in birds were investigated using RACE and real-time quantitative reverse transcriptase-PCR technology. The effects of FTO on glucose metabolism, growth and body composition were determined by fasting and various diet treatments, as well as association analysis in a F₂ resource population. The function of cFTO1 was further studied by overexpression in chick embryo fibroblast (CEF) cells.

RESULTS

Variant FTO transcripts were identified in chicken (cFTO1 to cFTO4), duck (dFTO1, dFTO2 and dFTO4) and goose (gFTO1, gFTO2 and gFTO5). In the chicken, the complete transcript (cFTO1) was predominantly expressed in the leg muscle, pituitary, hypothalamus and cerebellum. Fasting increased both cFTO1 and PGC1α gene expression in the cerebrum, liver, breast muscle and subcutaneous fat, but decreased expression in the pituitary and anterior hypothalamus. In all tested tissues in chickens, a high-glucose diet markedly increased cFTO1 and PGC1α expression. Feeding a high-fat diet increased both cFTO1 and PGC1α expression, except in the pituitary. Overexpression of cFTO1 in CEF cells significantly increased the expression of PGC1α (2.5-fold), STAT3 (2.2-fold) and HL (1.5-fold), a cluster of genes related to energy metabolism. A total of 65 single nucleotide polymorphisms (SNPs) were identified in chicken FTO, and 18 tested SNPs were significantly associated with traits of body weight, body composition and fatness.

CONCLUSIONS

These data collectively indicate that FTO is related to glucose metabolism, body weight, fatness and body composition in birds, thus expanding knowledge of FTO function to non-mammalian species.

Mutation bias is the driving force of codon usage in the Gallus gallus genome

Synonymous codons are used with different frequencies both among species and among genes within the same genome and are controlled by neutral processes (such as mutation and drift) as well as by selection. Up to now, a systematic examination of the codon usage for the chicken genome has not been performed. Here, we carried out a whole genome analysis of the chicken genome by the use of the relative synonymous codon usage (RSCU) method and identified 11 putative optimal codons, all of them ending with uracil (U), which is significantly departing from the pattern observed in other eukaryotes. Optimal codons in the chicken genome are most likely the ones corresponding to highly expressed transfer RNA (tRNAs) or tRNA gene copy numbers in the cell. Codon bias, measured as the frequency of optimal codons (Fop), is negatively correlated with the G + C content, recombination rate, but positively correlated with gene expression, protein length, gene length and intron length. The positive correlation between codon bias and protein, gene and intron length is quite different from other multi-cellular organism, as this trend has been only found in unicellular organisms. Our data displayed that regional G + C content explains a large proportion of the variance of codon bias in chicken. Stepwise selection model analyses indicate that G + C content of coding sequence is the most important factor for codon bias. It appears that variation in the G + C content of CDSs accounts for over 60% of the variation of codon bias. This study suggests that both mutation bias and selection contribute to codon bias. However, mutation bias is the driving force of the codon usage in the Gallus gallus genome. Our data also provide evidence that the negative correlation between codon bias and recombination rates in G. gallus is determined mostly by recombination-dependent mutational patterns.

Complementary deoxyribonucleic acid cloning of avian G0/G1 switch gene 2, and its expression and association with production traits in chicken

As a member of the G0/G1 switch genes, G0/G1 switch gene 2 (G0S2) is related to many regulatory processes in the human and mouse. For example, it interacts directly with adipose triglyceride lipase to active its triglyceride hydrolysis activities. In this study, G0S2 gene cDNA of the chicken (522 bp), zebra finch (420 bp), sparrow (417 bp), pigeon (417 bp), and Bengalese finch (416 bp) were cloned, and each of them was encoded as a protein of 99 amino acids. The expression of G0S2 mRNA was determined by real-time reverse-transcription PCR analysis in 20 tested tissues of 21- and 91-d-old chickens. The highest mRNA level was found in abdominal fat and subcutaneous fat in both stages. Considerable G0S2 mRNA was also observed in chicken heart and muscle tissues. Expression of the chicken G0S2 gene varied at different stages and sexes. The abundance of G0S2 mRNA on d 21 was far higher than that on d 91. The abundance in female chickens was higher than that in males at both stages. In the coding region, we found 4 SNP, among which only G197A led to a change in the amino acids (Arg66Gln); the rest were synonymous substitutions. Association analysis showed that both G102A and G255A were significantly associated with head width (P < 0.05) and were highly significantly associated with leg muscle color (P < 0.01). The G102A was significantly associated with shank diameter at 63 d (P < 0.05). The SNP G197A was significantly associated with shank diameter at 49 d; CP content of leg muscle; total weights of the heart, liver, gizzard, and glandular stomach; and small intestine length (P < 0.05). In conclusion, much higher G0S2 mRNA was detected in both male and female chickens at 21 d of age than at 91 d of age, and 3 SNP (G102A, G197, and G255A) were associated with chicken production traits.

Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery

Pig (Sus scrofa) is an important organism for both agricultural and medical purpose. This study aims to investigate the S. scrofa transcriptome by the use of Roche 454 pyrosequencing. We obtained a total of 558 743 and 528 260 reads for the back-leg muscle and ovary tissue each. The overall 1 087 003 reads give rise to 421 767 341 bp total residues averaging 388 bp per read. The de novo assemblies yielded 11 057 contigs and 60 270 singletons for the back-leg muscle, 12 204 contigs and 70 192 singletons for the ovary and 18 938 contigs and 102 361 singletons for combined tissues. The overall GC content of S. scrofa transcriptome is 42.3% for assembled contigs. Alternative splicing was found within 4394 contigs, giving rise to 1267 isogroups or genes. A total of 56 589 transcripts are involved in molecular function (40 916), biological process (38 563), cellular component (35 787) by further gene ontology analyses. Comparison analyses showed that 336 and 553 genes had significant higher expression in the back-leg muscle and ovary each. In addition, we obtained a total of 24 214 single-nucleotide polymorphisms and 11 928 simple sequence repeats. These results contribute to the understanding of the genetic makeup of S. scrofa transcriptome and provide useful information for functional genomic research in future.

Transcript variants, expression, and polymorphisms of the pig prosaposin gene

Prosaposin (PASP) is a sphingolipid hydrolysis protein that plays roles in both the nervous and reproduction systems. In this study, we cloned the pig PASP gene and studied its genomic organization, polymorphism, and expression pattern. Two PASP transcripts, TV1 (HQ245644) and TV2 (HQ245646), were identified in pig. TV1 was the complete transcript that encoded 527 amino acids, whereas TV2 was 9 bp shorter due to an exon 8 deletion. The pig PASP gene spanned over 34 kb in length on chromosome 14 (SSC14), and consisted of 15 exons and 14 introns. The pig PASP gene (TV1 and TV2) expressed predominantly in the cerebellum, lymphnode, pituitary, abdominal fat, hypothalamus, and cerebrum in both females and males. PASP TV1 expressed mainly in teh cerebrum, cerebellum, hypothalamus, pituitary, heart, subcutaneous fat, and foreleg muscle, while TV2 was expressed in the liver, spleen, lung, kidney, and lymphnode. In foreleg muscle, the predominant transcript was TV2 in males and TV1 in females. Some potential transcriptional elements were predicted in 5' flanking region (~3000 bp) of the PASP gene, and they were TATA boxes, RORE, Sp1, SRY, oct-1, Cdx A, and cap. Additionally, we identified 68 single-nucleotide polymorphisms and 9 indels in the pig PASP gene, and three single-nucleotide polymorphisms (C77932320T or L15F; C77928094T or P191L; A77917401G or K522R) were nonsynonymous substitutions. These results provide useful information for future functional investigations of the pig PASP gene.

Genetic effects of polymorphisms in candidate genes and the QTL region on chicken age at first egg

Background

The age at first egg (AFE), an important indicator for sexual maturation in female chickens, is controlled by polygenes. Based on our knowledge of reproductive physiology, 6 genes including gonadotrophin releasing hormone-I (GnRH-I), neuropeptide Y (NPY), dopamine D2 receptor (DRD2), vasoactive intestinal polypeptide (VIP), VIP receptor-1 (VIPR-1), and prolactin (PRL), were selected as candidates for influencing AFE. Additionally, the region between ADL0201 and MCW0241 of chromosome Z was chosen as the candidate QTL region according to some QTL databases. The objective of the present study was to investigate the effects of mutations in candidate genes and the QTL region on chicken AFE.

Results

Marker-trait association analysis of 8 mutations in those 6 genes in a Chinese native population found a highly significant association (P < 0.01) between G840327C of the GnRH-I gene with AFE, and it remained significant even with Bonferroni correction. Based on the results of the 2-tailed χ² test, mutations T32742394C, T32742468C, G32742603A, and C33379782T in the candidate QTL region of chromosome Z were selected for marker-trait association analysis. The haplotypes of T32742394C and T32742468C were significantly associated (P < 0.05) with AFE. Bioinformatics analysis indicated that T32742394C and T32742468C were located in the intron region of the SH3-domain GRB2-like 2 (SH3GL2) gene, which appeared to be associated in the endocytosis and development of the oocyte.

Conclusion

This study found that G840327C of the GnRH-I gene and the haplotypes of T32742394C-T32742468C of the SH3GL2 gene were associated with the chicken AFE.

The influence of recombination on SNP diversity in chickens

The association between recombination rate and diversity, but not divergence is considered to be driven mainly by natural selection: fixation of positively selected variants and associated hitchhiking effects and/or background selection eliminating deleterious alleles. In the present study, we investigated the relationship between recombination rate, SNP diversity and interspecies divergence for 29 loci in chickens. We found that recombination rate is positively correlated with nucleotide diversity but is not correlated with interspecies divergence. It appears that variation in recombination rate explains over 30% of the variation in levels of diversity among 29 loci. Our data suggested that natural selection is a main factor in shaping SNP diversity in chickens. Since SNP diversity is significantly lower at Z-linked than at autosomal loci, we argued that genetic hitchhiking might be more important than background selection in producing the observed correlation.

Size-normalized Robustness of Dpp Gradient in Drosophila Wing Imaginal Disc

Exogenous environmental changes are known to affect the intrinsic characteristics of biological organizms. For instance, the synthesis rate of the morphogen decapentaplegic (Dpp) in a Drosophila wing imaginal disc has been found to double with an increase of 5.9°C in ambient temprerature. If not compensated, such a change would alter the signaling Dpp gradient significantly and thereby the development of thewing imaginal disc. To learn how flies continue to develop "normally" under such an exogenous change, we formulate in this paper a spatially two-dimensional reaction-diffusion system of partial differential equations (PDE) that accounts for the biological processes at work in the Drosophila wing disc essential for the formation of signaling Dpp gradient. By way of this PDE model, we investigate the effect of the apical-basal thickness and antero-posterior span of the wing on the shape of signaling gradients and the robustness of wing development in an altered environment (including an enhanced morphogen synthesis rate). Our principal result is a delineation of the role of wing disc size change in maintaining the magnitude and shape of the signaling Dpp gradient. The result provides a theoretical basis for the observed robustness of wing development, preserving relative but not absolute tissue pattern, when the morphogen synthesis rate is significantly altered. A similar robustness considerqation for simultaneous changes of multiple intrinsic system characteristics is also discussed briefly.

Effects of the thyroid hormone responsive spot 14alpha gene on chicken growth and fat traits

The thyroid hormone responsive spot 14alpha (THRSPalpha) gene plays important roles in chicken growth and fat deposition. The aim of this study was to identify new variations in the gene to determine their effects on growth and fat traits in chicken and to observe the effects of the THRSPalpha gene on chicken lipid profile and lipoprotein and glucose and triiodothyronine effects on the THRSPalpha expression in liver and fat cells. Two new variations, namely A197835978G and G197836086A, and a reported 9-bp insertion-deletion (indel) of the THRSPalpha gene were genotyped by single-stranded conformational polymorphism in a Xinghua x White Recessive Rock F(2) full-sib resource population. The results showed that the A197835978G was significantly associated with hatch weight and BW at 28 d of age and breast muscle weight at 90 d of age in chickens (P < 0.05). The G197836086A was significantly associated with cingular fat width (P = 0.0349) and breast muscle crude fat content (P = 0.0349). The indel was significantly associated with abdominal fat weight (P = 0.0445). The above new THRSPalpha polymorphisms were also significantly associated with the total cholesterol and low-density lipoprotein, in which the THRSPalpha GA/AG genotype was associated with lipid and lipoprotein and the THRSPalpha BB indel genotype was significantly associated with liver weight in chicken breeds. The mRNA expression analysis in vivo and in vitro culture studies suggested that the THRSPalpha gene is more responsive to glucose than triiodothyronine. In conclusion, the 3 variations of the chicken THRSPalpha gene were associated with both growth and fat traits in this study. Such effects of the THRSPalpha gene were further supported from the data of observations in association analysis of the gene with phenotypic records and plasma lipid profiles, in the THRSPalpha gene expression in chicken development, and in vivo and in vitro cell culture observation of liver and abdominal fat tissues.

The correlation coefficient of GC content of the genome-wide genes is positively correlated with animal evolutionary relationships

In this study, we present a new method for evaluating animal evolutionary relationships. We used the GC% levels of genome-wide genes to determine the correlation between the GC% content and evolutionary relationship. The correlation coefficients of the GC% content of the orthologous genes of the paired animal species were calculated for a total of 21 species, and the evolutionary branching dates of these 21 species were derived from fossil records. The correlation coefficient of the GC% content of the orthologous genes of the species pair under study served as an indicator of their evolutionary relationship. Moreover, there was a decreasing linear relationship between the correlation coefficient and evolutionary branching date (R(2)=0.930).

The genetic effects of the dopamine D1 receptor gene on chicken egg production and broodiness traits

Background

The elevation of egg production and the inhibition of incubation behavior are the aims of modern poultry production. Prolactin (PRL) gene is confirmed to be critical for the onset and maintenance of these reproductive behaviors in birds. Through PRL, dopamine D1 receptor (DRD1) was also involved in the regulation of chicken reproductive behavior. However, the genetic effects of this gene on chicken egg production and broodiness have not been studied extensively. The objective of this research was to evaluate the genetic effects of the DRD1 gene on chicken egg production and broodiness traits.

Results

In this study, the chicken DRD1 gene was screened for the polymorphisms by cloning and sequencing and 29 variations were identified in 3,342 bp length of this gene. Seven single nucleotide polymorphism (SNPs) among these variations, including a non-synonymous mutation (A+505G, Ser169Gly), were located in the coding region and were chosen to analyze their association with chicken egg production and broodiness traits in 644 Ningdu Sanhuang individuals. Two SNPs, G+123A and C+1107T, were significantly associated with chicken broody frequency (P < 0.05). Significant association was also found between the G+1065A - C+1107T haplotypes and chicken broody frequency (P < 0.05). In addition, the haplotypes of G+123A and T+198C were significantly associated with weight of first egg (EW) (P = 0.03). On the other hand, the distribution of the DRD1 mRNA was observed and the expression difference was compared between broodiness and non-broodiness chickens. The DRD1 mRNA was predominantly expressed in subcutaneous fat and abdominal fat of non-broodiness chicken, and then in heart, kidney, oviduct, glandular stomach, hypothalamus, and pituitary. In subcutaneous fat and abdominal fat, the level of non-broodiness was 26 to 28 times higher than that of broodiness. In pituitary, it was 5-fold higher. In heart, oviduct, and kidney, a 2-3 times decrease from non-broodiness to broodiness was displayed. In glandular stomach and hypothalamus, the level seen in non-broodiness and broodiness was almost the same.

Conclusion

The polymorphisms of the DRD1 gene and their haplotypes were associated with chicken broody frequency and some egg production traits. The mRNA distribution was significant different between broodiness and non-broodiness chickens.

Localized Ectopic Expression of Dpp Receptors in a Drosophila Embryo

Receptor-mediated BMP degradation has been seen to play an important role in allowing for the formation of relatively stable P Mad patterns. To the extent that receptors act as a "sink" for BMPs, one would predict that the localized over-expression of signaling receptors would cause a net flux of freely diffused BMPs toward the ectopic, i.e., abnormally high concentration, receptor site. One possible consequence would be a depression of BMP signaling in adjacent areas since less BMPs are now available for binding with the same normal concentration of receptors at the adjacent areas. However, recent experiments designed to examine this possible effect were inconclusive. In this paper, we investigate the possibility of depression of Dpp signaling outside the area of elevated tkv in a Drosophila embryo by modeling mathematically the basic biological processes at work in terms of a system of nonlinear reaction diffusion equations with spatially varying (and possibly discontinuous) system properties. The steady state signaling morphogen gradient is investigated by the method of matched asymptotic expansions and by numerical simulations.

Multi-scale Modelling for Threshold Dependent Differentiation

The maintenance of a stable stem cell population in the epidermis is important for robust regeneration of the stratified epithelium. The population size is usually regulated by cell secreted extracellular signalling molecules as well as intracellular molecules. In this paper, a simple model incorporating both levels of regulation is developed to examine the balance between growth and differentiation for the stem cell population. In particular, the dynamics of a known differentiation regulator c-Myc, its threshold dependent differentiation, and feedback regulation on maintaining a stable stem cell population are investigated.

cDNA cloning, characterization, and variation analysis of chicken adipose triglyceride lipase (ATGL) gene

Adipose triglyceride lipase (ATGL) is an important triglyceride-specific lipase that catalyzes the initial step in triglyceride hydrolysis. In this study, cloning, sequencing, and mRNA real-time analyses were employed to characterize the chicken ATGL gene. We obtained a total of 1,528-bp long chicken ATGL cDNA fragment including 51-bp 5'UTR, 1,452-bp open reading frame (ORF), and 25-bp 3'UTR. The predicted chicken ATGL had 483 amino acids and a molecular weight of 53.5 kDa, giving rise to identities of 66.5%, 67.3%, 68.2%, 64.8%, and 66.5% with that of human, mouse, rat, pig, and cattle, respectively. The chicken ATGL gene spanned over 30,197 bp and comprised of nine exons and eight introns, in which the intron 1 (21,146 bp) was far longer than others. It predominantly expressed in subcutaneous fat and abdominal fat and then in kidney and lung. Very low but detectable mRNA level was also observed in other 15 tissues. However, no mRNA was detected in spleen. A total of 15 single nucleotide polymorphisms (SNPs) were identified in its complete cDNA sequences with an average of one SNP in every 102 bp and a summarized nucleotide diversity of 3.02 x 10(-3). Seven of the 15 SNPs were non-synonymous. All SNPs had allelic frequencies over 5% and could be considered as candidate markers for future marker-trait association analysis.

The PIT1 gene polymorphisms were associated with chicken growth traits

Background

With crucial roles on the differentiation of anterior pituitary and the regulation of the prolactin (PRL), growth hormone (GH) and thyroid-stimulating hormone-β (TSH-β) genes, the chicken PIT1 gene is regarded as a key candidate gene for production traits. In this study, five reported polymorphisms (MR1-MR5) of the PIT1 gene were genotyped in a full sib F₂ resource population to evaluate their effects on growth, carcass and fatty traits in chickens.

Results

Marker-trait association analyses showed that, MR1 was significantly associated with shank diameters (SD) at 84 days (P < 0.05), hatch weight (HW) and shank length (SL) at 84 days (P < 0.01), MR2 was significantly associated with BW at 28, 42 days and average daily gain (ADG) at 0–4 weeks (P < 0.05), and MR3 was significantly associated with ADG at 4–8 weeks (P < 0.05). MR4 was associated with SL at 63, 77, 84 days and BW at 84 days (P < 0.05), as well as SD at 77 days (P < 0.01). Significant association was also found of MR5 with BW at 21, 35 days and SD at 63 days (P < 0.05), BW at 28 days and ADG at 0–4 weeks (P < 0.01). Both T allele of MR4 and C allele of MR5 were advantageous for chicken growth. The PIT1 haplotypes were significantly associated with HW (P = 0.0252), BW at 28 days (P = 0.0390) and SD at 56 days (P = 0.0400). No significant association of single SNP and haplotypes with chicken carcass and fatty traits was found (P > 0.05).

Conclusion

Our study found that polymorphisms of PIT1 gene and their haplotypes were associated with chicken growth traits and not with carcass and fatty traits.

SNP mapping of QTL affecting growth and fatness on chicken GGA1

An F2 chicken population was established from a crossbreeding between a Xinghua line and a White Recessive Rock line. A total of 502 F2 chickens in 17 full-sib families from six hatches was obtained, and phenotypic data of 488 individuals were available for analysis. A total of 46 SNP on GGA1 was initially selected based on the average physical distance using the dbSNP database of NCBI. After the polymorphism levels in all F0 individuals (26 individuals) and part of the F1 individuals (22 individuals) were verified, 30 informative SNP were potentially available to genotype all F2 individuals. The linkage map was constructed using Cri-Map. Interval mapping QTL analyses were carried out. QTL for body weight (BW) of 35 d and 42 d, 49 d and 70 d were identified on GGA1 at 351–353 cM and 360 cM, respectively. QTL for abdominal fat weight was on GGA1 at 205 cM, and for abdominal fat rate at 221 cM. Two novel QTL for fat thickness under skin and fat width were detected at 265 cM and 72 cM, respectively.

Polymorphism of Growth-Correlated Genes Associated with Fatness and Muscle Fiber Traits in Chickens

Thirty single nucleotide polymorphisms (SNP) and one 6-bp insertion-deletion (indel) from 8 genes of somatotropic axis were used to study the association with chicken fatness and muscle fibers. The allele frequency difference between Xinghua and White Plymouth Rock chickens was observed, and their effects on fatness and muscle fiber traits were also evaluated by linkage analyses. The G143831A (G+1705A) SNP of the growth hormone (GH) gene was related to fat width, and the G144762A (G+119A) SNP of the GH gene was significantly associated with abdominal fat pad weight, abdominal fat pad ratio, and crude fatty content of the breast muscle. The 6-bp indel of the growth hormone secretagogue receptor (GHSR) gene was significantly linked with the fat traits. The C51978309T SNP of the insulin-like factor-I (IGF-I) gene was significantly linked with the transversal area of the leg muscle fiber and transversal area of the breast muscle fiber. There was significant linkage between the insulin (INS) gene and 2 traits of the transversal area of transversal area of the leg muscle fiber and transversal area of the breast muscle fiber. Association of 30 SNP and one 6-bp indel from 8 genes of somatotropic axis with chicken fatness and muscle fiber traits was analyzed in the present study. The GH, GHSR, and leptin receptor genes were significantly related to chicken fatness. The INS and IGF-I genes were linked with muscle fiber density. Therefore, the genes of somatotropic axis not only affected chicken growth and body composition but also were associated with fatness and muscle fiber traits.

An 8bp indel in exon 1 of Ghrelin gene associated with chicken growth

Ghrelin, acts as the endogenous ligand for growth hormone secretagogues receptor (GHS-R), is a novel growth hormone (GH) releasing peptide with reported effects on food intake in chickens. In this study, an 8 bp indel polymorphism in exon 1 of the chicken Ghrelin (cGHRL) gene was genotyped in a F(2) designed full-sib population to analyze its associations with chicken growth and carcass traits. Later, mRNA level in the proventriculus was determined by real-time PCR to reveal the expression feature of cGHRL gene. Result showed that this 8 bp indel was significantly associated with body weight at the age of 28 days (BW28) and 56 days (BW56), eviscerated weight (EW) and leg muscle weight (LMW) (P<0.05), highly significantly associated with hatch weight (HW), BW14, 21, 35, 42, 49, 90 and body length (BL), dressed weight (DW), eviscerated weight with giblet (EWG), wing weight (WW), breast muscle weight (BMW) and head and neck weight (HNW) (P<0.01). Meanwhile, A allele (with 'CTAACCTG') was positive for chicken growth as individuals with AA genotype had the highest value of all traits. Analysis on cGhrelin mRNA level revealed that it differed significantly among individuals with three genotypes (P<0.05). Individuals with AB genotype had the highest mRNA level, whereas that of AA had the lowest one. It was concluded that this 8 bp indel of cGHRL gene was significantly associated with most body weight and body composition traits, and negative effect of endogenous Ghrelin on chicken growth were indicated by this study.

Membrane-associated non-receptors and morphogen gradients

A previously investigated basic model (System B) for the study of signaling morphogen gradient formation that allows for reversible binding of morphogens (aka ligands) with signaling receptors, degradation of bound morphogens and diffusion of unbound morphogens is extended to include the effects of membrane-bound non-signaling molecules (or non-receptors for short) such as proteoglycans that bind reversibly with the same morphogens and degrade them. Our main goal is to delineate the effects of the presence of non-receptors on the existence and properties of the steady-state concentration gradient of signaling ligand-receptor complexes. Stability of the steady-state morphogen gradients is established and the time to reach steady-state behavior after the onset of morphogen production will be analyzed. The theoretical findings offer explanations for observations reported in several previous experiments on Drosophila wing imaginal discs.

High Diversity of the Chicken Growth Hormone Gene and Effects on Growth and Carcass Traits

The chicken growth hormone (cGH) gene plays a crucial role in controlling growth and metabolism, leading to potential correlations between cGH polymorphisms and economic traits. In this study, DNA from four divergent chicken breeds were screened for single nucleotide polymorphisms (SNPs) in the cGH gene using denaturing high-performance liquid chromatography and sequencing. A total of 46 SNPs were identified, of which 4 were in the 5' untranslated region, 1 in the 3' untranslated region, 5 in exons (two of which are nonsynonymous), with the remaining 36 in introns. The nucleotide diversity in the cGH gene ( theta = 2.7 x 10(-3)) was higher than that reported for other chicken genes, even within the same breeds. The associations of five of these SNPs and their haplotypes with chicken growth and carcass traits were determined using polymerase chain reaction-restriction fragment length polymorphism analysis in a F2 resource population cross of two of the four chicken breeds (White Recessive Rock and Xinghua). This analysis shows that, among other correlations, G+1705A was significantly associated with body weight at all ages measured, shank length at three of four ages measured, and average daily gain within weeks 0 to 4. Thus, this cGH polymorphism, or another polymorphism that is in linkage disequilibrium with G+1705A, appears to correspond to a significant growth-related quantitative trait locus difference between the two breeds used to construct the resource population.