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Zhang H.,Key Laboratory of Chicken Genetics and Breeding | Zhang H.,Northeast Agricultural University | Wang S.-Z.,Key Laboratory of Chicken Genetics and Breeding | Wang S.-Z.,Northeast Agricultural University | And 15 more authors.
BMC Genomics | Year: 2012

Background: Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF.Results: A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens.Conclusions: We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress. © 2012 Zhang et al.; licensee BioMed Central Ltd.


Zhang H.,Key Laboratory of Chicken Genetics and Breeding | Zhang H.,Northeast Agricultural University | Wang Z.,Key Laboratory of Chicken Genetics and Breeding | Wang Z.,Northeast Agricultural University | And 4 more authors.
Journal of Animal Science and Biotechnology | Year: 2012

Domestic animals are invaluable resources for study of the molecular architecture of complex traits. Although the mapping of quantitative trait loci (QTL) responsible for economically important traits in domestic animals has achieved remarkable results in recent decades, not all of the genetic variation in the complex traits has been captured because of the low density of markers used in QTL mapping studies. The genome wide association study (GWAS), which utilizes high-density single-nucleotide polymorphism (SNP), provides a new way to tackle this issue. Encouraging achievements in dissection of the genetic mechanisms of complex diseases in humans have resulted from the use of GWAS. At present, GWAS has been applied to the field of domestic animal breeding and genetics, and some advances have been made. Many genes or markers that affect economic traits of interest in domestic animals have been identified. In this review, advances in the use of GWAS in domestic animals are described. © 2012 Zhang et al.; licensee BioMed Central Ltd.


PubMed | Northeast Agricultural University and Key Laboratory of Chicken Genetics and Breeding
Type: Journal Article | Journal: Genetics and molecular research : GMR | Year: 2015

Intensive selection of broilers for improved growth rate is known to exert a negative effect on broiler health, such as an increase in body fat (and its related diseases). Excessive fat deposition in the liver can cause fatty liver hemorrhagic syndrome (FLHS); in addition, traits associated with liver fat have also been associated with FLHS. This study explored the genetic relationships among liver fat-related traits. Data was collected from 462 birds derived from 16th generation Northeast Agricultural University broiler lines divergently selected for abdominal fat content. The body weight at 7 weeks of age (BW7), abdominal fat weight (AFW), abdominal fat percentage, liver fat percentage (LFP), liver weight, and liver percentage were measured. The heritability of these traits and the phenotypic and genetic correlations were estimated, using the restricted maximum likelihood (REML) and Gibbs sampling (GS) methods. The REML and GS methods yielded similar heritability estimates for LFP (0.36 and 0.37, respectively). BW7 showed a high positive genetic correlation with AFW (rA(REML) = 0.74 and rA(GS) = 0.80), and a moderate positive genetic correlation with LFP (rA(REML) = 0.27 and rA(GS) = 0.39). Positive genetic correlations were also observed between AFW and LFP (rA(REML) = 0.35 and rA(GS) = 0.36). These results suggested that selection for growth may increase the AFW and LFP in broilers. LFP is directly related to FLHS; therefore, selection for broiler growth rate may increase the incidence of FLHS.


Chen X.,Key Laboratory of Chicken Genetics and Breeding
Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji | Year: 2012

The Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) were used in the current study to investigate the effects of Retinoblastoma1 (RB1) gene on chicken body weight (BW). The single nucleotide polymorphisms (SNPs) of the individuals were detected by MALDI-TOF-MS and PCR-RFLP methods and the genotypes of 27 SNPs were obtained. Haplotypes were constructed by liding window approach. Association analysis between single SNPs and haplotypes and body weight were conducted, respectively. Based on the results of single SNPs and haplotype association analyses. Four SNPs with significant effects on body weight at 1 week of age (BW1) and 2 SNPs with significant effects on BW1 and BW3 were determined. These results suggested that RB1 is an important candidate gene that affects chicken early growth and development.


PubMed | Key Laboratory of Chicken Genetics and Breeding
Type: | Journal: BMC genomics | Year: 2014

The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60 K SNP array, which is a high-throughput method widely used in chicken genomics studies.Using PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (including SLC9A3, GNAL, SPOCK3, ANXA10, HELIOS, MYLK, CCDC14, SPAG9, SOX5, VSNL1, SMC6, GEN1, MSGN1 and ZPAX) may be important for abdominal fat deposition in the chicken.Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken.


PubMed | Key Laboratory of Chicken Genetics and Breeding
Type: Journal Article | Journal: Acta biochimica et biophysica Sinica | Year: 2013

Krppel-like factor 7 (Klf7) has been extensively studied in the mammalian species, but its function in avian species is unclear. The objective of this study was to reveal the function of chicken Klf7 (Gallus gallus Klf7, gKlf7) in adipogenesis. The results of real-time reverse transcription polymerase chain reaction demonstrated that the relative mRNA level of chicken Klf7 (gKlf7/g-Actin) in the abdominal adipose tissue was significantly associated with the abdominal fat content and the age of broilers (P < 0.05), and gKlf7 was more highly expressed in preadipocytes than in mature adipocytes (P < 0.05). In addition, Oil red O staining showed that gKlf7 inhibited chicken preadipocyte differentiation, and MTT assay indicated that gKlf7 overexpression promoted preadipocyte proliferation. Additionally, luciferase assays showed that gKlf7 overexpression suppressed the chicken CCAAT/enhancer-binding protein (C/ebp), fatty acid synthase (Fasn), and lipoprotein lipase (Lpl) promoter activities (P < 0.05), and gKlf7 knockdown increased the chicken peroxisome proliferator-activated receptor (Ppar), C/ebp and fatty acid-binding protein 4 (Fabp4) promoter activities (P < 0.05). Together, our study demonstrated that chicken Klf7 inhibits preadipocyte differentiation and promotes preadipocyte proliferation.


PubMed | Key Laboratory of Chicken Genetics and Breeding
Type: | Journal: BMC genomics | Year: 2013

Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF.A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens.We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.


PubMed | Key Laboratory of Chicken Genetics and Breeding
Type: Journal Article | Journal: Genetics and molecular research : GMR | Year: 2015

In this study, we profiled gene expression in chicken liver and screened differentially expressed genes in the Baier layers and fat line broilers. Birds were derived from the 14th generation of Northeast Agricultural University fat broiler lines and Baier layers. Chicken genome arrays were used to screen differentially expressed genes in liver tissue from the Baier layers and fat line broilers. We screened 671 differentially expressed genes between broilers and layers at the ages of 2 and 4 weeks. We observed enrichment of a series of significant pathways, including the mitogen-activated protein kinase signaling pathway, cell cycle, mammalian target of rapamycin signaling pathway, and p53 signaling pathway. At 2 and 4 weeks, 94 shared differentially expressed genes were observed. We speculated that these genes regulate chicken lipid metabolism.


PubMed | Key Laboratory of Chicken Genetics and Breeding
Type: Comparative Study | Journal: Genetics and molecular research : GMR | Year: 2013

Liver fatty acid-binding protein (L-FABP) and liver bile acid-binding protein (L-BABP), in the liver intra-cytoplasm of chicken, are members of the fatty acid-binding protein subfamily. This study was designed to analyze and compare L-FABP and L-BABP expression levels between fat and lean lines in chicken liver tissue, and to determine the relationship between their expression and lipid metabolism. Real-time polymerase chain reaction (PCR) and Western blotting were used to detect the mRNA and protein expression in liver tissue between the lean and fat lines. Real-time PCR showed that L-FABP mRNA expression in fat male chickens was higher than that in lean male chickens at 2, 3, 4, 5, 6, and 10 weeks of age (P < 0.05), and L-BABP mRNA expression in fat male chickens was higher than that in lean male chickens at 1, 2, 3, 4, 8, and 10 weeks of age (P < 0.05). Western blotting showed that the L-FABP protein expression in fat male chickens was higher than that in lean male chickens at 3, 5, 6, and 7 weeks of age (P < 0.05), and L-BABP protein expression in fat male chickens was higher than that in lean male chickens at 3, 4, 5, and 6 weeks of age (P < 0.05). These results suggested that chicken L-FABP and L-BABP affect abdominal fat deposition through differences in their expression level, and the possible mechanism is that a high expression level of L-FABP and L-BABP leads to a high lipogenesis rate and, ultimately, to lipid deposition.


PubMed | Key Laboratory of Chicken Genetics and Breeding
Type: Journal Article | Journal: Animal science journal = Nihon chikusan Gakkaiho | Year: 2013

Krppel-like factor 7 (KLF7) has been extensively studied in mammalian species, but its role in birds is still unclear. In the current study, cloning and sequencing showed that the full-length coding region of chicken KLF7 (Gallus gallus KLF7, gKLF7) was 891 bp long, encoding 296 amino acids. In addition, real-time RT-PCR analysis showed that gKLF7 was broadly expressed in all 15 chicken tissues selected, and its expression was significantly different in spleen, proventriculus, abdominal fat, brain, leg muscle, gizzard and heart between fat and lean broilers at 7 weeks of age. Additionally, one novel single nucleotide polymorphism (SNP), XM_426569.3: c. A141G, was identified in the second exon of gKLF7. Association analysis showed that this locus was significantly associated with fatness traits in Arbor Acres broiler random population and the eighth generation of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) population (P<0.05). These results suggest that gKLF7 might be a candidate gene for chicken fatness traits.

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