Advances on genetic and genomic studies of ALV resistance

Avian leukosis(AL)is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus(ALV).No vaccine or drug is currently available for the disease.Therefore,the disease can result in severe economic losses in poultry flocks.Increasing the resistance of poultry to ALV may be one effective strategy.In this review,we provide an overview of the roles of genes associated with ALV infection in the poultry genome,including endogenous retroviruses,virus receptors,interferon-stimulated genes,and other immune-related genes.Furthermore,some methods and techniques that can improve ALV resistance in poultry are discussed.The objectives are willing to provide some valuable references for disease resistance breeding in poultry.

转录组测序揭示细胞周期通路参与鸡腹脂沉积

近年来,随着生长性状和饲料转化率的提高,中国地方品种肉鸡腹脂率不断增加,大大降低了肉鸡的品质。过多的腹脂沉积不仅降低了肉鸡的屠宰率和抗病力,而且由于脂肪较难处理,导致其被随意丢弃,污染环境。为了挖掘与中国地方品种肉鸡腹脂沉积相关的基因和调控通路,本研究对杏花鸡分别进行高脂和普通饲料的喂养,检测腹脂沉积情况,并利用转录组测序检测高脂饲养对肝脏和腹脂组织中基因表达的影响。结果表明,喂养两周后高脂组肉鸡腹脂重和腹脂率显著增加,且腹脂细胞的直径和面积也显著增大。对两组鸡的腹脂和肝脏进行转录组测序,发现在腹脂中显著差异表达基因主要富集于细胞周期通路、PPAR(peroxisome proliferator-activated receptor)信号通路和ECM(extracellular matrix)受体信号通路中;而在肝脏中,显著差异表达基因同样显著富集于细胞周期通路中,同时也显著富集于类固醇生物合成和PPAR信号通路中。通过分析腹脂和肝脏组织中共同差异表达的基因,发现这些基因同样显著富集于细胞周期中。进一步以鸡肝癌细胞系LMH(chicken hepatoma cell)细胞和鸡前脂肪细胞系ICP(immortalized chicken preadipocytes)细胞进行体外验证,利用高脂培养基和普通培养基进行培养,结果发现48h后,高脂培养基可显著促进细胞周期进程,增加处于S期的细胞数。同时,qRT-PCR结果发现高脂培养基可显著促进细胞周期相关基因的表达。综上所述,本研究通过基因表达差异分析,发现高脂饲养可能通过激活鸡脂肪组织的细胞周期来促进前脂肪细胞增殖,进而增加腹脂沉积。该研究结果为进一步了解优质肉鸡腹脂沉积的机制提供了理论依据。

Feed conversion ratio,residual feed intake and cholecystokinin type A receptor gene polymorphisms are associated with feed intake and average daily gain in a Chinese local chicken population

Background: The feed conversion ratio(FCR) and residual feed intake(RFI) are common indexes in measuring feed efficiency for livestock. RFI is a feed intake adjusted for requirements for maintenance and production so these two traits are related. Similarly, FCR is related to feed intake and weight gain because it is their ratio. Cholecystokinin type A receptor(CCKAR) plays an important role in animal digestive process. We examined the interplay of these three parameters in a local Chinese chicken population.Results: The feed intake(FI) and body weights(BW) of 1,841 individuals were monitored on a daily basis from 56 to 105 d of age. There was a strong correlation between RFI and average daily feed intake(ADFI) and a negative correlation between the FCR and daily gain(r_g=-0.710). Furthermore, we identified 51 single nucleotide polymorphisms(SNPs) in the CCKAR and 4 of these resulted in amino acid mutations. The C334A mutation was specifically associated with FI and the expected feed intake(EFI)(P < 0.01) and significantly associated with the average daily gain(ADG)(P < 0.05). G1290A was significantly associated with FI and EFI(P < 0.05).Conclusion: FCR is apply to weight selecting, and RFI is more appropriate if the breeding focus is feed intake. And C334A and G1290A of the CCKAR gene can be deemed as candidate markers for feed intake and weight gain.

circPTPN4 regulates myogenesis via the miR-499-3p/NAMPT axis

Background:Circular RNAs(circ RNAs)are a novel class of endogenous nc RNA,which widely exist in the transcriptomes of different species and tissues.Recent studies indicate important roles for circ RNAs in the regulation of gene expression by acting as competing endogenous RNAs(ce RNAs).However,the specific role of circ RNAs in myogenesis is still poorly understood.In this study,we attempted to systematically identify the circ RNAs involved in myogenesis and analyze the biological functions of circ RNAs in chicken skeletal muscle development.Results:In total,532 circ RNAs were identified as being differentially expressed between pectoralis major(PEM)and soleus(SOL)in 7-week-old Xinghua chicken.Among them,a novel circ RNA(novel_circ_002621),generated by PTPN4 gene,was named circ PTPN4 and identified.circ PTPN4 is highly expressed in skeletal muscle,and its expression level is upregulated during myoblast differentiation.circ PTPN4 facilitates the proliferation and differentiation of myoblast.Moreover,circ PTPN4 suppresses mitochondria biogenesis and activates fast-twitch muscle phenotype.Mechanistically,circ PTPN4 can function as a ce RNA to regulate NAMPT expression by sponging mi R-499-3p,thus participating in AMPK signaling.Conclusions:circ PTPN4 functions as a ce RNA to regulate NAMPT expression by sponging mi R-499-3p,thus promoting the proliferation and differentiation of myoblast,as well as activating fast-twitch muscle phenotype.

Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Background: Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence(WGS) data. However, sequencing thousands of individuals of interest is expensive.Imputation from SNP panels to WGS data is an attractive and less expensive approach to obtain WGS data. The aims of this study were to investigate the accuracy of imputation and to provide insight into the design and execution of genotype imputation.Results: We genotyped 450 chickens with a 600 K SNP array, and sequenced 24 key individuals by whole genome re-sequencing. Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. By increasing the sequencing cost from 24 X to 144 X, the imputation accuracy increased from 0.525 to 0.698 for Beagle and from 0.654 to 0.823 for FImpute. With fixed sequence depth(12 X), increasing the number of sequenced animals from 1 to 24, improved accuracy from 0.421 to0.897 for FImpute and from 0.396 to 0.777 for Beagle. Using optimally selected key individuals resulted in a higher imputation accuracy compared with using randomly selected individuals as a reference population for resequencing. With fixed reference population size(24), imputation accuracy increased from 0.654 to 0.875 for FImpute and from 0.512 to 0.762 for Beagle as the sequencing depth increased from 1 X to 12 X. With a given total cost of genotyping, accuracy increased with the size of the reference population for FImpute, but the pattern was not valid for Beagle, which showed the highest accuracy at six fold coverage for the scenarios used in this study.Conclusions: In conclusion, we comprehensively investigated the impacts of several key factors on genotype imputation. Generally, increasing sequencing cost gave a higher imputation accuracy. But with a fixed sequencing cost, the optimal imputation enhance the performance of WGP and GWAS. An optimal imputation strategy should take size of reference population, imputation algorithms, marker density, and population structure of the target population and methods to select key individuals into consideration comprehensively. This work sheds additional light on how to design and execute genotype imputation for livestock populations.

Identification and characterization of genes that control fat deposition in chickens

Background： Fat deposits in chickens contribute significantly to meat quality attributes such as juiciness, flavor, taste and other organoleptic properties. The quantity of fat deposited increases faster and earlier in the fast- growing chickens than in slow-growing chickens. In this study, Affymetrix Genechip~ Chicken Genome Arrays 32773 transcripts were used to compare gene expression profiles in liver and hypothalamus tissues of fast-growing and slow-growing chicken at 8 wk of age. Real-time RT-PCR was used to validate the differential expression of genes selected from the microarray analysis. The mRNA expression of the genes was further examined in fat tissues. The association of single nucleotide polymorphisms of four lipid-related genes with fat traits was examined in a F2 resource population. Results： Four hundred genes in the liver tissues and 220 genes hypothalamus tissues, respectively, were identified to be differentially expressed in fast-growing chickens and slow-growing chickens. Expression levels of genes for lipid metabolism （SULTIB1, ACSBG2, PNPLA3, LPL, AOAH） carbohydrate metabolism （MGAT4B, XYLB, GBE1, PGM1, HKDCl）cholesttrol biosynthesis （FDPS, LSS, HMGCR, NSDHL, DHCR24, IDI1, MEI） HSD17B7 and other reaction or pro- cesses （CYPIA4, CYP1A1, AKR1BI, CYP4V2, DDO） were higher in the fast-growing White Recessive Rock chickens than in the slow-growing Xinghua chickens. On the other hand, expression levels of genes associated with multicellular organism development, immune response, DNA integration, melanin biosynthetic process, muscle organ develop- ment and oxidation-reduction （FRZB, DMD, FUT8, CYP2C45, DHRSX, and CYP2C18） and with glycol-metabolism （GCNT2, ELOVL d, and FASN）, were higher in the XH chickens than in the fast-growing chickens, fiT-PCR validated high expression levels of nine out of 12 genes in fat tissues. The G1257069A and T1247123C of the ACSBG2 gene were significantly associated with abdominal fat weight. The G4928024A of the FASN gene were significantly associ- ated with fat bandwidth, and abdominal fat percentage. The C4930169T of the FASN gene was associated with ab- dominal fat weight while the A59539099G of the ELOVL 6 was significantly associated with subcutaneous fat. The A8378815G of the DDT was associated with fat band width. Conclusion： The differences in fat deposition were reflected with differential gene expressions in fast and slow growing chickens.

Porcine growth differentiation factor 9 gene polymorphisms and their associations with litter size

Growth differentiation factor 9 （GDF9） is expressed in oocytes and is thought to be required for ovarian folliculogenesis. Given this function, GDF9 may be considered as a candidate gene controlling pig ovulate rate. In this study, the complete coding sequence was cloned （encoding a 444 amino acid）, intron sequence and partial 5＇-UTR of pig GDF9. RT-PCR results showed that GDF9 mRNA is expressed in a wide range of tissues of the ruttish Erhualian pig. The expression levels of GDF9 mRNA in pituitary, ovary, uterus and oviduct are higher in the Erhualian pigs than those in Duroc pigs, especially in pituitary with a significant difference （P 〈 0.05）. Comparative sequencing revealed 12 polymorphisms, including 8 single nucleotide polymorphisms （SNPs） and one 314 bp indel in noncoding regions, and the other 3 SNPs in coding regions. Four polymorphisms, G359C, C1801T, T1806C and 314 bp indel, were developed as markers for further use in population variation and association studies. The G359C polymorphism segregates only in Chinese native pigs, Erhualian and Dahuabai, on the contrary, 314 bp indel segregates only in Duroc and Landrace. C1801T and T1806C sites seem to be completely linked and segregate in Erhualian, Dahuabai and Landrace. In a word, GDF9 may be not associated with pig litter size in extensive populations as per the studies of allele distributions of the four polymorphisms and pilot association in four breeds.

High expression of BCL6 inhibits the differentiation and development of hematopoietic stem cells and affects the growth and development of chickens

Background:B-cell CLL/lymphoma 6(BCL6)is a transcriptional master regulator that represses more than 1200 potential target genes.Our previous study showed that a decline in blood production in runting and stunting syndrome(RSS)affected sex-linked dwarf(SLD)chickens compared to SLD chickens.However,the association between BCL6 gene and hematopoietic function remains unknown in chickens.Methods:In this study,we used RSS affected SLD(RSS-SLD)chickens,SLD chickens and normal chickens as research object and overexpression of BCL6 in hematopoietic stem cells(HSCs),to investigate the effect of the BCL6 on differentiation and development of HSCs.Results:The results showed that comparison of RSS-SLD chickens with SLD chickens,the BCL6 was highly expressed in RSS-SLD chickens bone marrow.The bone marrow of RSS-SLD chickens was exhausted and red bone marrow was largely replaced by yellow bone marrow,bone density was reduced,and the levels of immature erythrocytes in peripheral blood were increased.At the same time,the hematopoietic function of HSCs decreased in RSS-SLD chickens,which was manifested by a decrease in the hematopoietic growth factors(HGFs)EPO,SCF,TPO,and IL-3,as well as hemoglobinα1 and hemoglobinβexpression.Moreover,mitochondrial function in the HSCs of RSS-SLD chickens was damaged,including an increase in ROS production,decrease in ATP concentration,and decrease in mitochondrial membrane potential(ΔΨm).The same results were also observed in SLD chickens compared with normal chickens;however,the symptoms were more serious in RSS-SLD chickens.Additionally,after overexpression of the BCL6 in primary HSCs,the secretion of HGFs(EPO,SCF,TPO and IL-3)was inhibited and the expression of hemoglobinα1 and hemoglobinβwas decreased.However,cell proliferation was accelerated,apoptosis was inhibited,and the HSCs entered a cancerous state.The function of mitochondria was also abnormal,ROS production was decreased,and ATP concentration andΔΨm were increased,which was related to the inhibition of apoptosis of stem cells.Conclusions:Taken together,we conclude that the high expression of BCL6 inhibits the differentiation and development of HSCs by affecting mitochondrial function,resulting in impaired growth and development of chickens.Moreover,the abnormal expression of BCL6 might be a cause of the clinical manifestations of chicken comb,pale skin,stunted growth and development,and the tendency to appear RSS in SLD chickens.

广东省地方鸡线粒体遗传多样性与母系起源

系统评估地方鸡的遗传变异水平并追溯其母系起源,可为保护利用优质家禽种质资源库提供科学依据。本研究测定了广东省和邻省共12个地方鸡品种的线粒体DNA D-loop序列,分析品种间的遗传距离与系统关系,并构建单倍型系统发生树和中介网络图。360份样品共检测到60个突变位点,均为转换。定义了85种单倍型,归属于单倍型类群A、B、C和E,在12个鸡品种中均有分布,其中B是优势单倍型类群(187个,51.94%),E次之(76个,21.11%)。B02和C01是优势单倍型(85个,23.61%;48个,13.33%),为12个鸡品种共有;E03位居第三(35个,9.72%),杏花鸡、黄郎鸡和宁都三黄鸡未见此单倍型。杏花鸡集中分布在单倍型类群B,惠阳胡须鸡和中山沙栏鸡则主要分布在单倍型类群E;怀乡鸡的单倍型数量最多,中山沙栏鸡的最少。广东地方鸡品种间遗传距离为0.012–0.015,单倍型多样性0.805±0.047至0.949±0.026,核苷酸多样性0.0102±0.0017至0.0138±0.0009。邻接树和中介网络图将85种单倍型划分为进化枝A、B、C和E,广东省与邻省地方鸡单倍型的地理分布模式相似。中性检验显示广东地方鸡未经历明显的群体历史扩张。结果表明广东地方鸡处于较好的保护状态,遗传多样性水平较高,品种的形成受到邻省和北方家鸡的影响,东南亚红原鸡对广东地方鸡也有重要的遗传贡献。

MicroRNAs Involved in Skeletal Muscle Differentiation

MicroRNAs （miRNAs） negatively regulate gene expression by promoting degradation of target mRNAs or inhibiting their translation. Previous studies have expanded our understanding that miRNAs play an important role in myogenesis and have a big impact on muscle mass, muscle fiber type and muscle-related diseases. The muscle-specific miRNAs, miR-206, miR-1 and miR-133, are among the most studied and best characterized miRNAs in skeletal muscle differentiation. They have a profound influence on multiple muscle differ- entiation processes, such as alternative splicing, DNA synthesis, and cell apoptosis. Many non-muscle-specific miRNAs are also required for the differentiation of muscle through interaction with myogenic factors. Studying the regulatory mechanisms of these miRNAs in muscle differentiation will extend our knowledge of miRNAs in muscle biology and will improve our understanding of the myogenesis regulation.

The genetic regulation of skeletal muscle development:insights from chicken studies

Skeletal muscle development is a complex multi-process trait regulated by various genetic factors.The chicken embryo is an ideal model system for studying skeletal muscle development. However, only a small proportion of the genetic factors affecting skeletal muscle development have been identified in chicken. The aim of this review is to summarize recent knowledge about the genetic factors involved in the regulation of skeletal muscle development in the chicken, such as gene polymorphisms, epigenetic modification, noncoding RNAs and transcription factors, which can influence skeletal muscle development at the genome, epigenome,transcriptome and proteome levels. Research on the regulation of skeletal muscle development in chicken is not yet comprehensive and most of the candidate genes and single nucleotide polymorphisms related to chicken muscle growth remain to be verified in experimental studies. In addition, the data derived from transcriptome sequencing and genome-wide association studies still require further investigation and analysis and comprehensive studies on the regulation of chicken skeletal muscle development will continue as a major research focus.

Genetic diversity and population structure of indigenous chicken breeds in South China

A total of 587 individuals from 12 indigenous chicken breeds from South China and two commercial breeds were genotyped for 26 microsatellites to investigate the genetic diversity and population structure.All microsatellites were found to be polymorphic.The number of alleles per locus ranged from 5 to 36,with an average of12.10±7.00(SE).All breeds,except White Recessive Rock,had high allelic polymorphism(>0.5).Higher genetic diversity was revealed in the indigenous chicken breeds rather than in the commercial breeds.Potential introgression from the commercial breeds into the indigenous chickens was also detected.The population structure of these indigenous chicken breeds could be explained by their geographical distribution,which suggested the presence of independent history of breed formation.Data generated in this study will provide valuable information to the conservation for indigenous chicken breeds in future.

Faster evolution of Z-linked duplicate genes in chicken

It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes in Drosophila melanogaster. However, whether this phenomenon is general and can be applied to other species is not known. Here we examined this issue in chicken that have heterogametic females （females have ZW sex chromosome）. We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes. We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications. Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression. These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function. The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z. Therefore, the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than autosomal duplications, regardless of the kind of sex determination systems.