| Growth performance,slaughter performance and meat quality are the critical focus traits in broiler industry.The growth rate,meat production performance and meat quality directly affect the economic benefits of broiler industry.With the rapid development of science and technology,the combination of traditional breeding methods with modern biotechnology,will greatly shorten the breeding cycle,which has become one of the important objects in current animal breeding programs.As a result,there are more and more researches on the genetic mechanism of growth and development rules and economic traits in broilers,which have been gradually resolving the molecular mysteries of these traits.Therefore,the only sure way for researchers to break through innovations is to choose appropriate research methods for complex traits.RNA-seq technology has the advantages of high efficiency,high precision and relatively low technical cost in transcriptomic research.It can perform global detection of transcriptomes of any cell type of any species.RNA-seq technology not only can analyze the structure of transcripts and expression patterns,but also can accurately identify single-nucleotide polymorphisms in the coding sequence(cSNP)and alternative splice sites.Therefore,RNA-seq technology is considered to be one of the most effective tools for the study of complex traits.In this study,Jinmao black chicken were used as experimental animals.Breast muscle samples of Jinmao black chicken at the age of 2 weeks,6weeks,10 weeks(close to growth inflection point)and 14 weeks(on-sale stage)were collected and used to explore the genome-wide gene expression levels in the process of growth in Jinmao black chicken and screen specific genes at different growth stages by using RNA-seq sequencing and Gene co-expression methods.Body weight,slaughter performance and meat quality of Jinmao black chicken at 14 weeks of age were detected and conducted by whole transcriptome association analysis to reveal the molecular genetic markers and genetic markers affecting the occurrence of these complex traits.This study would provide reference for the growth and development rules and molecular mechanism of the formation of important economic traits in Jinmao black chicken.The main findings were showed as follows:1.The study of growth regularity found that the Compertz model was most suitable for fitting the growth of the Jinmao black chicken,fitting degree reached more than 0.999.The growth inflection point of Jinmao black chicken was 11.12 weeks of age,and the inflection point weight was 979.6 g.The fitting results showed that the model had good characteristic in imitating curves,and the predicted results are in good agreement with the experimental values.2.It was found that there were 2341 differentially expressed genes between the four growth stages through pair wise comparison according to the results of RNA-seq,Among the differentially expressed genes,930 genes were up-regulated and 1411 genes were down-regulated.A total of 699 differentially expressed genes were found in W2_vs_W14 and there were at least 107 differentially expressed genes in W2 vs W6(FC≥2,FDR<0.05).3.Stage-specific modules were identified at four stages using gene co-expression analysis at different growth stages.One specific module was identified in each stage,and functional enrichment analysis was performed on important genes in specific modules.The stage-specific genes(two-week-age)were significantly enriched in ECM-receptor interactions,renin-angiotens in system and ErbB signaling pathway(P<0.05).The regulation of phagosomes,actin cytoskeleton and MAPK signaling pathway were significantly enriched in the six-week-age module(P<0.05).Phagosomes,TGF-β signaling pathway and MAPK signaling pathway were significantly enriched in the ten-week-age module(P<0.05).ECM receptor interactions,focal adhesions and insulin signaling pathways were significantly enriched in the fourteen-week-age module(P<0.05).These pathways had played an important regulatory role in the growth and development of breast muscle in Jinmao black chicken.4.Among the four specific modules,FGF22,NRG1 and SCD were considered as the important genes related to the growth and development of Jinmao black chicken at 2 weeks age;FGF16,APLNR1 and NGFR were related to the growth and development of the chicken at 6 weeks age.FGF10,SOCS2 and CTSG were important genes associated with growth and development when the chicken were at 10 weeks age;ACSL1,PRKCE and PP1R3C were important genes associated with growth and development of Jinmao black chicken at 14 weeks age.Functional analysis revealed that these genes played an important roles in regulating the growth and development of Jinmao black chicken at each stage.5.Whole transcriptome association analysis found 9 genes which were significantly associated with body weight,including BRDT,BPIFB4,NUP107,CFAP65,MC4R and CCDC152 genes.MC4R gene,as a candidate gene which affected body weight,may play an important regulatory role in the growth and development of Jinmao black chicken.As a common candidate gene which affected body weight and carcass weight,NUP107 gene participated in various biological developmental processes by regulating the transportation of substances between nucleoplasm.CCDC family genes were identified by whole transcriptome association analysis and CCDC152 gene was also significantly correlated with body weight at 14 weeks of age.6.Whole transcriptome association analysis found 28 genes which were significantly correlated with slaughter performance.SRP68 and PAXIP1 genes were significantly correlated with semi-eviscerated weight.GAK gene was significantly correlated with eviscerated weight.SPAG4,PKHD1 and ASB2 genes were significantly correlated with the head weight.GAK,NSUN6 and C70RF72 genes were significantly correlated with wing weight.As a common candidate gene related to wing weight and eviscerated weight,GAK gene plays a key role in regulating receptor transportation and receptor signal and function,which may affect the wing weight and eviscerated weight of the late growth period of Jinmao black chicken.Other genes of the CCDC family,such as the CCDC89 gene was significantly correlated with head weight,and CCDC65 gene was significantly correlated with gizzard weight.ACSL4 gene was significantly correlated with liver weight and spleen weight,which could be selected as candidate gene of liver weight and spleen weight for further study.7.Whole transcriptome association analysis of meat quality found that FFAR4 and TXK genes were candidate genes for IMP and might need further study.Expression of genes such as PLEKHS1 and MUC might affect meat color.LHX9,SPDEF and GRXCR1 were candidate genes for water holding capability,but there were no reports in poultry.NPY,POMC,FGF20,MGAT4C and GUK1 have rarely been reported as candidate genes for muscle pH in poultry,which might regulate lipid metabolism,glucose metabolism and phosphodiesterase hydrolysis while affecting the changes of muscle pH.HS6ST3 and EDAR were candidate genes for muscle shear force(tenderness)and indirectly affected the shear force of muscles by involving the deposition of muscle fibers and intermuscular fat. |
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