Regulation Mechanism Of Differences In Meat Production Traits Between Lean-and Obese-type Pigs And Heterosis Of Their Crossbreds

Pork production depends on the skeletal muscle development of pigs.Meanwhile,skeletal muscle development is a very complicated process.The dynamic expression and interaction of genes as well as transcription factors during muscle development play important regulatory roles in the formation of muscle phenotype.There are great differences in meat production traits between Chinese indigenous obese-type pigs and foreign lean-type pigs,which provide excellent materials for molecular mechanism study of pig skeletal muscle development.In this study,skeletal muscle of lean-type Landrace pigs(L),obese-typeTongcheng pigs(T),and their crossbreds LT pigs at 27 developmental time points(15 before birth and 12 after birth)were selected as materials.Molecular dynamics of porcine skeletal muscle development was exploredby transcriptome sequencing,and molecular mechanism of phenotypical differencesbetween L and T pigs and heterosis of meat production traits of LT pigs were also analyzed.The main results of this study are as follows:1.In this study,a total of 388.4 G clean data were obtained,averaging 4.8 G per sample.The average number of expressed genes per sample was 13,130(RPKM ? 1).The number of expressed gene decreased gradually with the development of skeletal muscle,suggesting that stronger transcriptional activity and more complicated molecular events are happened during prenatal stages than postnatal stages.However,there was no significant difference in the number of expressed gene among these three pig breeds(P> 0.05).2.Principal component and multidimensional scale analysis could divide the samples into two categories: before and after birth.Age effects could explain more than 50% variances of skeletal muscle development.Hierarchical clustering analysis showed that the neighboring time points were clustered together within breeds,indicating that the transcription difference between neighboring time points within breeds was less than that of different pig breeds at same time points.3.The expressions of some commonly used housekeeping genes(such as GAPDH,ACTB)had great fluctuationsduring skeletal muscle development,suggesting that these genes may not be suitable as internal reference genes for quantitative expression in skeletal muscle.At the same time,14 genes with stablyhighexpression in skeletal muscle were identified,and MKRN1 was the most stable one.These genes could be used as suitable reference genes for expression analysis in skeletal muscle development.4.Zf-C2H2 and CSD were the highest expressed transcription factor families in skeletal muscle at prenatal and postnatal stages,respectively.CSDA gene was the highest expressed transcriptional factor in the postnatal stage and was up-regulated during skeletal muscle development.There was a significantly negative correlation between the expression of CSDA and Myogenin(P<0.01).Compared to other transcription factors,transcription factors associated with muscle development tended to be highly expressed during skeletal muscle development,but still exhibited dynamic volatility before and after birth.There was no expressed difference in transcription factors associated with muscle development among different breeds.5.16 co-expression modules,which associated with distinct developmental stages or biological processes,were identified in this study,and hub genes that played key roles in different developmental stages were alsoappraised.The roles of many hub genes(such as CNN3,FSCN1,SFRP1,OLFML3)in skeletal muscle have been confirmed by our previous studies.Energy metabolism and neuromodulation played important roles in skeletal muscle maturation and fiber typeformation.6.2,471 novel lncRNAs were identified in skeletal muscle and a ceRNA regulatory network closely associated with porcine skeletal muscle development was constructed.Six lncRNAs were identified as putative ceRNAs through regulating the expression of skeletal muscle development-related genes.7.‘Associated genes' strategy was used to analyse the similarity map of gene expression between T and L pigs,indicating non-synchronization of expression regulation during skeletal muscle developmentbetween T and L pigs.The embryonic and neonatal periods might be the critical stages resulting in non-synchronization in skeletal muscle development between these two pig breeds.Gene ontology biological processes,such as nucleus mitosis and mitochondrial cell cycle,were highly enriched during E33-E60 stage in L pigs,but these processes only lasted to E45 in T pigs,indicating that in the embryonic stage of skeletal muscle development,cell cycle-related genes are expressed longer in L pigs than in T pigs,resulting L pigs having more primary fibers than T pigs.Functional analysis showed that non-synchronized genes played important roles in formation of theskeletal muscle phenotypic differences between T and L pigs.At the same time,we used two other methods,turning point and maximum spike,to certify the non-synchronization mechanism in skeletal muscle development between T and L pigs?8.This study explored the molecular mechanism of heterosis of meat production traits in LT pigs at transcription level.Compared with T pigs,the gene expression pattern of skeletal muscle in LT pig was more similar with that of L pigs.The transgressive and dominant up-regulated genes were closely related to the heterosis of meat production traits.Different gene expression patterns played important regulatory roles in heterosis at different developmental points or periods.In summary,the molecular events and possible regulatory mechanisms involved in the skeletal muscle development of different pig breeds were analyzed from two dimensions(breeds and time points).The heterosis of meat production traitsin LT pigs was analyzed at the transcription level.Key genes and transcription factors that play important roles in pig skeletal muscle development were identified,which provide a wealth of information for the study of functional genomics in pig skeletal muscle and a foundation for molecular design breeding for pork production and quality traits.