| Feed production,accounting for about two –thirds of the production cost,takes a large proportion of the economic cost in the pig industry.In recent years,the production of domestic grain grows very slowly compared to imported corn in china.These situations highlighted the increasing problems of food shortage.Improving the feed efficiency of pigs can reduce the feeding cost hence promote economic performance of pig industry as well as relieve competition for food between people and animals.Feed conversion ratio is a common index for measuring feed efficiency.Thirty years ago,great progress has been made for FCR in pig breeding,but the molecular mechanism of FCR variation was still unknown.In this study,we identified some SNPs associated with FCR using reduced-representation sequencing and genome-wide association study in pig and in mice,to provide the molecular markers for porcine feed efficiency improvement and to find candidate genes to uncover the genetic mechanism of feed efficiency.A previous study showed that muscle growth was related to feed efficiency,therefore,we investigated the molecular mechanism of muscle hypertrophy using the high throughput sequencing technology,expecting to find some important genes relevant to muscle growth,and then taking them as candidate genes of feed efficiency study,and thus provide the theoretical foundation to elaborate the correlation between muscle growth and feed efficiency at the same time.The results are as follows:(1)We selected 258 extreme individuals with high and low FCR from Duroc population,and found that the ADG,FI were significantly different between extremely FCR individuals(low FCR individuals: FCR=1.89±0.093,ADG=0.91±0.11(Kg),FI=1.71±0.22(Kg);high FCR individuals: FCR=2.34±0.097(Kg),ADG=0.84±0.097(Kg),FI=1.96±0.22(Kg))through comparative analysis of feed efficiency index and growth traits.Combined with the results of traits association analysis in this population and RNA-seq of extreme FCR individuals in large white pig worked by other colleagues,we found muscle growth and energy metabolism were the main factors influencing feed efficiency.(2)GBS was used in the extremely FCR duroc pig,309246 SNPs were identified by TASSEL software and 2338228 SNPs were identified by Stacks.Many new SNPs were identified.Six SNPs were identified suggesting association with FCR by GBS and GWAS,three of them were located in the QTL related to meat quality and fatty acid metabolism.Function analysis found 51 annotated genes nearby related to calcium binding,ATP binding,proteinase activity e.t.c.Further analysis of the genes near the six identified SNPs,found that some genes could be used as candidate genes to study FCR variation.Twelve 12 genes of S100 A family fall within the scope of 1 Mb around the site chr4:105296496.S100A10,A member of S100 A family was identified significant associated with feed efficiency,and the distance of this gene from the site is more than 1Mb.VGLL2 gene,near the site chr1:49709264,is related to muscle growth and located in the QTL which is related to ADG.(3)In the extremely FCR duroc pigs,4 SNPs were identified suggesting an association with ADG.These SNPs were mapped to the QTL which may influence meat quality traits,ADG,backfat and so on.Twenty-seven genes were found around these SNPs with the scope of 1 Mb,some of these genes related to ATP binding,such as ACSS2,AACS,DHX37,MYH7 B and so on.(4)We found the significant FCR and immune traits were different between KM and C57 mice through comparative analysis.We measured the feed intake and body weight gain of 28 female kunming mice(FCR=4.81±0.91)and 35 male C57 mice(FCR=10.35±2.37),afterwards,calculated the FCR.We selected 7 high FE female kunming mice mating with 7 low FE C57 male mice,and obtained 740 F2 mice(female mice:319,male mice 321).We measured the feed intake and body weight gain from the F2 population and calculated the FCR(female mice FCR=6.24±1.27,male mice FCR=5.84±1.63).(5)We selected 72 extreme individuals with high and low FCR from KM×C57 F2 population for RAD-Seq and 988717 SNPs was identified by GATK.67 SNPs were identified significantly associated with FCR by GWAS.These SNPs were mainly located in chromosome 2,13 and 15.We found 203 annotated genes near these SNPs.The functions of genes were related to muscle growth,redox reaction,cell cycle and so on.The genes related to muscle growth were Ret,Act19,Arpc5 l,Actbl2,Fgf10 and Dhpr.(6)We found 7 similar genes from FCR of pig and mice(slc28a9,Ppap2 a,Skiv2l2,Ccno,Gpx8,Gzma and Gzmk)and 3 similar genes from pig ADG and mice FCR by comparative genomics(Zswim6,Smin5 and Ndufaf2).Analysis the position of these genes found these genes were located in two identical regions in pig and mice.Comparative genomics analysis found the two region were conserved in pig(chr16:36.5Mb,chr16:43.1Mb)and mice(MMu13D2.2,MMu13D2.1).(7)Gene expression profiles associated with hypertrophic skeletal muscle in myostatin propeptide transgenic mice were investigated by RNA sequencing.A total of132 genes were identified and used for function annotation and gene enrichment analysis.The novel up-regulated genes were related to hypertrophic cardiomyopathy,focal adhesion,PA signaling pathway,and ROS removal processes,suggesting that myostatin directly affects these processes during the regulation of skeletal muscle growth and mass.Two new signaling pathways,the Ky/Mybph/Actins and PA signaling pathways,were uncovered,which may account for myostatin propeptide-induced muscle hypertrophy. |
