| In China,there is a great variety of cattle breeds with excellent adaptability,but the meat quality is poor by comparing with Japanese black cattle and Angus cattle,showing large space for improvement.This is the root cause of the fact that domestic high-grade beef will be long-term dependent on import.In addition,the aimless introduction and hybridization has caused the dramatic decrease of Chinese various local cattle breeds,and some breeds are even near extinction,such as Gayal.In recent years,the emergence of high-throughput sequencing technology provided opportunities and challenges for species protection and resource development and utilization,the breakthrough of which field could provide technical support for improving the breeding efficiency and comprehensively exploring the genetic information.In 2009,cattle genome sequence has been successful assembled,which offered theoretical basis for the functional genomic study of different cattle breeds.In this study,the next generation sequencing technology was utilized to conduct the genome and transcriptome sequencing of Qinchuan cattle(QCC),Japanese black cattle(JBC),Angus cattle(AGS)and Gayal,in order to reveal the genetic characteristics of these different breeds,and provide scientific basis for the improvement and protection of Chinese local cattle breeds.The main results are as follows:(1)A total of 343.69 G data was obtained by sequencing the genomes of QCC(n = 3),JBC(n = 3)and AGS(n = 3).The reference genome(UMD3.1)was 99.08% covered and the average sequencing depth was 11.14 ×.A total of 24562477 single nucleotide polymorphisms(SNPs),2764904 insertions / deletions(In Dels),27699 copy number variants(CNVs)and 429748 structural variants(SVs)were detected.The number of these types of genetic variation in QCC was significantly higher than that in JBC and AGS,indicating that QCC had higher genetic diversity.Of all the variations we detected,32.20% of the SNPs and 41.09% of the In Dels were not included in the db SNP140.Based on genome-wide scanning analysis,985 positively selected genes(PSGs)were detected in JBC,and these genes were significantly enriched in fatty acid metabolism related signal pathways and functional classification.In the AGS,1298 PSGs were found and they were significantly enriched in the thyroid hormone signaling pathway,insulin-related pathways,AMPK signaling pathway,oxytocin-signaling pathway and other important classical pathway and functional classification.In QCC,4622 genes with breed-specific missense mutation(BSMGs)were found,and they were enriched in functional classification,such as autoimmune response,antigen treatment and presentation,immune response,african pyramid disease,etc.The results above provided theoretical evidence to explain for the high beef quality and black coat of JBC,the excellent reproductive performance of AGS,the superior adaptability and the strong resistance of QCC.(2)A total of 42.77 G data was obtained by sequencing the genome of Gayal.The coverage rate was 98.44% and the sequencing depth was 13.06 ×.A total of 23828562 SNPs,1970270 In Dels,3659 CNVs and 70810 SVs were detected in Gayal;62.24% of the SNPs and 64.50% of the In Dels were novel.Our results showed that the distribution of SNPs on various chromosomes and the coverage of sequencing data were consisted with that of JBC and AGS(2n=60),suggesting that Gayal(2n=58)might experience a chromosome fusion event.A total of 6167 BSMGs were found,which were significantly enriched in the signaling pathways and functional classifications such as complement system,bio adhesive,external stimulus response and defense response,suggesting an intrinsic correlation with the excellent performance of Gayal strong resistance.In addition,demographic history analyses showed that Gayal has experienced two population expansions and two population shrinkages;meanwhile,the fluctuation of the population size might related to worldwide climate alteration.The phylogenic analysis based on single ortholog copy genes and mitochondrial genomes showed that Gayal might evolve from the descendant of the hybridization crossing male wild gaur with female domestic cattle.(3)We performed whole transcriptomic analysis of the longissimus dorsi of QCC,JBC and AGS.Compared with the other two breeds,36 differentially expressed genes(DEGs)were found in JBC,these genes were significantly enriched in the pathways and functional classification of lipid metabolism,which might be related to the high quality of beef.Additionally,37 DEGs were found in QCC,these genes were significantly enriched in the pathways and functional classification of immunization and susceptibility to pests and diseases,which revealed the genetic characterization of strong adaption of QCC.Similarly,162 DEGs were found in Angus cattle,but these genes were only enriched in four pathways and functional classification,two of which were immune related,reflecting the special immunity different from Angus cattle.(4)Considering the high meat quality of JBC and strong adaptability of QCC,we combined the transcriptomic analysis with genome analysis,screening the DEGs and PSGs related to lipid metabolism and immune response.As results,ELOVL6 is shared by the above two types of genes in JBC and BLA-DQB,as well as HBA,PRG4 and VWF in QCC.These five genes could be used as important candidate genes in cattle breeding to improve the meat quality and adaptability.The results of regulation network analysis showed close relationship between the PSGs and the DEGs,which would provide references for revealing the molecular mechanism of lipid regulation and immune response.In current research,we performed genomic and transcriptomic analysis of QCC,JBC and AGS,and investigated their genetic characteristics.Our results will provide scientific basis for the improvement of beef cattle and the cultivation of novel cattle breeds with high beef quality in China.In addition,the whole genome sequencing of Gayal revealed the potential genetic mechanism of strong adaptability,and further illuminated the evolutionary history,which will provide theoretical foundation for the protection and utilization of local germplasm resources. |
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