Genome-wide Association Study Of Growth And Carcass Traits And Target Sequencing Analysis For Detecting Function Genes In Beef Cattle

Growth and carcass traits of beef cattle is one of the most important commercial traits in pratice,which is crucial to the development of beef cattle industry.In 2016,China’s beef consumption per capita was only 5.6 Kg / person,well below the level of developed countries in the United States(36 Kg / person),Japan(10 Kg / person)and slightly below the world average(6.2 Kg / person).The main reasons leading to the lag of beef cattle industry in China include the high feeding cost,the low management level and especially the genetic resources which always obstruct the development of beef cattle industry in China.The aim of this study was to explore the genetic factors of growth and carcass traits by using genome-wide association analysis and target region sequencing,and to explore the major genes or QTLs of beef cattle growth and carcass traits from multi-strategy,multi-omics and multi-aspect.These can provide a reliable basis for genome selection,molecular marker-assisted selection,etc.This study leads to important conclusions as follows:(1)A total of 18 candidate genes and 4 QTL regions were detected in five growth and carcass traits of the Simmental beef cattle.The genes such as NCAPG and LCORL were reported in previous studies,the new candidate genes such as FGF9,SPIDR,LAMA4 and so on were detected.This result provided the theoretical basis and direction guidance for the molecular breeding program.(2)The genetic mechanism of the average daily gain trait of beef cattle was further explored by multi-strategy genome-wide association analysis.The three genome-wide association analysis was simultaneously mapped to the NCAPG-DCAF16 region,and the phenotypic variation was more than 4% explained by this region.Transcription factors binding sites predict result indicated that transcription factors binding sites related to cell proliferation and differentiation were enrichment in this region,suggesting that the average daily gain trait may be related to gene expression regulation.This conclusion provide a reliable direction for next explrosion.(3)Further linkage analysis of NCAPG-DCAF16 region were implemented to explore the possibility of daily gain candidate.The level of linkage disequilibrium in Simmental was significant higher than Chinese indigenous cattle,indicating strong selection in this region of Simmental.(4)We conducted association analysis between transcript expression of candidate genes and phenotypic trait.First,we verified that there were three transcripts in NCAPG in muscle cells,two of which has not reported previously.And then we found the total expression of NCAPG,and DCAF16 was significantly associated with the average daily gain phenotype.This study further demonstrated genetic mechanism of average daily gain trait in beef cattle.(5)There were 38 markers and 77 significant markers,mainly located in the upstream region of NCAPG gene,and no amino acid mutation sites were found by target region sequencing association analysis.