CNV Identification And Muscle Development Related Heredity Basis Of Australian Boer Goat

There is still a gap between the growth performance of Chinese native goats and foreign breeds.Determining the key molecular markers of muscle development is the basis for improving the productivity of Chinese native goat breeds.The Boer goat was first bred in South Africa.This breed of meat goat exhibits not only superior meat production performance,but also high fecundity and broad-spectrum adaptability.Since the early 19th century,when the South African Boer goat was introduced.Australia has implemented more stringent breeding techniques and developed,an excellent meat goat breed:the Australian Boer goat,which is currently highly sought after worldwide.Since the 1990s,herdsmen have introduced a large number of Australian Boer goats to China and hybridized them with local goats to improve the growth performance of native goats and increase their economic income.However,the genetic basis,specific genetic variation,and structural characteristics of the excellent meat production performance of Boer goats remain unclear.In this study,genome-wide data from 127 goats（46 Boer goats and 81 indigenous goats from different parts of the world）were used to mine specific copy number variations（CNVs）and muscle development-related candidate genes in Australian Boer goats.We identified the biological effects of candidate genes on skeletal muscle satellite cells（SMSCs）using cell biology methods,and analyzed the expression regulation pathways and mechanisms of candidate genes using RNA-Seq.The major results are as follows.（1）In this study,24826 CNVs were identified in the autosomal genome data of127 goats,with a total length of 95.1 Mb.In accordance with the F_ST parameters,25CNV candidate variants with a selection signal ranking of Top 0.1%(F_ST≥0.526755)were selected,and 22 candidate genes were identified through functional annotation.A large number of genes were enriched in pathways related to muscle development（TEAD1 and EDNRA）,metabolism（TPK1 and NR3C2）,and biological functions（NDST3 and FTMT）.（2）A highly selective signal(F_ST=0.918858)carried by Boer goat was identified as a 1.1 Mb CNV variation located on chromosome 17,including six genes（ARHGAP10,NR3C2,EDNRA,TMEM184C,PRMT9 and LOC108637893）.By using the combination of three-generation long-reading genome resequencing and Sanger sequencing,we clarified that the HSV mutation was formed through the reverse insertion of a 1.1 Mb（CHIR17:60062304-61171840 bp）genomic front and the replacement of a 5362 bp（CHIR17:60145940-60151302 bp）genomic region to form a chromosome rearrangement structure.In accordance with the gene frequency distribution,all individuals in the Australian Boer goat population carried this mutation,and 96%of the individuals were HSV multi-copy homozygotes（+/+）.In indigenous goats,HSV homozygous copy genotypes（+/+）were detected in only 4%of African native goats.（3）In this study,the effects of overexpression of 6 candidate genes covered by HSV on SMSCs were studied.We found that the overexpression of the ARHGAP10and NR3C2 genes promoted the proliferation of SMSCs.EDNRA,TMEM184C,PRMT9 and LOC108637893 exerted no significant effect on the proliferation of SMSCs.In addition,ARHGAP10 and EDNRA could significantly promote the differentiation of SMSCs,while the NR3C2 gene could inhibit their differentiation.（4）RNA-Seq technology was used to investigate the expression regulation mechanism of three candidate genes（NR3C2,EDNRA,and ARHGAP10）in SMSCs.A total of 272 significantly differentially expressed genes（DEGs）were identified between the NR3C2 overexpression group and the empty transfection group,including227 upregulated DEGs and 45 downregulated DEGs.The results of gene function annotation showed that 123 DEGs were enriched into 223 KEGG pathways,including a large number of signal transduction pathways,such as cell growth and muscle development.In addition,compared with the empty group,the EDNRA gene overexpression group significantly upregulated 6 DEGs（CFB,SAA3,C2,CYP26B1,SLC7A8,and SLPI）,and 4 DEGs were enriched in 6 KEGG pathways related to metabolism.Only the SAA3 gene was significantly upregulated in the overexpression group of the ARHGAP10 gene in SMSCs.But it’s worth noting that the three genes related to muscle cell development screened in this study significantly upregulated the expression of the SAA3 gene.In summary,this study used combined multiple sequencing techniques to identify the fine structure of CNV variation（HSV）with high-frequency specificity in the Australian Boer goat population.Cell biology and transcriptome sequencing technology constructed the candidate gene expression regulatory network.Therefore,this study not only laid a theoretical foundation for further revealing the genetic mechanism related to the excellent production performance of Boer goats,but it also provided data reference for the development of molecular genetic markers of goat growth traits.