JiaXian Red Cattle Genome Variation Map Construction And Selection Signal Analysis

Native cattle breeds are an important source of genetic resources of yellow cattle in China.The research on local cattle breeds is helpful for further protection,development and utilization.Jiaxian Red cattle,a superior local breed from Jiaxian County,Pingdingshan City,Henan Province,has achieved excellent production performance after years of cultivation.To further analyze the genetic characteristics of Jiaxian Red Cattle,in this study,genetic diversity,population structure,genome region and copy number variation of 30 Jiaxian Red cattle from core breeding farms were investigated using the whole genome resequencing data.In addition,combined analysis of 131 published worldwide yellow cattle genomes was conducted to investigate the variation of Jiaxian Red cattle genome.The results are as follows:（1）Jiaxian Red Cattle genomic sequencing analysisBased on resequencing data analysis of 30 Jiaxian Red cattle,24.8M biallelic allelic SNP was found in the Jiaxian Red cattle population.At the same time,the nucleotide diversity,linkage disequilibrium decay and runs of homozygosity of Jiaxian Red cattle were studied,it was found that compared with other cattle populations,Jiaxian Red cattle had higher nucleotide diversity,lower linkage imbalance degree and lower inbreeding degree,indicating that Jiaxian Red cattle have a high genome diversity.Meanwhile,it also indicated that the breeding intensity of Jiaxian Red cattle was weak and should be further improved.（2）Population structure analysis of Jiaxian Red cattlePopulation structure analysis based on Jiaxian Red cattle and other cattle populations in the world showed that there was a mixed pedigree of East Asian taurine（0.493）,Chinese indicine（0.379）,European taurine（0.095）and Indian indicine（0.033）.（3）Selective sweep in Jiaxian Red cattleSelective sweep were analyzed usingθπ,CLR,F_ST and XP-EHH to screen positive selection signals on Jiaxian Red cattle.By using different detection strategies,171common genes（θπand CLR）and 238 common genes(F_ST and XP-EHH)were identified.By functional annotation and enrichment analysis of these genes,we get 18significantly correlated GO terms,the results showed that these genes may be related to growth and feed efficiency（CCSER1）,meat quality traits（ROCK2,PPP1R12A,CYB5R4,EYA3,PHACTR1）,fertility（RFX4,SRD5A2）and immune system response（SLAMF1,CD84 and SLAMF6）.（4）Copy number variation of Jiaxian Red cattleA total of 1269 duplicate types,413 deletion types and 277 both types were detected in a study on copy number variation of Jiaxian Red cattle population.Functional annotation on the copy number variation,the distribution of exon region gene enrichment analysis,found that A large number of genes were found to be enriched in pathways related to immune response,such as BOLA,BOLA-NC1 and GZMB gene were associated with cattle disease resistance,suggests that the CNV in Jiaxian Red cattle may have important effects on their disease resistance and environmental adaptability.In conclusion,this study comprehensively evaluated the genetic variation of Jiaxian Red cattle and found that there was high genetic diversity and low inbreeding degree in Jiaxian Red cattle.Selective signals that may be related to important economic traits were detected in the Jiaxian Red cattle genome region.These results will provide the basis for further conservation and breeding improvement of this breed.