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The aim of this study was to use Y-chromosome gene polymorphism method to investigate regional differences in genetic variation and the population evolution history of the Chinese native cattle breeds.Six Y-chromosome short tandem repeat (Y-STR) loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404 and UMN0103) were analyzed using 1016 healthy and hetergenetic males and 90 females of nine native cattle breeds (Qinchuan, Jirnan, Zaosheng, Luxi, Nanyang, Jiaxian, Dabieshan, Yanbian, Menggu) in China.Allele frequency, gene diversity were calculated among various populations.The results indicated that Y-STRs in six loci have polymorphism and genetic diversity in Chinese cattle populations.According to genetic diversity analysis, Chinese cattle populations have a close genetic relationship.Based on analysis of INRA124, UMN2404 and UMN0103 loci, we might look into Chinese cattle original history to determine which cattle belong to Bos Taurus or Bos Indicus.Most notably, a declining Zebu introgression had been displayed from South to North and from East to West in Chinese geographical distribution, which implied that various region cattle population in China had been subjected to somewhat different evolution history.This conclusion supported other evidences such as earlier archaeological, historical research and blood protein polymorphism analysis.