Genetic Diversity Of The X Chromosome Genome In Domestic Cattle

The study of genetic diversity in the X chromosome genome is essential for understanding the evolution of species.Little is known about the genetic diversity of the X chromosome in domestic cattle worldwide.This study collected 258 whole-genome resequencing data from 42 domestic cattle breeds in Africa,Europe,and Asia.By analysing the genetic structure,genetic diversity,selection signals,and penetration of closely related species in the domestic cattle X chromosome population,the genetic characteristics and phylogeographic patterns specific to the domestic cattle X chromosome genome were revealed at the whole-genome level and the following main findings were obtained:1.Using a sliding window to scan the X chromosome genome,Pseudoautosomal region(PAR)was identified at the end of the X chromosome in the 133.4-139.0 Mb range,accounting for 4% of the total length of the X chromosome and 11.7% of the total number of SNPs on the X chromosome.2.Based on SNPs in the X-linked region of domestic cattle,it is possible to separate East Asian Bos indicus,African Bos indicus,South Asian Bos indicus,European Bos taurus,Eurasian Bos taurus,East Asian Bos taurus and African Bos taurus,whereas based on SNPs in the PAR region of domestic cattle,it is not possible to separate the Bos taurus and Bos indicus groups well.3.Genetic diversity in the X-lined region of domestic cattle is lower than autosomes,LD levels are higher than autosomes,and the number and average length of ROH are higher than autosomes.4.Studies of selection signaling in X-lined region of Bos indicus and Bos taurus populations identified functional genes associated with stress behavioral responses,nervous system development,apoptotic and skin morphology,with the IKBKG gene being strongly selected for and its two missense mutations(X:37593162A>G and X:37601697A>G)having significantly different haplotypes in Bos indicus and Bos indicus populations.The AR and EDA2 R genes were also strongly selected for and showed highly divergent haplotype patterns in Bos indicus and Bos taurus,possibly related to environmental adaptations,growth and development and reproductive traits in domestic cattle.5.Gene infiltration was detected in the X chromosome of the East Asian Bos indicus population in Banteng and Gaur,with a lower proportion of infiltration than in autosomes.Annotation and enrichment analysis of bison adaptive infiltration fragments revealed enrichment in signalling pathways associated with the nervous,endocrine and immune systems,with the SHROOM2 gene possibly associated with circadian rhythms,visual development or UV resistance traits,and the FRMPD4 gene possibly associated with neurodevelopment or cognition.It is hypothesized that the penetration of these genes contributes to the adaptation of Bos indicus to the tropical climate of southern East Asia.In conclusion,this study provides important information for understanding the genetic characteristics and evolution of the domestic cattle X chromosome through systematic analysis of its genetic structure,genetic diversity,selection and penetrance characteristics,and has important theoretical implications for understanding the relationship between functional genes and environmental adaptations of the domestic cattle X chromosome.