Analysis Of Mitochondrial Genetic Effects On Milk Production Traits In Chinese Holstein Dairy Cows

Chinese Holstein cattle have become the mainstream dairy cattle in China due to their high milk yield,docile character and easy feeding.The research on the genetic basis of Chinese Holstein cattle has been a hot topic in recent decades.At present,the research on nuclear genetic information is mainly focused on,and the research on the effect of extracellular genetic effect is less.Mitochondria,as the "energy factory" of cells,provide more than 90% of energy,regulate membrane potential,control programmed cell death,regulate cell proliferation and metabolism,synthesize cholesterol and some heme and other functions.Mitochondrial inheritance has a high mutation rate,and the mutation rate of mitochondrial DNA is about 10 times that of nuclear DNA.Therefore,even among species that diverge recently,a large number of mitochondrial nucleotide variations will be accumulated quickly,which can be compared and analyzed.Strict maternal inheritance,and no DNA recombination and other characteristics.With the development of sequencing technology,genome resequencing technology has been gradually applied in dairy breeding.This study aims to accurately obtain mitochondrial variation information from low-depth sequencing data,explore the genetic effect of mitochondrial DNA on milk production traits,analyze the proportion of phenotypic variation explained by mitochondrial variation,and analyze whether nucleo-plasmic interaction affects milk production traits.(1)NUMTs sequences in nucleus are highly similar to mitochondrial homologous sequences.Different methods to mask NUMTs sequences may affect the detection of mitochondrial variation.In this study,four kinds of NUMTs screening strategies of resequencing data were compared.By comparing the mitochondrial coverage of sequencing data and the heterogeneity rate of variation detection,it was found that the method of extracting mitochondrial sequence by comparing sequencing data to the whole genome reference sequence could obtain the mutation sites with higher mitochondrial coverage and lower heterogeneity rate.Therefore,this method was used to detect mitochondrial genome variation in dairy herds.(2)Through the double-genome association analysis,we excluded the false positives that might be caused by the nuclear effect in the analysis of mitochondrial genetic effect,and found that all the mitochondrial variation sites were significant enough to significantly affect the milk production character.Considering the small population of dairy cows and the small mitochondrial genetic effect may be obscured in the double-genome association analysis,further mitochondrial genome association analysis revealed that 12900(C→T)site located on mitochondrial ND5 gene was significantly associated with milk yield traits(FDR = 0.174334< 0.2,0.2 is the commonly used hypothesis test significance level in mitochondrial association analysis),so it is speculated that site 12900 May be related to milk production traits.In addition,double-genome association analysis of mitochondrial haplotype and copy number variation for milk production traits and mitochondrial genome association analysis showed that there was no significant correlation with the five milk production traits.(3)The proportion of phenotypic variation of milk production traits explained by mitochondria was calculated,and the proportion of phenotypic variation of milk production explained by mitochondria was 0.096%;Mitochondria accounted for 0.00403% of the variation of milk fat scale type.The proportion of mitochondria that could explain the variation of milk protein scale type was 0.00653%.The phenotypic variation of milk fat percentage explained by mitochondria was 0.00532%.Mitochondria accounted for 0.00438%of phenotypic variation in milk protein percentage.In conclusion,to obtain mitochondrial variation information from low depth resequencing data,mitochondrial homologous sequences in nucleus should be excreted first to improve the accuracy of results.Mitochondrial DNA has a certain genetic effect on milk production traits of Chinese Holstein dairy cows.