Study On Selection Signals Of Holstein And Jersey Cattle Based On Resequence Data

Holstein cattle have a large physique and high milk production,but are not heat-resistant;Jersey cattle have good heat resistance and high milk fat content,but their milk production is relatively low.They have undergone different breeding processes in history,informing their own distinct phenotypes.Studying their unique and shared selection signal characteristics can explain the molecular mechanisms underlying their phenotypic differences.The resequencing data of 462 cattles obtained from the 1000 Bull Genome Database include:150 Holstein cattle,70 Jersey cattle,50 Angus cattle,45 Charolais cattle,30 Limiousin cattle,40 Hereford cattle,50 Simmental cattle,and 27 Gelbvieh cattle.We studied the resequencing data of Holstein and Jersey cattle from different countries,as well as multiple European dual-use and meat-use breeds.At the same time,we analyzed the selection signal characteristics of Holstein cattle and Jersey cattle,and identified some candidate genes related to important economic traits combined with the c GTEx（Cattle genotype tissue expression）database.The results of this study are as follows:（1）After data quality control and mapping analysis with the bovine reference genome（ARS-UCD1.2）,a total of 12.19 million single nucleotide polymorphisms（SNPs）were obtained,mainly distributed in the inter gene region,accounting for 60.7%.（2）Calculate and statistically analyze the nucleotide diversity,linkage imbalance attenuation,the genomic genetic diversity of Holstein cattle and Jersey cattle is not abundant.The nucleotide diversity of Holstein cattle is at an intermediate level,while that of Jersey cattle is relatively low.The highest degree of linkage imbalance is found in Jersey cattle.The degree of genomic linkage imbalance in Angus cattle,Charolais cattle,Holstein cattle,Limiousin cattle,and Simmental cattle is very similar.The average length of homozygous fragments in different cattle populations is 1～2Mb.The above results indicate that the genome genetic diversity of Holstein cattle and Jersey cattle is not rich,and they may have been experienced a strong artificial selection.（3）Using Holstein cattle and Jersey cattle as test populations,and European dual use and meat use cattle as reference populations,detecting significant selection signals in Holstein and Jersey cattle by CLR,F_ST,θπ-ratio.In Holstein cattle,257 candidate genes were detected,of which 76.90～76.95 Mb on chromosome 4 were highly selected.The NPC1L1 and NUDCD3 genes contained in this region were related to lactation traits.There were three missense mutation in NPC1L1,and p.E732K and p.Y888C were highly conservative;p.V683M and p.E732K are located in the transmembrane domain of NPC1L1 protein,altering the physicochemical properties of amino acids.In Jersey cattle,152 candidate genes were detected,and 43.40～43.47Mb on chromosome7 was strongly selected.This region contains genes related to heat tolerance（MED16）and immunity（PRTN3,ELANE）,which may play an important role in the environmental adaptability of Jersey cattle.（4）Holstein cattle and Jersey cattle have 5 shared selected regions,including 1486 SNPs,which are matched with 137 cis e QTLs from 6 tissues and 3 trans e QTLs from 2 tissues.The genes involved in the shared selection region include C2CD4C,SHC2,FSTL4,BOP1,ADIPOQ,MROH1,GHR.MROH1 and GHR are significantly related to lactation traits and also have e QTLs.In summary,this study conducted population genetic diversity and genetic structure analysis on common cattle from multiple European countries,and analyzed the selection signal characteristics of Holstein cattle and Jersey cattle,and identified genes related to the excellent characteristics of cattles.This result provides a theoretical basis for further understanding the genetic basis and improvement of important traits in Holstein cattle and Jersey cattle.