Genetic Variations Of Y Chromosome And Their Associations With Male Fertility In Cattle

Reproductive efficiency is one of the most important economic traits in livestockproduction. It can generate huge economic benefit if we could select bull with high fertility atan early age. Y chromosome, because of its male sepefic characterization and important rolesin male reproduction, supplies us a valuable genetic resource to seek the molecular markersfor bull selection at early stage.The current study has done three different analyses to15different cattle breeds,including Holstein. First, we investigated the paternal pedigree of Holstein bulls in NorthAmerica for the purpose of understanding bovine Y chromosome (BTAY) diversity inmacroscopic level. Second, we analyzed the copy number varitions (CNVs) of three bovineY-linked multicopy genes using quantitative-PCR (qPCR). Last, we investigated the43SNPsof12single copy bovine Y-lined genes and98genetic variation loci of5Y-linked multicopygenes. The major findings are as follow:(1) The objective of this part is to investigate the effective population size of the HolsteinY chromosomes and the effects of the limited Y chromosome lineages on the malereproduction and the future of the breed. Paternal pedigree information of62,897Holsteinbulls born between1950and2013in North America were collected and carefully analyzed.The results indicated that the number of Y chromosome lineages in Holsteins have undergonea dramatic decrease during past six decades as a consequence of artificial selection and theapplication of the artificial insemination (AI) technology. These Holstein AI bulls in NorthAmerica were the descendants of only four ancestors, namely Hulleman (Registration No.886HHB, birth date3/27/1881), Neptune H (Registration No.711HHB, birth date3/23/1880),Netherland Prince (Registration No.716HHB, birth date4/1/1880) and Jacob (RegistrationNo.608HHB, birth date2/25/1880). We found that founder had no significant effect malereproductive traits of their descendant. Among three dominant founder families are present in2010s, HOUSA1441440had significantly worse milk performance than other two. In order toconserve Y chromosome diversity in Holstein population, the current study suggests the futurebreeding program should select elite AI bull within different Y-lineage, and importation of exogenous paternal origins can be implemented in Holstein breeding program.(2) The objective of this part is to investigate the CNV of PRAMEY within and acrossbreeds and to determine whether the CNV is associated with reproductive traits in Holsteinbulls. A quantitative real-time PCR method was applied to measure the copy number (CN) ofPRAMEY among460bulls using a Y-linked single copy gene, DEAD box polypeptide3,Y-linked (DDX3Y), as a reference. The results revealed that the median CN of PRAMEY was13, ranging from2to31. Significant variations in the PRAMEY CN were observed among15breeds investigated. Holstein bulls had the lowest median CN (12), whereas Limousin bullspossessed the highest median CN (26). Furthermore, bulls in the taurine lineage (13) had asignificantly lower median CN than those bulls in the indicine lineage (20). Associationanalysis revealed that the PRAMEY CN was correlated negatively with scrotal circumference(SC), relative scrotal circumference (RLSC), percentage of normal sperm (PNS), andnon-return rate (NRR), but had no significant association with post thaw motility (PTM),incubated motility (IM), percentage of intact acrosome (PIA), sire conception rate (SCR) andrelative breeding efficiency (RBE). The data from this study suggest that the CNV of thePRAMEY gene family is associated with male reproductive traits and may serve as one ofvaluable markers for sire fertility selection at an early age in cattle.(3) We investigated the copy number (CN) of the bovine HSFY and ZNF280BY in a totalof460bulls from15breeds using a quantitative PCR approach. We observed CNVs for bothgene families within and between cattle breeds. The median copy number (MCN) of HSFYamong all bulls was197, ranging from21to308. The MCN of ZNF280BY was236, varyingfrom28to380. Furthermore, bulls in the Bos taurus (BTA) lineage had a significantly higherMCN (202) of HSFY than bulls in the Bos indicus (BIN) lineage (178), while taurine bulls hada significantly lower MCN (231) of ZNF280BY than indicine bulls (284). In addition, the CN ofZNF280BY was positively correlated to that of HSFY on the BTAY. Association analysisrevealed that the CNVs of both HSFY and ZNF280BY were correlated negatively with testissize, while positively with sire conception rate. The study suggests that the bovine HSFY andZNF280BY gene families have extensively expanded on the Y chromosome during evolution.These variations were associated with testis size and bull fertility in Holstein, suggesting thatthe CNVs of HSFY and ZNF280BY may serve as valuable makers for male fertility selection incattle.(4) The study analyzed single nucletide polymorphsims (SNPs) of Y-linked single copygenes and genetic varitations of Y-linked multicopy genes in840bulls using VeraCode384OPA technology. A total of21Y-SNPs were identified in818Holstein bulls. Of those,17SNPs were significantly associated with concenption rate, sperm motility and sperm morphology, which can be severd as valuable markers in early selection of Holstein bulls. Inaddition, according to the analyzing genetic variation loci of Y-linked multicopy in22bullsfrom Bovine HapMap project and one Qinchuan breed, we found these loci can distinguishBos taurus and Bos indicus lineage, which confirmed that there are huge difference inY-ampliconic region between Bos taurus and Bos indicus.