Genome-wide CNV And High Altitude Candidate Genes Of Heme Oxygenase(Decycling) 1 In Yak(Bos Grunniens)

Domestic yaks(Bos grunniens) have great economic and scientific research value. In recent years, copy number variations(CNVs), which are associated with complex disease traits and quantitative phenotypes, are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity. Notwithstanding, little is known about the extent to which CNVs contribute to genetic variation in the yak. There is no SNP or CGH beadchip for detecting the genomic analysis in yak. So, an approach known as "cross-species analysis", whereby a hybridization chip of a closely related species is employed, can be used to circumvent this problem. Indeed, cross-species meta-analysis has previously been used to address many questions in biology and medicine. The cross-species approach has been employed for several studies in mammals. Human microarrays have been used to analyze closely related species, such as chimpanzees, orangutans and other primates.In this study, analyses of CNVs in the genomes of two domestic yak breeds(Tianzhu white yak and Qinghai yak) were performed using the Bovine HD Genotyping Bead Chip array with 777962 single nucleotide polymorphisms probes and an average spacing of 3.43 kb. Qinchuan cattle(Bos taurus) was selected as a concrol.Analyses of CNVs in Qinchuan cattle and two domestic yak breeds were performed using the Bovine HD Genotyping Bead Chip array, which led to our discovery of 367 unique CNV events from 6 Qinchuan cattles, and the average size was 35.5 kb. Taking into the consideration of some overlapping regions, the total of 365 autosomal CNVRs(131 losses and 234 gains) were identified with an average number of 60.8 CNV events per individual, which cover 13.13 Mb of the cattle genomic sequence and corresponding to 0.4 % of the whole cattle genome. The average and median sizes of CNVRs were 35.07 kb and 18.56 kb, respectively. The CNVRs map of Qinchuan cattle was first constructed based on the Bovine HD Genotyping Bead Chip array. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in molecular function ion(such as olfactory receptor activity, ion channel activity, substrate specific channel activity and channel activity passive), biological process(such as G-protein coupled receptor protein signaling pathway and cell surface receptor linked signal transduction) and pathway(Olfactory transduction). Comparison between results of the this study and results from other reported studies, that the same CNVRs were detected by 18.3 %, 5.6 %, 2.1 %, 8.7 %, 42.7 %, 0.7 %, 13.9 %, 0.9 %, 3.7 % and 2.1 %, respectively.We discovered 943 CNVs from 200 domestic yaks, with an average size of 120.76 kb. Taking into consideration overlapping regions, a total of 857 CNVRs were identified, including 558 losses, 297 gains, and 2 with both losses and gains, which cover 127.99 Mb of the bovine genomic sequence and correspond to 4.79 % of the autosomal genome sequence. The length of the CNVRs on autosomes ranged from 1.708 kb to 8.83 Mb with a mean size of 149.43 kb. A yak CNVRs map was constructed based on the Bovine HD Genotyping Bead Chip array. Functional analysis indicated that the CNVRs are significantly enriched for genes involved in olfactory receptor activity, the G-protein coupled receptor protein signaling pathway, and cell surface receptor-linked signal transduction; as well as genes integral to the membrane or intrinsic to the membrane and olfactory transduction. Seventeen CNVRs of “losses”, “gains” and “both” types were selected for validation, and 13 CNVRs were further experimentally confirmed by quantitative PCR. These results provide a resource for the identification of genetic factors that distinguish yak breeds that are better adapted to high altitude and for the understanding of ruminant biology and a further genetic improvement in yak breeds.Base on the results of beadchip in yak breeds, the heme oxygenase(decycling) 1(HO1) gene in the Tianzhu white yak is potentially adaptive for high altitude habitats. HO1 as a candidate gene, play a crucial role in normal cellular function in both laboratory animals and humans, and adapation in high altitude and hypoxia. In the present study, we amplified the c DNA of yak HO1 from liver by reverse transcription polymerase chain reaction(RT-PCR) and rapid-amplification of c DNA ends(RACE-PCR). The open reading frame(ORF) of c HO1 covered 867 bp encoding 289 amino acids. We have submitted the sequence to Genbank and got the succession number(KF 888632). A prediction of the secondary structure analysis of HO1 suggested that 139 amino acids was composed of 10 helical and 1β-sheets, 150 amino acids was formed of Random coil in HO1 protein. Predicted 3D structe comparison between yak, human and rat indicated that the single chain of c HO1 has the similar structure, however two main chain were overlaped respectively, another chain was distrubute in different spatial location. The heme iron, Fe2+ and gas molecule binding position were also predicted. All results revealed that yak, human and rat have silimlar single chain structure, but the spatial location struture were different from each other. Real-time quantitative PCR(q PCR) analysis indicated that c HO1 m RNA was predominantly expressed in yak lung tissues. Immunohistochemistry staining and Western blot analysis suggested that yak HO1 protein was also predominantly expressed in yak lung tissues. All results suggested that the function of HO1 have a closed relationship with respiratory system.