Discovery Of Gene Loci And Development Of Liquid Chip For Altitude Adaptation In Cattle

The improvement of Tibetan cattle began in the 1980s.At present,the progressive cross of Tibetan improved cows（Holstein×Tibetan cattle）has been carried out to F₃ generation or above.With the increase of improved generations,its plateau adaptability is significantly reduced,the mortality rate is about 20%,and the milk yield is only more than 2300 kg.Therefore,cross fixation and generation selection of improved populations must be carried out to retain the good lineage of Tibetan cattle for plateau adaptation.In this study,through population genomics analysis of continuous altitude cattle,we explored plateau adaptation loci of Tibetan cattle and created a low-cost high-throughput genotyping liquid chip to provide molecular means for rapid and accurate selection of plateau tolerant individuals.Findings were as follows:Firstly,cattle from five altitude gradients of 500 m（Yingjiang,Damaidi）,1500 m（Tengchong）,2500 m（Lijiang）,3000 m（Diqing）and 3500 m（Gongbujiangda）were selected as the research objects.By FST（3500-500 m）,MEMEA and Bay Pass analysis,10108 altitude associated loci were screened.The reference genome ARS-UCD1.2 was used for annotation and enrichment analysis of the selected sites,and 38 KEGG significant pathways and 436 related pathway genes were enriched.Eight genes,PIK3R5,VASP,EFNA5,NFATC4,CREB3,SPP1,CAMK2B and LAMP3,were significantly associated with hypoxia.Secondly,based on the 10108 altitude associated loci screened,combined with the animal QTL database and the filling sites necessary for the production of dairy chip,a dairy cow hypoxia functional liquid chip（10K,Yanxing-1）based on targeted capture sequencing was created.The microarray included 10108 hypoxia-related functional sites,3552 filled sites in the cow chip,and a total of 11637 sites after the two were checked.Finally,the chip was used to genotype 1551 Tibetan improved cattle,and a total of10138 high-quality SNPs were detected after filtering.The average capture efficiency of target SNPs was relatively high,which was 87.12%,and the average sequencing depth of target SNPs was 5×.At the same time,the GWAS analysis combined with the blood physiological indicators of Tibetan improved cattle showed that CRTC3,GADD45A and MZF1 genes were related to HIF and related pathways.The results showed that the association between altitude related loci and blood physiological phenotypes was not significant,and further studies are needed to expand the fitness indicators such as heart and lung.In conclusion,in this study,through population genome analysis of continuous altitude cattle,altitude related genes and loci were screened,and based on these loci,a bovine hypoxia functional liquid chip（10K）was created.The chip has the advantages of accurate typing,low cost and rich functional loci.The results prove the reliability of the chip.This chip can be directly used for cross fixation and generation selection of improved dairy cows in plateau.