Genome-wide Genetic Diversity And Selection Signature Of Qinghai Yak

Yak(Bos grunniens),a "unique" bovine species,lives in Qinghai-Tibet Plateau and adjacent highlands.Qinghai Province is located in the northeast of Qinghai-Tibet Plateau with rich yak genetic resources.At present,there are few systematic studies on genetic diversity,population structure and genomic selection signature of yak breeds(populations)in Qinghai Province.Based on the previous researches of molecular genetic markers of Qinghai yak,the current study taked 8 Qinghai yak breeds(populations)with special genetic information and rich genetic diversity as the research object.A total of 42yaks(i.e.6 Datong yaks,6 Yushu yaks,5 Xueduo yaks,5 Huanhu yaks,5 Geermu yaks,5 Qilian yaks,7 Tongde yaks and 3 Huzhu white yaks)were resequenced with high-depth genome re-sequencing technique(21.92X~28.60X)and then analyzed together with reported genome re-sequencing data of 71 yaks(19 wild yaks,23 Datong yaks,16 Yushu yaks,7 yaks around the lake,3 Geermu yaks and 3 Qilian yaks).The genome-wide genetic diversity,population structure and selection signatures of Qinghai yaks were revealed by comprehensive analysis of 113 yak genome data sets(average sequencing depth of 12.3X)from one wild yak population and 8 Qinghai yak breeds(populations)in China.The results are as follows:1.The nucleotide diversity(Pi),heterozygosity(H),runs of homozygosity(ROH),linkage disequilibrium(LD)and inbreeding coefficient(F)of 9 yak breeds(populations)were analyzed.The results showed that wild yak and Qinghai yak breeds(populations)had rich genomic genetic diversity and different inbreeding degree.Except that the nucleotide diversities of wild yak,Qilian yak and Geermu yak were lower(0.0006~0.0009),the nucleotide diversities of other domestic yak breeds(populations)were higher(0.0011~0.0015).The nucleotide diversities from big to small were: Huzhu white yak > Tongde yak > Xueduo yak > Datong yak > Huanhu yak > Yushu yak > wild yak > Qilian yak > Geermu yak.There was a little difference in heterozygosity among 9yak breeds(populations).Huzhu white yak population had the highest observed heterozygosity(0.3454)and expected heterozygosity(0.4752),while Datong yak breed had the lowest observed heterozygosity(0.1443)and expected heterozygosity(0.2699).The results of ROH showed that the count and length of ROH of Geermu yak and wild yak populations were both small,but the count and length of other yak breeds(populations)were higher.The order of count and length of ROH were: Datong yak >Yushu yak > Huanhu yak > Tongde yak > Huzhu white yak > Xueduo yak > Qilian yak >wild yak > Golmud yak.In linkage disequilibrium(LD)analysis,Huzhu white yak had the highest linkage disequilibrium,followed by Xueduo,Tongde,Qilian,Yushu,Huanhu,Datong and Geermu yaks,while the wild yak population had the lowest LD.Analysis of inbreeding coefficient(F)showed that the F values of Huzhu white yak,Tongde yak,Xueduo yak and Datong yak were higher(0.1747 ~ 0.2841),but that of the other yak breeds(populations)were lower(-0.0394 ~ 0.0687).2.The comprehensive studies of ancestral component,principal component and phylogenetic analyses showed that 9 yak breeds(populations)were clustered into three clusters: wild yak population,Geermu yak population,and the other 7 yak breeds(populations)(Datong,Huanhu,Yushu,Qilian,Xueduo,Tongde and Huzhu yak).9 yak breeds(populations)were composed of two big genetic lineages(i.e.Lineage Ⅰ and Lineage Ⅱ),so it was speculated that yak has two origins.3.Analysis of genetic differentiation among 9 yak breeds(populations)showed that the fixation index(Fst)among breeds(populations)were between 0.007 and 0.076.Except that the wild yak and Geermu yak populations were moderately differentiated from the other seven yak breeds(populations)(0.05< Fst <0.15),the differentiation among the other breeds(populations)were weak(0 < Fst < 0.05).The results of cluster and multi-dimensional scale analysis based on Fst value showed that 9 yak breeds(populations)could be divided into six categories/groups(wild yak,Geermu yak,Huan yak and Qilian yak had each one category,Yushu yak and Datong yak had one category,and Xueduo yak,Tongde yak and Huzhu white yak had one category).Based on the results of genetic differentiation and cluster analysis,Geermu yak and Qilian yak could be used as potential new genetic resources for in-depth research,development and utilization.4.Based on two methods(CLR and π),64 candidate genes were identified in Qinghai yak breeds/populations.These genes related to disease resistance(WARS1,COPS7 B,and SLC25A48),hypoxic adaptation(CLUH,NFAT5 and CBL),melanosis(MCAM,RNF26 and BOP1),fecundity(RFX4,RNF17 and WDR25),milk quality(OPLAH,GRINA and PARP10),immunity(NOD1,FBXL20 and SLC4A11),neurodevelopment(PAFAH1B1,ITPA and TOM1L2),environmental adaptation(CAMK,SUSD4 and HSF1)and meat quality(ZRANB1).At the same time,the pathways related to substance metabolism,smell,digestion and absorption,heat production,vasoconstriction and disease resistance were also identified.The above results systematically revealed the genome-wide genetic diversity,differentiation,clustering relationship,genetic background and selection signatures of Qinghai yak breeds(populations)at genome-wide leveland provided genetic information and basic data for a comprehensive understanding of the genome-wide genetic diversity,differentiation,phylogeny,classification and selection of Qinghai yak.At the same time,it laid a theoretical foundation for the exploration,rational protection and utilization of Qinghai yak genetic resources and the corresponding practice of molecular breeding.