Study On The Genomic Structural Variation Of Wild Yak And Domestic Yak Based On Resequencing Technology

The yak is an important livestock in the Qinghai-Tibet plateau of China and plays an irreplaceable role in the development of animal husbandry.Since its domestication,the yak has evolved into a range of breeds showing diverse phenotypes,reproductive physiology,and behavior characteristics due to natural and artificial selection.It is reported that genomic structural variation(SV)with a key determinant in the economic trait and adaptation of livestock.These studies are helpful to understand the genetic mechanism of the breeds’ formation and explore genes that are related to economic trait and plateau adaptation to allow for more targeted breeding of yak.In this study,nextgeneration sequencing was used to determine the genomic structural variations of four representative Chinese yak populations: wild yak,Datong yak,Qinghai Plateau yak,and Tianzhu white yak.We explored the features of structural variations(SVs)and their effects on the phenotypes of the yak.(1)A total of 99 yaks were selected in this research,which included 9 wild yaks and 30 yaks of each population of Datong yak,Qinghai plateau yak,and Tianzhu white yak.Genomic DNA was pooled by population.A total of 59.25 to 65.34 million high quality reads were obtained after filtering raw reads and 97.39% to 98.98% of these reads were mapped to the reference genome with a coverage of 94.35% to 94.43%.(2)A total of 168,063 SVs involving 12,911 genes were identified using Manta.These included deletions,insertions,duplications,inversions,and translocations,of which the latter comprised most of the SVs.Most SVs length ranged from 50 bp to 1000 bp.After subtracting the overlapping genes in different yak populations,we distilled 222 genes that were specific for wild yak,227 genes for Datong yak,140 genes for Qinghai plateau yak,and 198 genes for Tianzhu white yak.Gene ontology(GO)and signalling pathways analysis revealed that population specific genes were significantly enriched in processes involving muscle development,adaption to hypoxia,spermatogenesis,energy metabolism,and osteogenic differentiation.We identified 25 genes related to economic and plateau adaption by integration with the Animal Quantitative Trait Loci Database(Animal QTLdb).Genes such as NCAPG,CTNNBL1,DLX6,TPX2,FOXO4,and IGF1 were found to be related to growth and development and PPP2R5 A,GGNBP2,HMGB,KDM3 A and SBF1 to fertility.Plateau adaptation was linked to CREB3L1,EGLN3,CEP164,PCTP and PDGFA.(3)Furthermore,a total of 122,898 copy number variations(CNVs)involving 8,176 genes were identified using CNVnator.Loss of repeats was detected more often than gains.The length of the CNVs mostly ranged from 1Kb to 5Kb.After compared the CNV genes,we obtained 134 genes specific for wild yak,106 genes for Datong yak,845 genes for Qinghai plateau yak,and 104 genes for Tianzhu white yak.GO and signalling pathways analysis revealed that population specific genes were significantly enriched in processes involving muscle development,skeletal system,spermatogenesis,lipid metabolism,nervous system,and brain development.Integration with the Animal QTLdb identified 27 genes related to economic and plateau adaption and temper.Genes such as WNT7 A,COL1A1,ASB2,MECP2,and PCSK1 were found to be related to growth and development and SPACA7,TAF7 L,and BMP15 were related to fertility.Plateau adaption was linked to HCN4,FABP2,GADD45 A,KRT71,and NRP1,CACNA1 H,GPR88,and NLGN3 were related temper,whereas ADIPOQ influenced meat quality.