Genome-wide Characterization Of The Sudanese And Chinese Indigenous Sheep Populations By High Density SNP Arrays

Through long term natural and artificial selection,domestic sheep(Ovis aries)have become adapted to a diverse range of ecological environments and display multiple phenotypic traits.Characterization of diversity and selection signature is essential for genetic improvement,understanding of environmental adaptation,as well as utilization and conservation of sheep genetic resources.The rapid development of high throughput genotyping such as high density SNP Bead Chip arrays and whole genome re-sequencing allow us to discover million SNPs of the individuals' genome and quantify genome-wide genetic variation in sheep population.However,comprehensive researches are still limited and uncovered in Sudanese sheep as well as Chinses sheep to some extent.Here,we aimed to assess genetic diversity,population structure,and genomic selection among Sudanese native sheep and Chinese native sheep breeds using 600 K HD Bead Chip data.We collected a total of 280 individuals representing five Sudanese desert sheep AL-Ahamda(n =25),Buzee(n = 23),Hammri(n = 24),Kabashi(n =25)and Shanbali(n =24)with four Chinese sheep breeds Black Tibetan(n = 15),Oula(QOL =15),Tan(TS =18)and Zeku(n=15).Moreover,we compared five Chinese sheep breeds from extreme dry environments Hetian(n=19),Yabuyi(n= 20)and Karakul(n=20)and extreme humid environments Hu(n=17)and Wadi(n=17)sheep.In the second chapter,we provided a comprehensive literature review including the origin and domestication of sheep genetic resources in Africa and Asia,overview and distributions of Sudanese indigenous sheep,techniques and importance of molecular characterizations that make them importance targets for research,breeding and conservation.In third chapter,we investigated genome diversity,evolutionary relationship,population structure and genome-wide selection signatures between the five Sudanese thin-tailed desert sheep and four Chinese sheep breeds by using 600 K SNP Bead Chip in order to clearly characteristics the population and properly understand their genomics potential which provides a good opportunity for sustainable utilization,conservation and maintenance for genetic resources improvements in Sudanese sheep population.The analysis has revealed the low genetic diversity in the five Sudanese thin-tailed desert sheep ecotypes.PCA,phylogenetic analysis and ADMIXTURE analysis revealed AL-Ahamda slightly genetically differentiated.Unexpectedly,a few individuals of the Kabashi ecotype had a unique genetic background at K = 2.By comparing Sudanese thin-tailed desert with Chinese fat-tailed Tan sheep,selection signature analysis identified 41 candidate regions spanning 72 potentially novel and known genes that are associated with the response to heat stress(HSPA5,DNAJB14,and YTHDF1),lifespan(GAK and CPLX1),growth regulation(CSMD1,FGFR3,and BRCA1),body weight and height variation(DIS3L2 and TP53),fat deposition and tail growth(NPR2,ADD1,and SNORA73),metabolic pathways(ATP1B2,G6 BC,U2,STRT3,MYT3,and GLI1),production(FGF9 and LATS2),reproduction(TET2,H2 AFZ,OVOL1,SPAG4,EEF1A2,NPTX1,MELK,FGF2,PPP2R5 D,MAPKAP1,and LGR5),proliferation(PDE6B,XRN2,and EFNB3),immunity(COMMD4,ADPP1,FGB,SIGLEC1,and ELF4A1)and disease resistance and inflammatory responses(POLR2A,TNFSF13,CD68,SAT2,GAA,PPT2,RABEPK,SCAI,and LHX2).Our findings have offered insights into the genome architecture of Sudanese thin-tailed desert sheep,which call for the further investigations to determine whether the observed genome structure can characterize other African thin-tailed sheep.In the fourth chapter,we aimed to assess genetic diversity,population genetic structure and genome selection signatures among five Chinese native sheep breeds using 600 K HD Bead Chip in order to breeds characterization and a greater understanding their potential adaptation to diverse range of ecological environments as well as utilization,conservation and its essential for genetic improvement of Chinese sheep from extreme dry and humid environments.A total of 96 animals were selected from different geographical locations with extremes dry and humid environments.We found a high proportion of informative SNPs,ranging from 93.3% in Yabuyi to 95.5% in Wadi,Hu and Hetian breeds.The average estimated pairwise genetic differentiation(FST)among the population was 0.048%,ranging from 0.022% to 0.054% and indicating low to moderate genetic differentiation.PCA,ADMIXTURE,and phylogenetic tree analyses revealed a clustering of five Chinese sheep breeds according to geographical distribution,tail types,coat color,body size and breeding history.The regions of putative signatures of selection frequently overlapped with FST and XP-EHH approaches across the breeds,including candidate genes associated with disease resistance traits,defenses,innate and adaptive immunity response,digestive metabolism,growth,body size,milk production,wool production,and reproduction traits.The selective signature analyses suggested that,at least partially,a selection for economic traits and environmental adaptation into extreme arid and humid lands.The present study offer novel insights into genomic adaptation to arid and cold climates in sheep and other animals,and provides a valuable resource for further investigations.Moreover,it provides useful information for sustainable utilization and maintenance of genetic resource.In the fifth chapter,our aim was to investigate the occurrence and distribution of ROHs to characterize autozygosity of each breed,as well as to identifying the genomic regions with high ROH frequencies within individuals using 600 k HD Bead Chip to assessment the inbreeding and allows inferences the past demographic history and determine the genome-wide linkage disequilibrium(LD),the extent of effective population size(Ne).In total,96 animals were selected from five Chinese sheep breeds,from different geographical locations extremes dry and humid environments.In total,3046 ROHs were identified in all individuals,among which longer segments(>1-5Mb)were predominated.On the average,approximately 12% of the genome was covered by ROH segments;with the lowest coverage on OAR20 and the highest coverage on OAR2;Analysis of distribution ROH showed that,the majority of detected ROH were ranged >26 to 28 Mb,the lowest two breeds are Hetian and Hu sheep.The levels of ROH that were estimated reflect to the recent and ancient inbreeding history,which had an impact on the genome of the sheep breeds and suggesting that several animals experienced recent autozygosity events(YY,KK,and WD).The regions of putative signature of selection frequently overlapped with high ROH across the breeds,included candidate genes associated with disease resistance traits(5S_rRNA),innate and adaptive immunity response(HERC2 and CYFIP1),digestivemetabolism(CENPJ),Growth(SPP1),body size and developments(GJB2 and GJA3).Chapter five provides new insights into ROHs distribution patterns for future conservation strategies of Chinese sheep populations.Overall,the thesis provides valuable genome-wide information of genetic diversity,population relationship and structure,and selection signatures,which could be good opportunity for sustainable utilization and maintenance for the Sudanese and Chinese indigenous sheep populations.