Genetic Diversity Analysis Of Domestic And Wild Geese Breeds Based On STR Markers And The Correlation Between Growth Related Genes And Body Weight Of Geese Breeds

This study aimed to get a comprehensive understanding,better visualization of the genetic diversity,population structure and population relationship,the present situation of universal breeds and variety of geese breed with a trial to connect all these breeds to its ancestor.In the present study,we collected 26 universal geese breeds based on geographical distribution samples were gathered from:8 Chinese breeds(Yangzhou,Shitou,Yili,wanxi,Zhedong,Zhejiang and Taihu and Sichuan),10 European breeds(Landes,Roman,Leime,Carolas,Emden,Toulouse,Czech,white hungerian,Pomeranian and Hortobagy),4 African Egyptian breeds(grey Egyptian breed,black Egyptian breed,grey hybrid Egyptian breed and black hybrid Egyptian breed),2 wild breeds(graylag,pilgrim and white swan)and 1 American breed(Canada).the samples were collected on 2 steps from all across the world,one step was made in China(14 breeds)and the second was in the Arab republic of Egypt(12 breeds).Thesis framework was built on 2 experiments using two type of markers short tandem repeat markers(STR)and single neucleotide polymorphism markers(SNP);first experiment(divided on 3 phases depending on samples availability and place of conducting the experiment;each phase was named according to the number of available breeds 14 goose breeds,9 goose breeds and 8 goose breeds)was to determine ecological situation of 21 breeds,with a total of 1019 individuals,depending on 9 microsatellite loci were detected by STR-PCR.Allele frequency,expected heterozygosity(He),effective number of alleles(Ne)and polymorphism information content(PIC),genetic distance between groups were analyzed.The genetic diversity,phylogenetic tree structure and population genetic structure analysis including population clustering,population distribution and relationship between populations were preformed using Structure,xlstat and MATLAB program.To reveal the genetic diversity of domestic and wild goose based on STR markers.In the other hand,there are big differences in the types of domestic and wild geese breeds and their situation from extinction.Second experiment was to further explore the relationship between 2 key genes of growth and the body weight which will be helpful for the utilization and improvement of geese production.The SNPs of growth related genes(GH gene and PIT1 gene)were investigated and the effect of the different genotypes observed at each site and their relation to body weight were analyzed.The results will supply foundation for the development,utilization of an efficient breeding program of geese production.The results were summarized as follows:1.The genetic diversity of domestic and aboard geese based on STR markersSTR primers have been selected upon the principle of the number of alleles is high and highly polymorphic.microsatellite primers for 9 loci WWX1,CKW13,CKW14,CKW21,G10,TTUCG5,G07,CKW49 and CKW32.The results showed that the average range of Exp He ranged from 0.43±0.17 to 0.7±0.1.The lowest value were detected at Wanxi geese breed;while highest value were detected at white Emeden geese breed.on the other hand,at the 9 loci level the average range of Exp He ranged from 0.086 to 0.941.The lowest value were detected at CKW13 locus;while highest value were detected at TTUCG5 locus.The average range of Obs He ranged from 0.345±0.224 to 0.62±0.2.The lowest value were detected at Hortobagy geese breed;while highest value were also reported at Emeden geese breed.While on the loci level Obs He lowest value were detected at CKW13 locus by 0.088,and the highest value were also reported at TTUCG5 locus by 0.853.6 loci was reported highly polymorphic PIC>0.5.G1O,CKW21,TTUCG5,CKW49,GO7 and CKW32;2 loci reported medium polymorphic PIC>0.25.WWX1 and CKW14;and only one locus reported low polymorphism PIC<0.25 CKW13.The Ne number of the entire population ranged from 2.54± 1.533 to 4.868±3.024.The lowest value were detected at Hortobagy geese breed;while highest value were reported at white swan geese breed.The Ne number of the nine loci lowest value were detected at CKW13 locus by 1.09;while highest value were reported at TTUCG5 locus by 11.56.MATLAB was used to estimate Reynolds' genetic distance between groups.First part concerning the 14 goose breeds for the first experiment the closest distance between Canada and Hortobagy geese breed(1.28)and the highest between Yili geese breed,and Gray lag geese breed(6.3).second part concerning the 9 goose breeds;The 9 goose populations were divided into two clades.The first cluster was subdivided into two clusters containing the Egyptian grey breed population,and the other cluster contained the three Chinese breeds(Zhejiang,Wanxi and Sichuan).The second clade was subdivided into three clusters.The first was for the Pilgrim population,the second was for the Egyptian black breed population and the third was for the European breeds(Roman tufted head,Toulouse and Emden).third part concerning the 8 goose breeds,The eight populations were divided into two main branches.One for the European breeds;Czech,Pomeranian,and White Hungarian.The second one had three sub-divisions containing first one for Local Egyptian breed of black color,second one for commercial hybrid of Toulouse goose and Local Egyptian breed of black color(HY1)while the last branch had commercial hybrid of Toulouse goose and Local Egyptian breed of grey color(HY2),Local Egyptian breed of grey color,and Zhedong White breeds.Different bio-informatics methods were used to detect clustering among different goose breeds,The results would help to reveal the origin of domestic and aboard geese.STRUCTURE program was used in 2 experiments to determine population clusters;the first part(14 goose breeds)Some groups revealed a visual cluster but with interference of other groups.k=10 can seen a clear clustering for Hortobagy,Canada,grey Egyptian breed,gray lag,white swan,Yangzhou,Shitou,Leime,Carolas and Landes.K=11 was the same as K=10 except for more interference between the breeds.K=12 the clusters with clear identification were graylag,white swan,Yangzhou,Shitou,Leime,Carolas and Landes,K=13 can see clusters for only graylag,white swan,Yangzhou,Leime,Carolas and Landes.K=14 the clearest clusters were for graylag,white swan,Yangzhou,Shitou,Carolas and Landes.The second part(9 goose breeds)suggesting clustering numbers from k=5 to k=9.Some populations showed a definite cluster as did the three Chinese breeds(Sichuan,Zhejiang and Wanxi)for all of the assigned cluster numbers.The remaining 6 goose populations demonstrated definite clusters at K=5 and K=6,while Toulouse,Pilgrim and Egyptian black breed continued to give definite clusters(with some individual interference).The Roman tufted head,Egyptian grey breed and Emden breeds showed high individual interference from k=7 to k=9.Principal coordinates analysis(PCoA)was used in the second experiment(9 goose breeds)showing three clusters,The first cluster was for the three Chinese breeds,The second cluster was for the European breeds,while both the Egyptian local breed and Pilgrim were in the third cluster.3D clustering was performed using MATLAB in the second experiment(9 goose breeds)resulted in revealed that the Pilgrim,Emden,Toulouse,Egyptian black and Roman tufted goose populations formed the first cluster.On the other hand,the Egyptian grey breed,Zhejiang breed,Wanxi and Sichuan goose populations formed a more scattered second cluster.Principal component analysis(PCA)was calculated in second(9 goose breeds)and third experiment(8 goose breeds)reporting 9 definite clusters representing each population.A few scattered individuals were also noted for the Pilgrim and Sichuan populations within the Emden and Egyptian grey breed populations,respectively for the second experiment and definite eight population clusters divided into two levels.The first level showed Czech,White Hungarian and Pomeranian breeds clustering near each other;while the second level showed Local Egyptian breed of black color,HY1,and Zhedong White populations along with some interaction between HY2 and Local Egyptian breed of grey color populations for the third one.self-organising map(SOM)was constructed for the second(9 goose breeds)and third experiment(8 goose breeds);concerning the 9 goose breeds relationships among the breeds were presented by node number as follows:node(1)Pilgrim,Emden and Roman tufted breeds;node(2)Emden,Roman tufted,Egyptian black breed and Egyptian grey breed breeds;node(3)Roman tufted,Pilgrim,Emden and Egyptian black breeds;node(4)Egyptian black breed,Emden,Toulouse and Egyptian grey breed breeds;node(5)Toulouse,Egyptian grey breed and Egyptian black breeds;node(6)Egyptian grey breed,Emden,Egyptian black breed and Toulouse breeds;node(7)Zhejiang,Egyptian grey breed,Toulouse and Sichuan breeds;node(8)Sichuan,Toulouse and Zhejiang breeds;and finally node(9)Wanxi,Zhejiang and Sichuan breeds.As for the 8 goose breeds where(1)White Hungarian,Pomeranian,and Local Egyptian breed of black color populations,(2)Pomeranian,White Hungarian,Local Egyptian breed of black color,and Local Egyptian breed of grey color populations,(3)Local Egyptian breed of black color breed with White Hungarian,Pomeranian,Hyl and Local Egyptian breed of grey color populations,(4)HY1 breed with Local Egyptian breed of black color,HY2,Local Egyptian breed of grey color and Zhedong White populations,(5)HY2 breed with HY1,Local Egyptian breed of grey color,Czech and Zhedong White populations,(6)L2 breed with Local Egyptian breed of black color,HY1,HY2 and Pomeranian populations,(7)Czech breed with HY1 and HY2 populations(8)Zhedong White breed with Czech and HY2 populations.2.The diversity of geese based on growth related genes and correlation with their weightThe primers were designed to amplify growth related genes(GH gene and PIT1 gene).To detect 4 SNP C123T,and C158T for GH gene;A161G and T282G for PIT1.Exp He was recorded high in HY1 breed(0.49)for both C123T(GH gene)and G161A(Pit-1 gene)loci.Some loci showed homozygous genotyping.Obs He showed high values in HY1 breed for all the four SNPs loci 0.62(C123T),0.53(C158T)for GH gene and 0.66(G161A),0.48(G282T)for Pit-1 gene.Four breeds had moderate polymorphic loci:HY1 breed 0.4(C123T),0.28(C158T),0.48(G161A)and 0.42(G282T)and HY2 breed 0.36(C123T),0.4(C158T),0.3(G161A)and 0.37(G282T).Four SNP loci were reported to have a significant effect on geese body weight.They were CT genotype for C123T locus,TT genotype for C158T locus,GG genotype for G161A locus,and GG genotype for T282G locus.