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The Genetic Diversity, Genetic Differentiation of Six Cattle Populations in Bovidae in China and the Statistical Methods of Genetic Diversity Research

Author: MaoYongJiang
Tutor: ChangHong;YangZhangPing
School: Yangzhou University
Course: Animal Genetic Breeding and Reproduction
Keywords: Chinese yellow cattle breeds Buffalo Yak Blood protein loci Microsatellite Genetic diversity Genetic differentiation Weitzman genetic diversity Genetic distances Beyes theory
CLC: S823
Type: PhD thesis
Year: 2006
Downloads: 545
Quote: 4
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Abstract


Applying the method of simple random sampling in typical colony, 346 individuals from 6 cattle populations (Luxi, Bohai black, Minnan, Qinhai yak, Chinese Holstein and buffalo) in 4 species in Bovidae were sampled. The genetic diversity for 21 blood protein (enzyme) loci and 12 microsatellite were studied using polyacrylamide gel electrophoresis (PAGE) and starch gel electrophoresis (SGE) and the results were analyzed using different statistical methods. In the meantime, the genetic diversity of 20 indigenous Chinese yellow cattle populations were analyzed with Weitzman approach based on the information of FAO-domestic animal diversity information system (FAO-DAD-IS) and standard genetic distances from 6 polymorphic blood protein loci. The results were as following:1. The genetic diversities within and between populations were calculated using the data of 21 blood protein (enzyme) loci, the NJ and UPGMA phylogenetic trees were constructed by standard genetic distance and DA genetic distances and the divergence times among Bos, POephagus and Bubalus bulalus (swamp type) were estimated by standard genetic distance. The results showed that, 13 protein (enzyme) loci were polymorphic across 6 cattle populations in 21 loci. Minnan showed the highest genetic variability, the observed number of alleles (Na), mean effective number of alleles (MNA), mean heterozygosity (He) and the proportion of polymorphic loci were 2.1538, 1.5072, 0.2788 and 47.62%, respectively. The Buffalo showed the lowest genetic variability, the observed number of alleles (Na), mean effective number of alleles (MNA), mean heterozygosity (He) and the proportion of polymorphic loci were 1.3846, 1.2032, 0.1279 and 23.81%, respectively. The global heterozygote deficit across 6 cattle populations (Fit) amounted to 67.0%(p<0.001). The overall significant (p<0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 26.9%. The 6 cattle populations were highly differentiated (Fst=54.5%, p<0.001) with all loci. The heterozygote deficit within population (Fis) showed significant level for Luxi, Bohai, Minnan and Buffalo (p<0.001 or p<0.01). The average number of effective migrants exchanged per generation (Nem) was highest (7.8933) between Luxi and Bohai, and lowest (0.0700) between Yak and Buffalo. Luxi, Boahai and Minnan showed relative close kinship from the NJ and UPGMA phylogenetic trees constructed by standard genetic distance and DA genetic distance as comparison with Holstein, Yak and Buffalo, and this implied that Luxi, Boahai and Minnan probably have same or similar origin. It was estimated to have diverged about 1.4570 million years ago (MYA) between Bos and P(?)ephagus, about 2.9475 MYA with Bubalus bulalus(swamp type), and about 5.4288 between P(?)ephagus and Bubalus bulalus (swamp type).2. The genetic diversities within and between populations were estimated using 12 microsatellite markers. The phylogenetic trees were constructed byδμ2 and DA distances and the divergence times among Bos, P(?)ephagus and Bubalus bulalus (swamp type) were estimated byδμ2. The results showed that, 144 microsatellite alleles and 24 private alleles were identified for 12 microsatellites in 6 cattle populations. The private alleles ranged from 2 in Bohai and Buffalo to 10 in Holstein. Holsein had the highest genetic variability, the observed number of alleles (Na), mean effective number of alleles (MNA), mean heterozygosity (He) were 7.7500, 4.9722 and 0.7719, respectively. Buffalo and Yak showed low genetic variability, and mean heterozygosity were 0.5400 and 0.5325, respectively. The global heterozygote deficit across 6 cattle populations (Fit) amounted to 57.6%(p<0.001). The overall significant (p<0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 42.5%. The 6 cattle populations were highly differentiated (Fst=26.1%, p<0.001) with all loci. The average number of effective migrants exchanged per generation (Nem) was highest (1.149) between Luxi and Holstein, and lowest (0.449) between Yak and Buffalo. Luxi and Holstein grouped first, followed by Bohai and Minnan, Yak branched next and Buffalo emerged as the most divergent population from other cattle populations. It were estimated to have diverged about 0.1867 million years ago (MYA) between Bos and P(?)ephagus, about 0.4792 MYA with Bubalus bulalus(swamp type), and about 0.3272 between P(?)ephagus and Bubalus bulalus (swamp type).3. Using the information of 25 markers for 13 blood protein and 12 microsatellite, the linkage disequilibrium analyse showed that, Luxi, Holstein, Minnan and Buffalo were in linkage disequilibrium, Bohai and Yak were in linkage equilibrium. The global heterozygote deficit across 6 cattle populations (Fit) amounted to 65.73%(p<0.001). The overall significant (p<0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 42.81%. The 6 cattle populations were highly differentiated (Fst=40.58%, p<0.001) with all loci. The average number of effective migrants exchanged per generation (Nem) was highest (0.9785) between Luxi and Bohai, and lowest (0.1963) between Yak and Buffalo. Luxi, Boahai and Minnan showed relative close kinship from the NJ and UPGMA phylogenetic trees constructed by DA genetic distance as comparison with Holstein, Yak and Buffalo, and this implied that Luxi, Boahai and Minnan probably have same or similar origin. There were some differences in genetic variability, genetic differentiation, phylogenetic trees and diverged time between blood protein loci and microsatellite loci. The observed number of alleles (Na) of microsatellite was from 3.1 to 3.55 times than Na of blood protein loci. The mean effective number of alleles (MNA) of microsatellite was from 1.97 to 3.77 times than blood protein loci, the expected mean heterozygosity (He) of microsatellite was from 1.71 to 3.16 times than blood protein loci, the observed mean heterozygosity (Ho) of microsatellite was from 2.03 to 4.55 times than blood protein loci, the PIC of microsatellite was from 2.18 to 4.94 times than blood protein loci. The coefficient of gene differentiation among cattle populations from blood protein loci was 2.1 times than microsatellite. The ascription of Bohai cattle was different in the phylogenetic trees constructed from blood protein loci and microsatellite markers. The diverged time among among Bos, POephagus and Bubalus bulalus (swamp type) from blood protein loci was about from 6 to 16 times than microsatellite. It’s superior to access the genetic diversity and genetic differentiation between different species in Bovidae using microsatellite than using blood protein loci. The observed number of alleles (Na) were equal or larger than 4, and PIC were above middle level for 3 microsatellite (IDVGA-2, TGAL-122 and BM1824), this implied that these 3 microsatellite were more appropriate to access the genetic diversity and genetic differentiation between different species in Bovidae than other microsatellite markers.4. 6 genetic distances (DA, DC, Ds, Dsw, (σμ)2and DTL) and 2 cluster methods (UPGMA and NJ) were adopted to evaluate the reliabilities of reconstruction of phylogenetic trees, (σμ)2 and DTL genetic distances were used to estimation of genetic differentiation based on the microsatellite data of 6 cattle populations in China. The results showed that, the reliabilities of reconstruction of phylogenetic trees were affected significantly by the heterozygosity of loci. DA genetic distance generally showed higher reliability than other distances to obtain the correct phylogenetic tree, but it was difficult to confirm which is better for NJ and UPGMA to obtain the correct phylogenetic tree. DTL genetic distance needed to been improved to construct the phylogenetic tree. It cann’t to estimate the divergence times between different sapeics with DTL genetic distances from microsatellite. The divergence time derived from (σμ)2 distances should compare with the divergence time derived from mtDNA, palaeontology and historical records in order to get proper results. At last, usefulness and limitations were discussed to reconstruct of phylogenetic trees and estimate genetic differentiation from microsatellite.5. The data about 12 microsatellite for 6 cattle populations were analyzed with 3 software (GENECLASS, STRUCTURE and BAPS) based on the Beyes Theory from individual and population level. The results showed that, the probabilities calculated by GENECLASS were highest from individual and population level, and they were equal almost by STRUCTURE and BAPS. The clustering figure can been reflected dynamically by the variable inferred clusters, and the distributing figure of estimated membership probabilities of each individual to different genetic clusters for different inferred clusters can visible for STRUCTURE and BAPS. But when the inferred clusters were small (K<4) for BAPS, it is difficult to get an accurate conclusion, and this problem needs further improvement. For the running time, STRUCTURE was slowest, and GENECLASS was fastest. With the application of these 3 software, on the one hand, it can provide new evidences for the revealing of the true genetic structure and kinship of among populations. On the other hand, it can put into individual level from population level in the study of population genetics and genetic diversity. In the meantime, these 3 software can apply to the implication of crossing breeding in animal, individual identification and the protection of wild animal.6. The extinction probability, current and expected future diversity, breed contribution, marginal diversity and conservation potential of 20 yellow cattle breeds in China were calculated, and the maximum likelihood tree was constructed with Weitzman approach. 3 allocation methods of conservation funds were introduced and the optimal allocation of conservation funds was simulated. The results showed that, significant positive correlations existed between the total population size (POS), distribution of the breed (DIS), breeding organization and protecting measures (ORG), special traits (SPE) and extinction probability (p<0.01 or p<0.05). The current diversity of 20 yellow cattle breeds was 1.2650, the expected future diversity was 0.8813 after a given time (50 years). The maximum likelihood tree was similar with the UPGMA tree, but there were some differences between them. The breed contributions of Hainan (14.29%) and Dabieshan (12.96%) were highest. The marginal diversities and conservation potentials of Fuzhou, Dabieshan and Hainan were highest. The conservation funds were averaged to each cattle breed under model C. Significant positive correlations exited between the priority, allocated shares of conservation funds and the conservation potential for one cattle breed under model A and model B (p<0.001). Most shares of conservation funds were allocated to Fuzhou, Dabieshan and Hainan under model A and model B. The expected diversity was largest for model C (1.2650) and was least for model A (0.8920). The returns in terms of expected diversity to investment are diminishing for all 3 models. The real objects for animal protection should include the genetic diversity between breeds, but also genetic diversity within breeds, breed special traits, present and expected economic utilization. Weitzman genetic diversity concept was similar with the systematic conservation theory presented by Prof. Sheng Zhilian, but in the meantime some differences existed between them. Now it looks very attracted to reveal the animal genetic diversity in China and to allocate the conservation fund with Weitzman approach, because some works about the animal genetic diversity in China with molecular markers have been finished. At last, the limitation and development of this method were discussed.

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