Estimation of Genetic Variability between Populations (Lab Report Sample)

New England University
( BINF 550 )
127028956000
Estimation of Genetic Variability between Populations
(Diversity of Genetic Between Three types of cattle)
127046990000
Faten Alrashaid
May 18, 2014
Contents TOC \o "1-3" \h \z \u LIST OF TABLES PAGEREF _Toc415854373 \h iiiLIST OF ABBREVIATIONS PAGEREF _Toc415854374 \h iv1. Introduction PAGEREF _Toc415854375 \h 12. Background information PAGEREF _Toc415854376 \h 2Contribution by other authors (critical) PAGEREF _Toc415854377 \h 32. Literature review PAGEREF _Toc415854378 \h 33. Method PAGEREF _Toc415854379 \h 34. Presentation of results PAGEREF _Toc415854380 \h 5Variability relationship between eight of the breads PAGEREF _Toc415854381 \h 55. Discussion of the results PAGEREF _Toc415854382 \h 76. Conclusion PAGEREF _Toc415854383 \h 7References PAGEREF _Toc415854384 \h 9
LIST OF TABLES
TOC \h \z \c "Table" Table 1, Distribution of the heterozygote alleles in the population PAGEREF _Toc415853063 \h 7
Table 2, heterozygosity in the breeds PAGEREF _Toc415853064 \h 7
Table 3: Calculation on frequencies in each population PAGEREF _Toc415853065 \h 8
LIST OF ABBREVIATIONS
SNP – single nucleotide polymorph
FST – F-Statistics
USA – United States of America
Abstract
Genetic variation is the diversity within gene frequencies; the variation can lead to differences among a population or between populations. Mutation, Sexual reproduction and gene flow are activities that contribute to genetic variations in a given species. Mutation is the change that occurs in the DNA of an organism, gene flow like genetic drift is an activity that contributes to variation by movement of genes from one population to another (Andersson & Lönn, 2007).The research project will estimate the level of variability existing between Angus, Brahman and Santa cattle breeds: the aims will include establishing whether Santa and Angus cattle breeds show significant genetic variation from the Brahman cattle breeds’ .The research assumed that there was no significant variation between the genotypes of the three breeds to be able to test the variation if it exist. The null hypothesis stated that there was a significant genetic variation in the Angus and Santa cattle breeds as compared to the Brahman breed. While the alternative hypothesis stated that there was no significant genetic variability between Angus and Santa cattle breeds and the Brahman breed. Studying their genetic variability will certainly help researchers in considering whether the latter on discussed factors, contributed to an improved beef production or not, which was the objective of the research study. The gene pool considered in the study could be established with the aim of carrying out selection for genetic variability in animals. Results obtained in this research paper indicated the possibility of a strong correlation between cattle breeds selected for beef and increase in genetic variability.
1. Introduction
Giving a particular focus on sexual reproduction as the source of Variability, genetic variation will result from mating of any two potential parents so that their inheritable different characters are distributed throughout the succeeding generations in a population Ashley, Wilson, Pergrams, Dowd, Gende & Brown (2003). Currently in a given research study it was noted that variation can be used in the treatment of hepatitis c virus, which is a blood born infection. The research was done in the United States of America. Hepatitis c virus infection was noted to be the most common blood borne viral infection. The variation was noted to contribute to the manner in which the immune system responded to the drugs meant for treatment of hepatitis c virus; this variation was linked to differences in resistance and clearance of the virus among different individuals David L. T, Chloe L. T, Maureen, Ying, Donglian., Colm, Judith, Kenneth, Salim, Graeme, James, Gregory, Sharyne, Hugo, Leslie, Michael John David & Mary (2009).
Brahman is a European ancestral breed that might have undergone variations in its genotype due to ecological conditions it experienced. Their origin was traced back to India, but natural selection has been complimented by selective breeding that peaked in the last century with the development of well-defined breed types with a large genetic diversity (Porto-Neto, 2014). Santa cattle breeds were developed by mating Brahman bulls with pure breeds of beef shorthorn varieties. They were bred to achieve a genetically based progress in weight and hence arrive at a desired breed type (Santa Gertrudis). Brahman breeds developed remarkable adaptations for survival (Ok State Education), which was explored for selective breeding particularly in USA. Selective breeding have been done in USA to produce beef varieties of Brahman and polled varieties. Therefore, the Angus, Santa and Brahman cattle breeds have been developed for beef in different environments.
2. Background information
Genetic variation contributes to species evolution over time. Such distribution in freely breeding species result in genetic variability in the population thereby, molding the evolution of species across all taxa (Porto-Neto & Barendse ( 2014).Genetic variations emanate from variations in the genotypes of mating partners which occur under the influence of a number natural selection although human tailored selections are also prevalent (Lush, 1943). genomic signatures of selection is a contemporary scientific method which will help in discerning and studying genetic changes in the gene pool of a given population. This research study will focus on genetic variability in three cattle breeds and will be discerned using scientific computational methods. In recent research study, genetic variation have been used to show the impact of brains anterior cingulate cortex, in brain network when mediating a conflict Fan, Fossella, Sommer, Wu, & Posner (2003). The main challenge is mapping the genes.
Contribution by other authors (critical)
2. Literature review
During sexual reproduction, gene frequency has to be studied in order to ascertain genetic variability in a given species Vines & Rees (1974). The genes of each parent during fertilization combine to bring about variability among the off spring. Following homozygous and heterozygous frequencies as obtained by the Hardy -Weinberg equation, these conditions remain constant in the population until varied or changed by other factors such as selection, immigration or emigration, mutations and genetic drifts Vines & Rees (1974). These factors bring about phenotypic variations, irregularities and fluctuations in the population. Changes in the homozygote or heterozygote conditions result in changes in the gene proportions in the gene pool. This happens in both Autosomal and Sex-linked genes. This ultimately ends up varying the genome of the population. Furthermore, in domesticated animals, the natural factors that would be able to impose selective pressure are often overshadowed by human intervention. Intensive human-oriented selection for increased milk and beef production lead to genomic changes and gene variations that are called signatures of selection (Porto-Neto,2014)
3. Method
The research study, a total of 300 cattle; 100 from each of the three breeds were used in the analysis. All were genotyped using Bovine 50k map. More than 5460000 Single Nucleotide Polymorphism (SNP) Markers were used in the analysis in each of the cattle breeds. There were a total of 1099023 missing markers too. This was a limitation in the use of this method when establishing genetic variability. It was not possible to determine the alleles that were missing and yet these contributed significantly to selection and variations in the population. Each S.N.P provided 100 pairs of alleles for every cattle that was under research. 100 cattle were considered from each of the three breeds hence each population was having at least 5460000 pairs of alleles.The research study utilized, single nucleotide polymorph (S.N.P) and F – statistics (FST) in estimating genetic variability. High density (S.N.P) chips were used to determine the genotype of the animals. 100 animals from each breed were used in determining the SNP’s. Individual Fst for each SNP was not worked out but rather an average value for the breed population. Fst was conducted on the three breeds to determine their genetic variability. This was a more appropriate tool that would easily give genetic differentials between the alleles of the breeds. It gave a measure of the correlation between gametes drawn from the same sub population relative to the total (Gondro & Et-al,2013) Detection of Signatures of Selection using Fst, 2013). The larger the value obtained for Fst, the more varied the species are. The Angus and the Santa cattle breeds were compared to the Brahman breed in terms of variability to each other by their pair-wise Fst analytical results and heterozygosity.
4. Presentation of results
Table SEQ Table \* ARABIC 1, Distribution of the heterozygote alleles in the population




allele$ frequency$ in$

allele$ frequency$

allele$ frequency$

$$

Angus$

Brahman$

Santa$

Angus$

in$Brahman$

in$Santa$








AG$

1120728$

894139$

1080082$

0.20522771$

0.163734732$

0.197784614$








AC$

255133$

288220$

247916$

0.046719955$

0.052778846$

0.045398378$








GC$

29593$

22106$

27878$

0.00541907$

0.004048051$

0.005105019$








MISS...