Linkage Disequilibrium

Genes underpin the molecular basis of phenotypic variation among individuals. By identifying the position underlying gene via gene mapping, it is possible to uncover the evolutionary principles which account for phenotypic variations. In this practical, we associated ten simple sequence length polymorphism (SSLP) markers with three phenotypes to identify any possible association between a marker and certain phenotype in Arabidopsis. Those three phenotypes were: did the plant show flowering, did cell death observe in the plant and finally the rosette diameter. The first two phenotypes were qualitative traits scored with yes or no answer whereas the later was a quantitative phenotype with a continuous distribution and measured in centimeter.

Chi-square test was conducted to account for the association between SSLP markers and the qualitative phenotypes which had a discrete distribution. Since our sample size was 12, there was 10 degrees of freedom as we would need to account for two variations of whether it flowered or displayed cell death. An outcome with a Chi-square value of 18.31 or more would be interpreted as significant at 5% confidence level. Hence, it would mean that the marker was highly associated with a particular trait. Firstly, the flowering trait was scored as this trait was more obvious as compared to scoring the plant’s cell death. The FRIGIDA (FRI) alleles were shown to account for natural variation in flowering time in Arabidopsis. FRI exhibited linkage disequilibrium with the flowering trait as they tend to be inherited together to the next generation.

However, our empirical result contradicted the literature as the Chi-square value for this trait was 7.922 with a P-value of approximately 0.75.This implied t...

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... Thus, scoring a simple and easy trait appeared to be the strength of our study.

However, low sample size was one of the demerits of our study which might have resulted in the insignificance of our results. Our experimental subject comprised of only 12 Arabidopsis plants with a unique accession stock number whereas Caporaso’s study involved over two thousands human subjects. A low sample size would definitely be unfavourable as some outliers could bias the outcome of statistical analysis.

Works Cited

1. Caproraso N, Gu F, Chatterjee N, Sheng-Chih J, Yu K, et al.(2009) Genome-wide and candidate gene association study of cigarette smoking behaviors. PLoS ONE 4(2): e4653.

2. Johnson U, West J, Lister C, Michaels S, Amasino R, et al.(2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290:344-347.