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Exploring the Effect of Climate Factors on SNPs within FHA Domain Genes in Eurasian Arabidopsis Ecotypes

Author

Listed:
  • Tamer Aldwairi

    (Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA
    Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA)

  • David J. Chevalier

    (Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
    Department of Biology, East Georgia State College, Swainsboro, GA 30401, USA)

  • Andy D. Perkins

    (Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA)

Abstract

The rapid developments in high-throughput sequencing technologies have allowed researchers to analyze the full genomic sequence of organisms faster and cheaper than ever before. An important application of such advancements is to identify the impact of single nucleotide polymorphisms (SNPs) on the phenotypes and genotypes of the same species by discovering the factors that affect the occurrence of SNPs. The focus of this study is to determine whether climate factors such as the main climate, the precipitation, and the temperature affecting a certain geographical area might be associated with specific variations in certain ecotypes of the plant Arabidopsis thaliana . To test our hypothesis we analyzed 18 genes that encode Forkhead-Associated domain-containing proteins. They were extracted from 80 genomic sequences gathered from within 8 Eurasian regions. We used k-means clustering to separate the plants into distinct groups and evaluated the clusters using an innovative scoring system based upon the Köppen-Geiger climate classification system. The methods we used allow the selection of candidate clusters most likely to contain samples with similar polymorphisms. These clusters show that there is a correlation between genomic variations and the geographic distribution of those ecotypes.

Suggested Citation

  • Tamer Aldwairi & David J. Chevalier & Andy D. Perkins, 2021. "Exploring the Effect of Climate Factors on SNPs within FHA Domain Genes in Eurasian Arabidopsis Ecotypes," Agriculture, MDPI, vol. 11(2), pages 1-10, February.
    • Handle: RePEc:gam:jagris:v:11:y:2021:i:2:p:166-:d:501208
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    References listed on IDEAS

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    1. Xiangchao Gan & Oliver Stegle & Jonas Behr & Joshua G. Steffen & Philipp Drewe & Katie L. Hildebrand & Rune Lyngsoe & Sebastian J. Schultheiss & Edward J. Osborne & Vipin T. Sreedharan & André Kahles , 2011. "Multiple reference genomes and transcriptomes for Arabidopsis thaliana," Nature, Nature, vol. 477(7365), pages 419-423, September.
    2. Daniel M. Scolnick & Thanos D. Halazonetis, 2000. "Chfr defines a mitotic stress checkpoint that delays entry into metaphase," Nature, Nature, vol. 406(6794), pages 430-435, July.
    3. Robert J. Schmitz & Matthew D. Schultz & Mark A. Urich & Joseph R. Nery & Mattia Pelizzola & Ondrej Libiger & Andrew Alix & Richard B. McCosh & Huaming Chen & Nicholas J. Schork & Joseph R. Ecker, 2013. "Patterns of population epigenomic diversity," Nature, Nature, vol. 495(7440), pages 193-198, March.
    Full references (including those not matched with items on IDEAS)

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