IDEAS home Printed from https://ideas.repec.org/a/gam/jagris/v11y2021i2p166-d501208.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2077-0472/11/2/166/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/2077-0472/11/2/166/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    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)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Christina L Richards & Ulises Rosas & Joshua Banta & Naeha Bhambhra & Michael D Purugganan, 2012. "Genome-Wide Patterns of Arabidopsis Gene Expression in Nature," PLOS Genetics, Public Library of Science, vol. 8(4), pages 1-14, April.
    2. Jie Liu & Xuehua Zhong, 2024. "Epiallelic variation of non-coding RNA genes and their phenotypic consequences," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Minghui Kang & Haolin Wu & Huanhuan Liu & Wenyu Liu & Mingjia Zhu & Yu Han & Wei Liu & Chunlin Chen & Yan Song & Luna Tan & Kangqun Yin & Yusen Zhao & Zhen Yan & Shangling Lou & Yanjun Zan & Jianquan , 2023. "The pan-genome and local adaptation of Arabidopsis thaliana," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Xi Wang & Fan Zheng & Yuan-yuan Yi & Gao-yuan Wang & Li-xin Hong & Dannel McCollum & Chuanhai Fu & Yamei Wang & Quan-wen Jin, 2022. "Ubiquitination of CLIP-170 family protein restrains polarized growth upon DNA replication stress," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jagris:v:11:y:2021:i:2:p:166-:d:501208. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.