Preprint Communication Version 1 Preserved in Portico This version is not peer-reviewed

In-silico Discovery of Genetic Diversity in Cucumis sativus var. hardwickii: A Wild Relative of Cultivated Cucumber

Suniti Rawat
,
Vikas Kumar Singh
ORCID logo ,
Rahul Kumar
,
Meenakshi Sharma
,
Anil Kumar Delta
,
Parmdeep Singh Dhanda
,
Alpa Yadav
,
Prashant Kaushik
*
Version 1 : Received: 4 July 2023 / Approved: 4 July 2023 / Online: 4 July 2023 (08:55:12 CEST)

How to cite: Rawat, S.; Singh, V.K.; Kumar, R.; Sharma, M.; Delta, A.K.; Dhanda, P.S.; Yadav, A.; Kaushik, P. In-silico Discovery of Genetic Diversity in Cucumis sativus var. hardwickii: A Wild Relative of Cultivated Cucumber. Preprints 2023, 2023070167. https://doi.org/10.20944/preprints202307.0167.v1 Rawat, S.; Singh, V.K.; Kumar, R.; Sharma, M.; Delta, A.K.; Dhanda, P.S.; Yadav, A.; Kaushik, P. In-silico Discovery of Genetic Diversity in Cucumis sativus var. hardwickii: A Wild Relative of Cultivated Cucumber. Preprints 2023, 2023070167. https://doi.org/10.20944/preprints202307.0167.v1

Abstract

Genome-wide sequencing data play an important role in evaluating the genomic level differences between superior and poor-quality crop plants and improving our understanding of molecular association with desired traits. We analyzed the obtained 92,921,066 raw reads from genome-wide resequencing of Cucumis sativus var. hardwickii through in-silico approaches and mapped to the reference genome of Cucumis sativus to identify the genome-wide single nucleotide polymorphisms (SNPs) and Single nucleotide variations (SNV). Here, we report 19, 74,213 candidate SNPs including 1,33,468 insertions and 1,43,237 deletions and 75 Indels genome-wide. A total of 2228224 identified variants were classified into four classes including 0.01% sequence alteration, 5.94% insertion, 6.37% deletion and 87.66% SNV respectively. These variations can be a major source of phenotypic diversity and sequence variation within the species. During the present study these variants were also utilized to resolve orthologous relationships among the genomes of C. melo and C. sativus var. hardwickii. Overall, the discovery of SNPs and genomic variants may help predict the plant response to certain environmental factors and can be utilized to improve crop plants' economically important traits.

Keywords

Cucumis sativus var hardwickii; VEP; Genomic variation; SNP; SNV

Subject

Biology and Life Sciences, Biology and Biotechnology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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