Genetic variation of Nang Thom Cho Dao rice variety based on whole genome sequencing-Reference-Cited by-同舟云学术

Genetic variation of Nang Thom Cho Dao rice variety based on whole genome sequencing

Published:2022-11-29 Issue:3 Volume:14 Page:40-44
ISSN:2815-5602
Container-title:Can Tho University Journal of Science
language:
Short-container-title:CTUJS

Author:

Huynh Ky,Van Quoc Giang,Nguyen Loc Hien,Nguyen Chau Thanh Tung,Huynh Nhu Dien,Nguyen Nhut Thanh,Vo Cong Thanh,Yeap Swee Keong

Abstract

High-performance sequences are generating increasingly comprehensive catalogs of crop genetic variation. To make optimal use of this vast collection of data for research purposes, a robust and reproducible analytical pipeline discipline is required that is capable of accurately detecting and favoring variants. The entire genome sequencing data from the rice variety Nang Thom Cho Dao was analyzed using the appropriate bioinformatic pipeline. A total of 21 million reads with 6,6 GB of data were analyzed. SNPs and indels from the Nang Thom Cho Dao genome were found to be variable when compared to the Nipponbare reference rice genome. The result showed that the novel Indel of BADH2 gene in Nang Thom Cho Dao genome. The study will contribute valuable information to the development of genetic markers for rice breeding strategies using Nang Thom Cho Dao rice varieties.

Publisher

Can Tho University

Subject

General Medicine

Reference16 articles.

1. Barton, H. J., & Zeng, K. (2019). The impact of natural selection on short insertion and deletion variation in the great tit genome. Genome Biology and Evolution, 11(6), 1514-1524. https://doi.org/10.1093/gbe/evz068

2. Bolser, D., Staines, D. M., Pritchard, E., & Kersey, P. (2016). Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. In D. Edwards (Ed.), Plant Bioinformatics: Methods and Protocols (pp. 115-140). Springer New York. https://doi.org/10.1007/978-1-4939-3167-5_6

3. Chandler, V. L., & Brendel, V. (2002). The maize genome sequencing project. Plant Physiology, 130(4), 1594. https://doi.org/10.1104/pp.015594

4. Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6(2), 80-92. https://doi.org/10.4161/fly.19695

5. Cock, P. J. A., Fields, C. J., Goto, N., Heuer, M. L., & Rice, P. M. (2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic acids research, 38(6), 1767-1771. https://doi.org/10.1093/nar/gkp1137