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      저자 : Berdugo-Cely Jhon A. (검색결과 1 건)
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        Selection of a CTAB protocol for high-quality DNA extraction in Oryza sativa L. validated for application in genotyping process based on Illumina sequencing

        Pérez-Pazos Jazmin Vanessa,Romero-Ferrer Jorge Luis,Berdugo-Cely Jhon A. 한국작물학회 2023 Journal of crop science and biotechnology Vol.26 No.4

        Rice genotypes with possible tolerance to biotic and abiotic stresses are interested in genomic studies for their use in breeding programs. Colombian Plant Germplasm Bank (CPGB) has preserved local rice genotypes without genomic analysis yet. Considering the need to develop genomic studies with these genotypes and minimize costs in the genotyping process, in this research, fve CTAB DNA extraction protocols (P1-P5) were evaluated and compared with a commercial kit. Four local rice accessions from the CPGB were used, and DNA concentration (fuorescence and absorbance), quality (absorbance, integrity, and enzymatic digestion), and cost analysis were determined. A selection index (SI) was established to choose the best DNA protocol. Finally, the selected protocol was validated in 14 local rice genotypes through Illumina sequencing. The six evaluated DNA extraction protocols presented signifcant diferences in quantifcation and quality variables. From the SI established, the protocol selected was the P4 (SI=147.7); this protocol allows obtaining DNA with high concentrations and quality levels at a 50% lower cost than the commercial kit. The sequences generated from the DNA obtained with the P4 protocol presented 7 million reads with high levels of quality (Q30) and length (>50 pb) per evaluated accession; On average, 98.9% of these sequences mapped to the rice genome and identifed up to 15,436 SNP markers without missing data. These results confrm that the DNA from rice local genotypes obtained with the P4 CTAB protocol has the requirements for routine use in genomic studies based on genotyping processes that require Illumina sequencing.

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