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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.
Oscar Burbano‑Figueroa1,Jazmin Vanessa Pérez‑Pazos,Milena Moreno‑Moran 한국작물학회 2022 Journal of crop science and biotechnology Vol.25 No.3
Cassava · Commercial inoculants · Data envelopment analysis · DEA · Technical efciency · NPK · Yield gaps · Nutrient-limited yieldPlant growth promoting microorganisms (PGPMs) are inhabitants of the rhizosphere that are able to provide better growth and biomass accumulation. Current agronomic practices have depleted these communities, which has created the opportunity for the development of commercial inoculants. These products use strains that are able to interact with a wide range of plant species and survive in diverse environments. The use of these generalist strains is required for providing a widespread solution that aggregates enough demand to reach market scale. Growth promotion by generalist strains may be suboptimal in comparison to the efect provoked by native and host-specifc populations, but these specialist strains are not a marketavailable solution. In this work, we assess the nitrogen, phosphorus and potassium (NPK) use efciency provided by commercial inoculants to cassava plants using Data Envelopment Analysis (DEA) to demonstrate the advantages of conceiving nutrient-limited yield as a production function. We also estimate the prospective production frontier that commercial inoculants can provide to cassava plants. Our results suggest that commercial inoculants have potential for improving cassava yields via improved NPK use efciency. The methods presented here ofer an ecological/economic production framework for the assessment of PGPMs and PGPMs-based commercial inoculants that can be extended to other laboratory, greenhouse or feld situations. The simple, intuitive and graphical approximation that DEA ofers will facilitate the understanding of the concept of technical efciency and the role of commercial inoculants on closing yield gaps