High-throughput sample collection and DNA extraction using PlantTrak and oKtopure systems at IRRI's [International Rice Research Institute] genotyping services laboratory
2015
Jarana, A.P. | Carandang, S.L. | Tandayu, E.S. | Cariño, G.A. | Sanchez, G.S.B. | Llantada, K.J. | Dizon, C. | Layaoen, G.A.M. | Castaneda, N.V. | Dilla-Ermita, C.J. | Reveche, M.Y.V. | Dwiyanti, M.S. | Thomson, M.J.
Plant tissue sampling and DNA extraction are the major bottlenecks in high-throughput SNP genotyping activities. While several SNP genotyping platforms have been developed to cater to high-throughput SNP genotyping, plant tissue sampling and DNA extraction are still considered low to medium throughput. To increase throughput and efficiency but coupled with decrease error, GSL recently adopted automated leaf sampling and high-throughput DNA extraction using the Brooks' PlantTrak and LGC Genomics' oKtopure systems. These systems have been tested with plants of varying age, differing numbers of leaf punches, and changes to the extraction protocol to optimize the DNA sample quantity and quality as compared to two previously optimized DNA extraction protocols utilized by the laboratory (magnetic bead-based Thermo King Fisher sup(R) Flex and manual CTAB) and manual sample collection using glassine bags. The efficiency of this new workflow was compared in terms of producing quality SNP calls. After several tests and optimization of these two systems, it has increased productivity more than twice from previously used technologies and has proven to be cost effective for processing large numbers of samples without compromising the quality.
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