Rapid ID Technology (RIDT) in Plants: High-Speed DNA Fingerprinting in Grain Seeds for the Identification, Segregation, Purity, and Traceability of Varieties Using Labautomation Robotics

Abstract

A rapid and inexpensive DNA diagnostic platform for fingerprinting Cdn. registered, wheat varieties has been developed. Two current, real-time applications being used in Canada include the determination of purity (% contamination) of grain shipments in rail cars and the monitoring of field plots that represent a midge varietal blend. The quantification of a sample is accomplished by fingerprinting single seeds and a sample having a mixture of varieties can be assayed. The Rapid ID Technology (RIDT) platform enables high-speed, high-throughput, robotic labautomation and low-cost single nucleotide polymorphism (SNP)-DNA fingerprinting in wheat. The inexpensive seed DNA extraction method, rapid PCR amplification, and miniaturization of the Invader assay for SNP scoring are all paramount for fingerprinting millions of single seeds per year in numerous rail cars/field plots at a low cost. The cost factor is the dominant concern in any fingerprinting program and the total cost for consumables for a single marker tested is estimated at less than $0.60 per seed. The RIDT platform can also segregate closely related cultivars, an important characteristic since many varieties have a common genetic background. The results ''from seed to fingerprint data'' at a central lab can then be transferred electronically to any location using a laboratory information management system. ( JALA 2009;14:221e231)

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

“…All these techniques can acquire 100–1000s of SNPs on a daily basis. With the increasing requirement of higher throughput data, the Taqman and Invader technologies have been significantly improved by enhancing the microtiter plates from 96 to 1536 wells ( Procunier et al, 2009 ).…”

Genotyping-by-Sequencing in Plants

“…These technologies originally allowed data collection of hundreds to up to a few thousand SNP/samples per day/machine. With the increasing need for higher throughput, end-point fluorescent assays such as Taqman and Invader have been significantly enhanced by the use of array tape technology in place of 96, 384 or 1,536-well microtiter plates, reducing cost per assay to a fraction of the original reaction and increasing throughput in a format that allows the PCR processing of the equivalent of hundreds of microtiter plates on one roll of tape [ 17 ].…”