Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

Table 2

Cost breakdown of standard marker genotyping and exploration of marker genotyping cost reduction opportunities.

Situation	Step	Consumables (US $)	Labor (US $)	Cost per marker (US $)
Standard cost	DNA	0.051	0.437	1.001
	PCR	0.211	0.076
	Gel	0.052	0.174
Scenario 1—multiplex loading	DNA	0.051	0.437	0.910
	PCR	0.211	0.076
	Gel	0.000	0.043
Scenario 2—multiplex PCR	DNA	0.051	0.437	0.500
	PCR	0.211	0.076
	Gel	0.052	0.174
Scenario 3—MAS pyramiding	DNA	0.051	0.437	0.676
	PCR 1	0.211	0.076
	Gel 1	0.052	0.174
	PCR 2	0.211	0.076
	Gel 2	0.052	0.174
	PCR 3	0.211	0.076
	Gel 3	0.052	0.174
Scenario 4—DNA extraction performed by research technician	DNA	0.051	0.040	0.604
	PCR	0.211	0.076
	Gel	0.052	0.174

(i) Standard cost calculated based on the genotyping of 96 samples using a single SSR marker at IRRI from Collard and Mackill [8].
(ii) Data in this section of the table are reported for the second marker; hence, the gel cost for consumables is zero. The calculation was performed using the data for a standard marker plus the second marker (gel consumable cost = 0) and dividing by two.
(iii) Multiplex loading by sequential loading of PCR samples, assuming different DNA samples are run in all lanes. Labor would require an extra 20 minutes for sequential loading, but gel preparation and assembly are no longer required in this scenario.
(iv) If direct pooling of PCR products is possible, only a single loading is required for 96 samples (extra 5 minutes of labor). Gel labor costs are reduced to US $0.011 and the total cost per marker is $0.893.
(v) Multiplex PCR (i.e., duplex PCR) in which two markers can be genotyped in the time and effort required for a single marker.
(vi) For MAS pyramiding, the genotyping of three loci was considered. For simplicity, it was assumed markers could not be multiloaded, but obviously, if this was possible, it would indicate a further cost reduction per marker screened.
(vii) The DNA extraction step is the most costly from our data analysis. There are considerable savings in expense, if genotyping efforts of a postdoctoral researcher are coordinated with those of a research technician at IRRI.