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However, plant breeders and agricultural scientists face many challenges to integrate and exploit these newmolecular and genomics-related technologies for more rapid and efficientvariety development [15, 16]. In this article, we review the current globalrice molecular breeding lab with an emphasis on recent research and the impactof rice genomics resources. We also review some current genomics research andpromising new genotyping methodologies with high potential for appliedoutcomes. Finally, we consider the obstacles to the successful application ofmolecular genetics and genomics research in rice breeding programs and proposeideas on how some of these problems should be solved.
Since marker genotyping methods were first developed in the 1980s, numerous protocolsand variations now exist. Many protocols have been refined and optimizedspecifically for the lab in which marker genotyping is conducted and willdepend on budget, equipment, and personnel. One feature of rice molecular breedinglabs is their diversity. Molecular breeding labs require a large initialcapital investment and since many labs are based in developing countries, theequipment and resources often differ markedly from those of well-funded labs indeveloped countries. The cost of marker genotyping is, therefore, a criticalfactor for the extent of MAS in rice, and this is likely to continue to be thecase for years to come given the unlikely dramatic decrease in costs.
In the context of plant breeding,there are several important considerations. Cost is critical due to the largenumber of samples breeders evaluate. Furthermore, 3 to 6 target traits usually segregatein a single population so the frequency of lines with all the desirable genecombinations is very low. This could undermine the suitability of some high-throughputwhole-genome profiling programs, although there could be numerous applicationsin basic research.
Despite the enormous potential for developing and using markers in rice, the cost ofgenotyping is still a prohibitive barrier to the wider application of MAS. Evenwith the global importance of rice, many developing countries have limitedresearch and development capability. Therefore, cost optimization of currentgenotyping protocols and the development of new cost-effective protocols shouldbe a major priority for breeding research and especially the rice molecularbreeding lab. These improvements might involve simple optimizations of current laboratorypractices, adopting new more efficient methods, or developing new MASstrategies and schemes.
QTL application research activities represent an extensive amount of time, effort,and resources. In practice, it seems that molecular breeders will ultimately have to perform this research insituations, in which important data for the application of MAS are notavailable. From experience, it is clear that breeding programs that do notundertake these activities risk wasting considerable time and resources. However,in practice, QTL application research activities may be constrained by funding,time, and resources; in some cases, these activities may be beyond the capacityof many rice molecular breeding labs. Furthermore, a breeder may decide that,based on the importance of the target trait, such QTL application research stepsdo not worth the investment in time, resources, and money, since, at the end, themarkers may not turn out to be useful for selection in their own breedingprogram.
Many activities will occur in the future ricemolecular breeding lab. Obviously, the primary objectives will be to supportand assist the breeding program in the evaluation and selection of breedingmaterial. To fulfill this duty, organizational and maintenance activities suchas organizing protocols, marker data, supplies of consumables, equipmentmaintenance, and LIMS will be critical. In-house data records for markeroptimization and parental screening will be critical; generally, the more detailedthe records, the better. This must include