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The study has application in micropropagation and selection of elite materials of P. japonicum by LC MS method.
For example, this marker could be used to introgress the high oil/low protein seed composition quantitative trait locus into elite materials.
Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations.
Such a "rapid cycling" scheme would accelerate the fixation rate of favorable alleles in elite materials and should increase the genetic gain per unit of time, as described by Heffner et al. (2009).
A deficiency of rare alleles is expected under the pronounced bottlenecks that lead to the origin of inbred lines and the increased in pairwise differences can result from the divergent nature of the elite materials selected for this study.
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Efforts in marker assisted introgression of root QTLs from landraces into elite material go back to 2001 (Shen et al. 2001) with mixed effects on yield in target environment in some cases (Steele et al. 2007).
Cornell uses the C6AIR chip for pre-breeding, to develop introgression lines using the rice wild relatives O. rufipogon and O. meridionalis, for QTL mapping, and to genotype elite material used in US breeding programs, mainly tropical japonica varieties.
Since European elite material was included in this study, LD was expected to span whole genes.
However, the diversity lost in the elite material is somewhat preserved in crop gene banks.
WK, DS and NB tested the EST-SSR primer sequences to detect polymorphisms in elite material.
Of these, 579 SNPs in 162 loci were polymorphic within elite material.
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