Selective advance for accelerated development of recombinant inbred QTL mapping populations

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Quantitative trait locus (QTL) mapping resolution of recombinant inbred lines (RILs) is limited by the amount of recombination they experience during development. Intercrossing during line development can be used to counter this disadvantage but requires additional generations and is difficult in self-pollinated species. It is desirable to improve mapping resolution for success of marker-assisted selection and map-based cloning. Here we propose a way of achieving this through recombination enrichment. This method is based on genotyping at each generation and advancing lines selected for high recombination and/or low heterozygosity. In simulations, the method yields lines that represent up to twice as many recombination events as RILs developed conventionally by selfing without selection, or the same amount but in three generations, without reduction in homozygosity. Compared to methods that require maintaining a large population for several generations and selecting lines only from the finished population, the method proposed here achieves up to 25% more recombination. The precision of QTL location is increased by up to 10% with negligible drop in QTL detection power at average marker intervals of 5 cM or less.

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