Nested Association Mapping in Rice

Nested-Association Mapping (NAM) is a very efficient design that allows gene or QTL mapping with unparalleled precision and power. The concept has been developed by Edward Buckler’s group at Cornell University (Yu et al, 2008; see http://www.panzea.org and http://www.maizegenetics.net for more information), as a very powerful tool to link genomics approaches and plant breeding. A NAM metapopulation is subdivided in several SSD populations of ~200 lines that share a common parent. This allows to genotype the common parent-specific alleles and to project the high-density marker information from the founders to the progenies, and thus to infer the ancient, very dense recombination events. This property is the key concept of high-resolution mapping of QTLs. Due to its structure (large number of alleles, high recombination information), NAM nicely combines the advantages of both conventional linkage fine-mapping and association mapping, providing the ability (i) to tackle a large number of alleles for each QTL, (ii) to perform genome-wide QTL detection, (iii) to efficiently detect QTLs for segregating traits, (iv) to determine QTL positions with ultra-high resolution, and (v) to avoid the sensitivity to genetic heterogeneity inherent to association mapping populations. In 2008, in collaboration with IRD and AfricaRice, we initiated the construction of a NAM population of rice, thanks to the support of the Generation Challenge Programme (www.generationcp.org). The populations are ready to distribute by now, and consist in 25 inter-subspecific crosses involving one common O. sativa ssp indica parent (cv. IR64) and 25 tropical japonica accessions from Asia, Africa and Latin America. These materials have been scored at CIAT and AfricaRice for a series of morphological and phenological traits, and the lines will be genotyped by GBS in the frame of the France Génomique-IRIGIN project led by IRD (www.france-genomique.org). We expect to obtain at least 20,000 SNPs per population, representing a total of 50 million datapoints, which should be able to finely map the expected 128,000 recombination breakpoints, and will provide one of the most saturated and precise genetic map ever generated in plants. Ultra-precise mapping of stable QTL for traits of interest is the main expected outcome of rice NAM-based studies.