Rice Breeding in Latin America - Plant Breeding Reviews - page 210

yield potential through GWAS. Working within the rice subspecies is
intended to remove part of the natural structure that exists within the
species. However, to adjust for any remaining strati

cation, we test the
options to account for population structure (Q) and kinship (K) (Pasam
et al. 2012), as well as the principal component analysis (PCA) correction
method (Price et al. 2006; Hall et al. 2010).

5. Nested Association Mapping. Nested association mapping (NAM)
is a very ef cient design that allows gene or QTL mapping with un-

paralleled precision and power. The concept has been developed by
Edward Buckler s group at Cornell University (Yu et al. 2008; visit www

.panzea.org and www.maizegenetics.net for more information) as a very
powerful tool to link genomics approaches and plant breeding. A NAM
population consists of several RIL populations that share a common
parent. This allows SNP genotyping of the common parent-speci

'

c
alleles and each of the RIL parents (founder lines) to project high-density
marker information from the founders to the progenies, and thus infer-
ring the ancient recombination events. In maize and other outcrossing
species, there are many historical recombination events. This property
underlies the potential for high-resolution mapping of QTLs using
GWAS. Because of the structure of NAM populations (a large number
of alleles segregating across populations, high recombination informa-
tion), these populations effectively combine the advantages of both
conventional linkage mapping (marker trait associations easily detected

with relatively sparse marker coverage, control of genetic background in
biparental inheritance) and association mapping (many alleles segregat-
ing, higher resolution because historical recombination is generally
higher than in biparental crosses), providing the ability (1) to tackle a
large number of alleles, provided that NAM founders cover a large allelic
diversity, for each QTL, (2) to perform genome-wide QTL detection,
(3) to ef

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ciently detect QTLs for segregating traits, (4) to determine QTL
positions with high resolution, and (5) to avoid the sensitivity to genetic
heterogeneity inherent to association mapping populations. In 2008,
in collaboration with IRD and AfricaRice, we began constructing a
NAM population of rice, thanks to support from the CGIAR Generation
Challenge Programme (GCP). The populations are now ready, and con-
sist of 25 intersubspeci c crosses involving one common Oryza sativa

subsp. 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 framework of
the France Génomique-IRIGIN project led by IRD. We expect to obtain