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Bridging Genomics and Genetic Diversity: Linkage Disequilibrium Structure and Association Mapping in Maize and Other Cereals

^a UMR 8120 Génétique Végétale, INRA UPS INA-PG CNRS, Ferme du Moulon, 91190 Gif sur Yvette, France
^b UMR 1097 Diversité et Génomes des Plantes Cultivées, INRA Domaine de Melgueil, 34130 Mauguio, France

View larger version (22K): [in this window] [in a new window]   Figure 1. Structure among all accessions as revealed by principal component analysis (PCA) on the among open pollinated varieties variance–covariance matrix of allele frequencies (data from Dubreuil et al., 2006). Axis 1 can be interpreted as the opposition between Northern Flint and tropical materials. Axis 2 can be interpreted as the opposition between the non-Northern Flint origins of northern American and European materials, respectively. Northern American populations were identified according to racial classification (ASW, American southwestern; ASD, American southern Dent; ACB, American Corn Belt; ANF, American Northern Flint). Other American origins were identified according to the country of origin: Arg, Argentina; Bol, Bolivia; Chl, Chili; Cos, Costa Rica; Cub, Cuba; Dom, Dominican Republic; Ecu, Ecuador; Gua, Guatemala; Mex, Mexico; Pan, Panama; Per, Peru; Uru, Uruguay; Ven, Venezuela; Win, West Indies. European origins were identified according to the country or region of origin (Als, Alsace; Bul, Bulgaria; Cze, former Czechoslovakia; Fra, central France; Gal, Galicia; Ger, Germany; Ita, Italy; Pol, Poland; Pyr, Pyrenean; SpS, southern Spain; Ukr, Ukraine; Yug, former Yugoslavia).

View larger version (47K): [in this window] [in a new window]   Figure 2. Models for population structure at three steps of maize selection history: open pollinated varieties, also called landraces (seven groups), first cycle inbreds (five groups), and whole inbred panel (five groups). Groups for each panel are represented by colors as indicated at the bottom of the figure. For the inbred panels, each inbred line is represented by a vertical line divided into colored segments, the length of which indicates the proportion of the genome attributed to the different groups. For the landrace panel, each population is represented by the mean proportions estimated for the five inbred lines simulated to represent it. Plain arrows stand for filiation relationship between clusters and have been established on the basis of either STRUCTURE assignments (in the joint study of landraces and first cycle inbreds) or genetic distances between groups of inbred line panels. Dotted arrows indicate lower contributions (less than three inbred lines with a high genome proportion (>0.80) attributed to a group obtained in the STRUCTURE joint analysis of landraces and first cycle inbred lines). From (Camus-Kulandaivelu et al., 2006).

View larger version (79K): [in this window] [in a new window]   Figure 3. Result of the analysis of the genes D3, D8, and Id1 (data from Remington et al., 2001) using our Hidden Markov Model (HMM)-based algorithm. The haplotypes are sorted according to their leaf position in a neighbor-joining tree based on their euclidean distance matrix. For each gene the left part of the figure depicts the pattern of mutation in the raw data set and the right part the ancestral origins of marker along the gene. At the top of each figure, the inferred ancestral haplotypes are displayed (i.e., four for D3 and Id1, and three for D8). The average diversity between ancestral haplotypes for D3, Id1, and D8 are 0.50, 0.48, and 0.61, respectively. The extra spaces between single nucleotide polymorphism (SNP) sites are based on a block structure of the haplotype inferred by the HMM-based algorithm of Anderson and Novembre (2003). If some ancestral fragments line up with the block boundaries (for D8 the block structure and our model give a similar pattern), for D3 and Id1 some recombination events detected by our model occur within blocks.