An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

Abstract

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F_7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.

Keywords: Lactuca sativa; linkage analysis; microarray; recombination.

Figure 1

Frequency distribution of number of SPP calls per polymorphic unigene.

Figure 2

Dot plots of marker orders comparing the maps of LG1 generated by Joinmap, Record_Win, and MSTMap.

Figure 3

Heat map showing linkage along linkage group 1 displayed using Checkmatrix. Each chromosome is plotted in the linear order of the loci against itself and the degree of linkage between each locus indicated by a color. Red indicates <0.1 cM; yellow, 0.1−0.4 cM; green, 0.4−0.49 cM; blue, >0.51 cM. The first column at the right lists the locus name. The second column indicates the genetic distance. The red and blue bars at the bottom indicate the allelic composition at each locus. Red indicates Salinas allele; blue, L. serriola allele; yellow , distortion toward the Salinas allele; light blue, distortion toward L. serriola allele. Figures for each linkage group can be viewed at high magnification at http://chiplett.ucdavis.edu/map_2012. The insert in the bottom right corner illustrates a high magnification view of a subset of the data.

Figure 4

Distribution of 831 loci exhibiting distorted segregation on the nine chromosomes of lettuce. Orange and green lines indicate distortion at a significance level of P < 0.05. Red and blue lines indicate distortion at a significance level of P < 0.01. Distortions toward the L. sativa cv. Salinas and L. serriola alleles are in red/orange and blue/green, respectively.

Figure 5

Average distribution of loci in intervals of 5 cM along LG1. Deviation from the mean value for LG1 (x = 51) is shown by bars. Similar analyses for the other LGs are shown in Figure S5.

Figure 6

Distribution of haplotypes along linkage group nine displayed vertically for 213 RILs using Checkmatrix. The RIL families are arranged along the x-axis and the loci displayed in linear order along the y-axis. Red indicates L. sativa haplotype; blue, L. serriola haplotype. Gray, no allele called; missing data. The first column at the right lists the locus name. The second column indicates the genetic distance. The number of double cross-overs and the proportions of each haplotype are shown below each RIL. Displays for each linkage group can be viewed at high magnification at http://chiplett.ucdavis.edu/map_2012. The insert in the bottom right corner illustrates a high magnification view of a subset of the data.

Figure 7

Frequency distribution of the number of cross-overs. Numbers of cross-overs detected per RIL (0 to >8) are displayed chromatically for each linkage group, which are organized by genetic size (longest at top, shortest at bottom).

Figure 8

Distribution of haplotype diversity across the nine linkage groups for butterhead (yellow line), romaine (blue line), crisphead (green line), and leafy (red line) lettuce types and between L. sativa and L. serriola (gray line). Each y-axis indicates the average number of polymorphic loci in a sliding 5-cM window (from 0 to 16). Turquoise ellipse: example of region with low level of diversity in cultivated types relative to L. serriola. Orange ellipses: examples of regions with low diversity specific to one type, in this case butterhead. Purple ellipses: regions associated with clusters of NBS-LRR-encoding genes.

Figure 9

Dot plot of the syntenic positions of genes in grape and lettuce. The nine chromosomes of lettuce are ordered along the x-axis and the 17 chromosomes of grape along the y-axis. The positions of 10,552 loci mapped in lettuce on the grape genome are displayed.