Therefore, hybridization among different horticultural types has been used to develop new cultivars and breeding lines. Lindqvist Selleckchem SAHA HDAC pointed out that most lettuce breeding occurred between butterhead and leaf types, since they have very similar leaf texture and midrib appearance [48]. Genealogy of contemporary North American lettuce shows that 52% of lettuce cultivars were bred using two parents, 31% from selection within a cultivar, 7% from three parents, 7% from backcrossing, 2% from four or more parents, and 1% from inter-specific crosses [49] and [50]. Recognizing the population structure in our collection will enable

us to apply the linkage disequilibrium (LD)-based association mapping to accurately identify DNA markers closely linked to genes

and genomic regions associated with desirable traits. Our results for population structure and cluster analysis agree with previous studies involving cultivated lettuce germplasm [30]. Genotyping of 258 homozygous lettuce genotypes with 322 SNP markers allowed a preliminary genome-wide analysis of marker-trait association. We found that seed coat color was significantly associated with four markers on linkage group 7; CLS_S3_Contig8254-1-OP4 (88.3%), CLS_S3_Contig7479-10-OP5 (80.0%), QGC12P16-4-OP1 (77.3%) and Contig10156-1-OP1 (76.0%). Two SNP markers from linkage group 9, CLS_S3_Contig5434-3-OP4 (69.3%) and CLSY4478.b1_K16-8-OP4 Staurosporine in vitro (67.0%), were significantly associated with anthocyanin on stems or leaves. These markers are potentially useful in MAS in lettuce improvement when they are validated with segregating populations, and they also can be used as the starting point to identify candidate genes underlying the respective phenotypic

traits. With the recent release of the draft lettuce genome sequence from the Compositae Genome Project website (http://compgenomics.ucdavis.edu/) that was supported by the USDA IFAFS program and NSF Plant Genome Program, we could locate most of the SNP sites in the genome. For example, lettuce seed coat color is a simply inherited trait [51] and a seed coat color locus buy Docetaxel (br) was mapped onto a linkage group with four AFLP markers using a recombinant inbred line population [52]. However, the br locus has not been assigned to a lettuce chromosome. The current study found that four SNPs associated with seed coat color are on chromosome 7. The lettuce genomeViewer website (http://gviewer.gc.ucdavis.edu/cgi-bin/gbrowse/lechuga_version_1_2/) indicates that the assembled lettuce chromosome 7 is approximately 240 Mb in length. Three of the four SNPs associated with seed coat color, QGC12P16-4-OP1, CLS_S3_Contig8254-1-OP4 and CLS_S3_Contig7479-10-OP5 are located at positions 69,873,871, 80,636,383 and 81,871,389, respectively. In other words, these three SNP sites are physically resided within a segment of 12 Mb, which most likely harbors the br locus conditioning the seed coat color.