High density molecular linkage maps of the tomato and potato genomes.

TLDR

Currently tomato and potato are among the most thoroughly mapped eukaryotic species, and the availability of high‑density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker‑assisted breeding, and evolutionary studies in these two important crop species. High‑density linkage maps were constructed for tomato and potato using over 1,000 markers spaced on average 1.2 cM (~900 kb). Using the common probe set, the authors precisely mapped five centromere‑proximal inversions that flip entire chromosome arms, found that recombination is uniformly distributed by chromosome size but highly heterogeneous within chromosomes—with centromeric, heterochromatic, and some telomeric regions showing up to ten‑fold lower rates—so that 28 % of loci lie in suppressed recombination zones, underscoring practical and evolutionary implications.

Abstract

Abstract High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.