Brief History of Comparative Mapping

Comparative mapping in plant genomes originated in the Solanaceae, through the early work of Tanksley and colleagues (Bernatzky and Tanksley 1986; Bonier-bale et al. 1988; Tanksley et al. 1988). In these studies, isozyme and RFLP markers were placed onto maps of tomato and its close relatives within the Solanaceae, pepper, and potato (Solanum tuberosum). Orthology of loci, or identity by descent from a common ancestral sequence, was determined based on map position. For example, if a tomato marker was within a block of markers, all showing conserved synteny between tomato and pepper, then that marker was orthologous to the corresponding marker in pepper. This criterion is still used today.

These early studies were modest in terms of numbers of molecular markers, but they provided the first evidence for the existence of highly conserved syntenic blocks of loci in higher plant

Table 8. Chromosomal rearrangements in the Solanaceae as determined by comparative mapping. Data from Bonierbale et al. (1988), Tanksley et al. (1992), Prince et al. (1993), Livingstone et al. (1999), and Doganlar et al. (2002a)

Taxon

No. of

No. of chromosomal

chromosomes

rearrangements in comparison

(2n)

to tomato

Tomato (Solanum lycopersicum)

24

_

Potato (Solanum tuberosum)

48

5 paracentric inversions

Pepper (Capsicum spp.)

24

30 chromosome rearrangements

Eggplant (Solanum melongena)

24

23 inversions, 5 translocations

Tobacco (Nicotiana tabacum)

48

naa

Petunia (Petunia hybrida)

14 or 18

na

a Not available, molecular linkage maps have been published for tobacco and petunia (e.g., Strommer et al. 2002; Bindler et al. 2006; Julio et al. 2006), but the markers used do not allow for comparison with any tomato maps a Not available, molecular linkage maps have been published for tobacco and petunia (e.g., Strommer et al. 2002; Bindler et al. 2006; Julio et al. 2006), but the markers used do not allow for comparison with any tomato maps genomes. Some of this information is summarized in Table 8. Comparative mapping is still proceeding in the Solanaceae (see Sect. 1.6.2). In most of these works tomato is central, and other plants' genomes are referenced against it. A variety of chromosomal rearrangements are postulated to have occurred during divergence from a common ancestor; this is based on breaks in conserved blocks of synteny when comparing maps of different genera within the family (Table 8). The effort that has gone into tomato mapping and sequencing has outpaced other members of the family, but tools and markers developed for tomato often work very well across many members of the family.

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