Markers and Orthology

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Sixmaj or types of DNA markers have historically been used for genetic linkage mapping in higher plants including Solanaceae: RFLPs, RAPDs, AFLPs, SSRs, sequence characterized amplified regions (SCARs), and

SNPs. In addition, COS markers have been specifically designed for comparative mapping. By comparing tomato EST sequences to the Arabidopsis genome sequence, Fulton et al. (2002b) identified a set of 1,025 genes, which they referred to as COS markers. COS markers are single or low-copy in both genera, thus probably orthologous, and potentially very useful for comparative mapping. Both computationally and through Southern hybridizations, Fulton et al. (2002b) found the COS markers to be present in many plants, including dicots and monocots. A potential disadvantage of the COS markers is that, because they are well conserved, they may show low polymorphism. Wu et al. (2006) followed up on COS marker development by designing a set of COSII markers, which are similar to the COS markers but have additional phylogenetic evidence to support orthology of sequences. In addition, a set of "universal PCR primers" has been designed which may enable amplification of these markers from a broad range of plant species. Attributes of DNA marker types used in comparative mapping are provided in Table 9.

The utility of a molecular marker for comparative mapping depends on level of polymorphism and ease of establishment of orthology when examining different crosses. Two loci in different individuals are orthologous if they have descended from a common ancestor. Orthology can be established fairly easily if the DNA marker detects only one locus. For multi-locus markers, orthology is determined based on map position. Inferences about marker synteny in comparative genomics cannot be made unless the orthology of loci in different genomes can be determined with high confidence. Orthology is most commonly determined based on a combination of two factors: (i) presence of a single DNA fragment upon hybridiza-

Table 9. DNA markers used for comparative mapping. General properties are listed, but exceptions occur

Marker type

Polymorphism

Dominant

Number of

or codominant

loci detected

RFLP

Low

Codominant

Usually 1 to 2

RAPD

Low

Dominant

5 or more

AFLP

High

Dominant

50 to 100

SSR

High

Codominant

Usually 1

SCAR

Low

Variable

1

SNP

High

Codominant

1

COS

Low

Variable

Usually 1 to 2

Table 10. Comparative mapping of some genes and QTLs in the Solanaceae. Chromosomal locations, when known, are given by "c." followed by chromosome number

Category of QTLs

Tomato

Potato

Pepper

Eggplant

Petunia

Tobacco

Reference

Physiology/ Morphology

Disease resistance invGE, Lin5, fruit sugar, c.9

ovate, c.2

QTL for fruit weight fw2.2,fw9.2,fwll.l Ovate gene for fruit shape

Fruit shape QTLfslO LeafC mutant for leaf shape Various color genes/mutants

Resistance to true fungi, multiple locations, overlapping with potato and pepper Verticillium resistance, c.9

Nematode resistance PCR-NRm

Invertases, cold sweetening, chip quality, c.9 Tuber skin color QTL, fruit shape QTL, c.10

Various color genes/mutants

Phytophthora resistance, multiple locations

Verticillium resistance, c. 2,6,9, and 12 PCR-NRh and Globodera resistance, c.9

Potato leafroll virus resistance, c.ll

Anthocyanin loci, fruit shape QTL fslO.l, c.10 Fruit size and shape fw2.1,fs2.1, c.2

Fruit shape QTLfslO

Phytophthora resistance, multiple locations

QTL for fruit weight fw2.1,fw9.1,fwll.l Gene for fruit length fl2.1

Fruit shape QTL ovs4.1 Lobing QTL Uob6.1

Multiple loci

Various color genes/mutants an2

Meloidogyne incognita resistance loci Me3 and Me4, c.12

Fridman and Zamir 2003;

Li et al. 2005a Ben-Chaim et al. 2003

Zygier et al. 2005; Ben-Chaim et al. 2006 Doganlar et al. 2002b

Doganlar et al. 2002b

Doganlar et al. 2002b Frary et al. 2003 a

De Jong et al. 2004

De Jong et al. 2004 Grube et al. 2000b; Thabius et al. 2003; Ogundiwin et al. 2005

Simko et al. 2004a, b

Bradshawet al. 1998; Dijian-Caporalino et al. 2001; Caromel et al. 2003; Bryan et al. 2004 N gene for TMV Marczewski et al. 2001 resistance

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tion or PCR in both genomes being compared, and (ii) position on the linkage map relative to other markers of known (or presumed) orthology.

The detection of a single fragment upon PCR or Southern hybridization in two or more plant genomes is taken as evidence that the fragments are ortholo-gous, barring any evidence to the contrary. Contrary evidence could include a firm map position that is not linked to any other locus that is linked to the putative ortholog in the other genome (although this could be evidence for fine-scale rearrangements) or DNA sequence that does not match.

Map position can allow one to distinguish between orthologous and paralogous loci corresponding to markers that detect multiple fragments. Figure 6 shows a simple hypothetical example of determining orthology vs. paralogy for an RFLP marker that has one copy in tomato and two in pepper. Because CD422b is in approximately the same map position in pepper as is CD422 in tomato, while CD422a is not, the most parsimonious interpretation is that CD422b is the ortholog to CD422 in tomato, while CD422a is the paralog.

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