Genetic Linkage Maps

The first Mendelian tomato linkage group was published by Hedrick and Booth (1907), where the dwarf and ovate loci were shown to be linked in an F2 cross between S. lycopersicum varieties Livingston Stone and Dwarf Aristocrat (Tanksley 1993a). By 1934,20 morphological markers had been mapped to ten linkage groups. This study scored over 48,000 plants derived from crosses among ten varieties that were homozygous for spontaneous mutations (MacArthur 1926,1934). During the same decade researchers began to implement crosses with wild tomato species as a source of disease resistance. These disease resistance genes were also quickly located to linkage groups since the parents of the hybrid populations were more polymorphic compared to intraspecific S. lycopersicum crosses. For example, Langford (1937) generated data indicating Cf loci on chromosomes 6 and 11 using S. pimpinellifolium. By 1973, 257 morphological and disease resistance markers had been mapped (Linkage Committee 1973).

Molecular markers were adopted the following year when isozyme Aps-1 was linked to the nematode resistance gene Mi on linkage group six (Rick and Fobes 1974). Seven loci of Est, Prx, and Got were added in 1977 using S. pimpinellifolium (Rick and Fobes 1977). In the mid-1980s, DNA-based RFLP markers were starting to be mapped, for example, in an interspecific cross between S. lycopersicum cv. VF36 and S. pennellii accession LA716 (Table 6, pop 8) (Bernatzky and Tanksley 1986; Vallejos et al. 1986). Chromosomal assignments of genomic clones by tri-somic analysis were also confirmed using this population (Young etal. 1987). An IL population from a cross between S. lycopersicum cv. M82 and S. pennellii accession LA716 (Table 6, pop 9) also used RFLP markers (Eshed and Zamir 1995). PCR-based markers (RAPD, AFLP, SSR, CAPS) were added to tomato maps in the late 1990s (Table 6, pop 6, 8 -11, 13 -14, 17-19, 21) (Grandillo and Tanksley 1996a; Pillen etal. 1996a, b; Bonnema etal. 1997; Areshchenkova and Ganal 1999; Haanstra et al. 1999). The advent of the complete Arabidopsis thaliana genome sequence facilitated development of PCR-based COS markers using genes shared between distantly related plant taxa (Table 6, pop 10) (Fulton etal. 2002b). Additional recent reviews have listed tomato genetic link-

Table 6. Tomato linkage mapping populations. Crosses are listed in alphabetical order by species. Populations are numbered and maps of these populations are listed chronologically. Markers used for each map are listed, and whether the map is available in an online format

Linkage mapping population Poptypea Pop size No. of Marker type(s) Onlineb Reference markers

S. lycopersicum :■ S. cheesmaniae

1.UC204B LA483

S. lycopersicum :■ S. chmielewskii

2. UC82B LA1028

S. lycopersicum :■ S. habrochaites

5. lycopersicum :■ S. lycopersicoides 5. VF36 LA2951

5. lycopersicum :■ S. lycopersicum var. cerasiforme

8. VF36 LA716

BCi BCi

BCi F7 RIL

f2 f2

149 145

135 171

84 1,030 368 1,050 909

20 375 140

RFLP

RFLP, Isozyme

RFLP SGN

RFLP,

Resistance Gene Analog (RGA)

Isozyme, NCBI

Morphological (Morph), RFLP

RFLP, RAPD, AFLP, Morph RFLP

RFLP NCBI

Isozyme, Morph, RFLP SGN, NCBI

RFLP, SSR

RFLP, EST

AFLP

RFLP SGN

T-DNA

CAPS

Paterson et al. 1991

Paterson et al. 1988

Bernacchi and Tanksley 1997 Zhang et al. 2002

Chetelat and Meglic 2000; Chetelat et al. 2000

Saliba-Colombani et al. 2000

Fulton et al. 2000

Bernatzky and Tanksley 1986 Tanksley et al. 1992 Broun and Tanksley 1996 Pillen et al. 1996b Haanstra et al. 1999 Areshchenkova and Ganal 1999 Areshchenkova and Ganal 2002 Eshed and Zamir 1995 Gidoni et al. 2003 Yang et al. 2004

a IL introgression line; IBL inbred backcross line; RIL recombinant inbred line b SGN http://www.sgn.cornell.edu/cview; NCBI http://www.ncbi.nlm.nih.gov/mapview; TMRD (Tomato Mapping Resources Database) http://www.tomatomap.net

Table 6. (continued)

Linkage mapping population

Pop typea

Pop size

No. of markers

Marker type(s)

Onlineb

Reference

11. Allround :: LA716 F2

S. lycopersicum :■ S. peruvianum

12. E6203 LA1706 BC3

13. Solentos LA2157 F2 S. lycopersicum :■ S. pimpinellifolium

14.M82 :: LA1589 BCi

15.NC84173 LA722 BCi

16. E6203 LA1589 BC2F6, IBL

17. Sunl642 LA1589 F2

19. Rio Grande LA 1589 F2

20. LA2157 LA2172 BCi

21. PI 128650 PI 128657 BCi

84 80 84

241 314

257 119 196 46 142 94

152 2,112

2,222 1,579 77 707 38

120 151 127 101 112 87

73 13

CAPS, SSR

RFLP, SSR

RFLP, AFLP

RFLP, SSR

RFLP

RFLP, CAPS

RFLP, RAPD

RFLP

RFLP

RFLP, CAPS SSR

SSR, CAPS, SNP

RFLP

RFLP, RAPD

SGN, NCBI Fulton et al. 2002b Fraryetal. 2005 Arens et al. 1995 Haanstra et al. 1999 Bai et al. 2004a

Fulton et al. 1997 Bonnemaet al. 1997

SGN Grandillo and Tanksley 1996a

Chen and Foolad 1999 SGN Doganlar et al. 2002c

TMRD Yang et al. 2004

Liu et al. 2005

Gonzalo and van der Knaap, unpublished; see Sect. 1.4.4 and Fig. 2

NCBI Van Ooijen et al. 1994

Pillen et al. 1996a age maps (Foolad and Sharma 2005; Villalta et al. 2005).

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