Use of SNP markers to genotype commercial hybrids and Spanish local cultivers of tomato
García-Gusano, M.; García-Martínez, S.; and Ruiz, J.J.
Escuela Politécnica Superior de Orihuela. Universidad Miguel Hernández
Carretera de Beniel, km 3,2. -03312- Orihuela (Alicante)
The low diversity of tomato cultivars is reflected by a poor level of polymorphisms for
proteins, isoenzymes, and most types of DNA markers (Bredemeijer et al., 1998). Several systems
such as RFLPs, AFLPs, CAPSs, SSRs, have been used in tomato to study its level of
polymorphism. In order to facilitate the conservation and management of tomato germplasm, we
have studied the genetic variability of some traditional tomato cultivars from Spain, using both
simple sequence repeats (SSRs) and sequence related amplified polymorphisms (SRAPs) markers
(Ruiz et al., in press). Both types of markers resolved the cultivars from different groups, but failed
to distinguish some of those classified under the same group. It seems that these markers systems
are unable to completely differentiate closely related cultivars. One of the most common forms of
genomic variation is single nucleotide polymorphisms, or SNP. Its utility in genetic variability studies
has already been demonstrated (Rafalski, 2002). In crops such as maize, wheat, soybean or melon
(Bhattramakki et al., 2002; Cregan et al., 2002; Morales et al., 2004), collections of SNPs have
already been identified. However, there are scarce studies published about SNPs in tomato. Yang
et al. (2003) detected 43 SNPs by electronic searching using collections of EST sequences of the
cultivars ‘Rio Grande’ and ‘TA496’, and they have confirmed these SNPs in other L. esculentum
cultivars. Also, Baldo et al. (2004) recently reported the electronic discovery of 2,527 potential
SNPs, and they are in the process of verifying these polymorphisms in the laboratory.
We have used 20 SNPs in order to try to find differences between 47 accessions of
Lycopersicon (Table 1 and 2). Most accessions are different cultivars of the main traditional types of
tomato cultivated in southeastern Spain. Most SNPs have been selected from those already
identified by Yang et al. (2003).
Table 1. Cultivars and accessions studied.
Local Spanish cultivars
Cultivar type
Cultivars
De la pera
Per1, Per7, Per16, Per19, Per21, Per22, Per25, Per43,
Per44
Muchamiel
Much4, Much11, Much18, Much29, Much30, Much128,
Much198, BN4, BN5
Morunos
Mor207, Mor208, Mor209, Mor231, Mor234
Other types
Valenciano, Teticabra, Flor de Baladre, CA13, CA16,
CA17, Raf
Commercial cultivars
Hybrids F1
Bond, Anastasia, Odisea, Royesta, Tirade, Evita, Vision
Other cultivars
Malpica, Roma, Ch89 (Cherry), Sali, Zapotec,
Moneymaker, EPSO42
Wild species
L. pimpinellifolium LA2853 and LA1610; L.e. var
cerasiforme LA2617
SNPs were analyzed as cleaved amplified polymorphic sequence markers. The fragments
amplified were digested with restriction enzymes, obtaining different band patterns for each one of
the accessions. In some cases the fragment amplified by the same couple of primers had more than
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