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Microsatellite markers for genome analysis of rubber tree (Hevea spp.)

Seguin M., Gay C., Xiong T.C., Rodier-Goud M.. 2001. In : Sainte-Beuve Jérôme (ed.). Biotechnology and rubber tree : Proceedings of IRRDB symposium, 25-28 September 2001, Montpellier, France. Montpellier : CIRAD. IRRDB Symposium, 2001-09-25/2001-09-28, Montpellier (France).

Genetic markers are defined as simple variable (polymorphic) traits, governed by a single gene (monogenic trait) and whose expression is independent of the environmental conditions, of the organ and of the developmental stage. Thanks to these properties, genetic markers allow to directly infer the genotype of individuals, by unequivocal relationship between a state of the trait and an allelic composition of the corresponding gene. The markers can be morphological, biochemical (such as isozymes) or based on DNA sequence variations (molecular genetic marker = MGM). In rubber tree no morphological genetic marker have been clearly identified, and the recent development of MGMs in this species led to a rapid progress in knowledge on genetic organization and provided new tools for breeders (Seguin et al. 1996a). The different kinds of MGM used in rubber tree genetics have specific properties or limits: Isozyme markers were proved to be efficient for rubber clone identification and genetic diversity studies (Chevallier 1988; Leconte et al. 1994; Yeang et al. 1998) but remain very limited in number (14 loci in Hevea genus). RFLPs (Restriction Fragment Length Polymorphism) are also efficient for identification (Besse et al. 1993a) or genetic diversity (Besse et al. 1994; Besse et al. 1993b; Seguin et al. 1995; Seguin et al. 1999). In addition, they are potentially unlimited in number and opened to the field of Hevea genome mapping ( Seguin et al. 1996b ; Lespinasse et al. 2000b). Nevertheless, RFLPs manipulations are relatively heavy and time consuming. RAPDs and AFLPs are PCR based MGMs: use of PCR amplification of DNA samples allow more rapid, routine application of MGM genotyping. RAPDs were proved to be applicable to clone identification (Varghese et al. 1997); but the low reliability of this kind of MGMs, based on non specific random amplification of DNA fragments, limits the possibility of technical transfer from one laboratory to another. AFLPs are more reliable and were very useful for rapid identification of a great number or MGMs and allow the establishment of a saturated genetic map of Hevea brasiliensis and H. benthamiana (Lespinasse et al. 2000b). But, AFLPs, like RAPDs, are genetically less informative compared to RFLPs or isozymes: they are non locus specific, i.e. they can't be transferred from one genotype (rubber clone) to another, and in practice, AFLPs only bi-allelic markers, i.e. markers that can exhibit only 2 states in a species (presence versus absence of a band). Microsatellites (alias SSRs for Simple Sequence Repeats or STMS for Sequence Tagged Microsatellite Site) have been also developed on rubber tree (Seguin et al. 1997). Microsatellites can be considered as ideal MGM as they combined good biological and technical properties such as: PCR based MGMs like AFLPs and RAPDs, locus specific and multi-allelic such as RFLP or isozymes, potentially unlimited in number like RFLPs and AFLPs, they show very high levels of polymorphism in populations, with a number of alleles per locus greater than for any other kind of MGM. It is the reason why Cirad decided to put effort on the identification of rubber specific microsatellite sequences, which is the critical step for the availability of such MGM. In this paper we present the progress of microsatellite development in rubber tree and present a rapid overview of our current works on microsatellite applications to Hevea molecular genetics....
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