Assessment of Inter Simple Sequence Repeat Markers to Differentiate Sympatric Wild and Domesticated Populations of Common Bean

1996) and amplified fragment length polymorphisms (AFLPs) (Tohme et al., 1996; Papa and Gepts, 2003). Efficient assessment of genetic diversity is important for conservaThe ISSR marker technique involves polymerase chain tion and utilization of genetic resources. We sought to assess the abilreaction (PCR) amplification of DNA using a single ity of inter simple sequence repeats (ISSRs) as molecular markers to primer composed of a microsatellite sequence, such as identify genetic diversity both within and among sympatric populations of common bean, Phaseolus vulgaris L. One wild and four domesti(GACA)4, anchored at the 3 or 5 end by two to four cated populations originating from the Sierra Norte de Puebla, Mexarbitrary, often degenerate, nucleotides (Zietkiewicz ico, were chosen because they were growing in the same region or et al., 1994). The ISSRs have proven to be a rapid, field. The ISSR diversity was assessed using four primers that revealed simple, and inexpensive way to assess genetic diversity a higher number of strong, polymorphic bands in preliminary analyses. (Kantety et al., 1995; Tsumura et al., 1996; Esselman Fifty of these bands could be mapped onto the core linkage map in et al., 1999; Gilbert et al., 1999; Sarla et al., 2003; Tanyopopulation BAT93 Jalo EEP558, whereas four were unlinked. The lac, 2003; Jin et al., 2003), to identify closely related mapped bands were distributed over nine of the 11 linkage groups, cultivars (Fang and Roose, 1997; Fang et al., 1997, 1998; suggesting that they were broadly distributed in the genome. On the Eiadthong et al., 1999; Prevost and Wilkinson, 1999; basis of a sample of 50 intense bands in these five populations, ISSRs Martins et al., 2003), and to study evolutionary prowere able to clearly distinguish all populations. Most of the variation was distributed among populations rather than within populations, cesses, such as reproductive systems (Liston et al., 2003) consistent with the predominantly selfing nature of the species. Differand gene flow (Wolfe et al., 1998). A recent paper by entiation among domesticated populations was much higher (FST ≈ Galván et al. (2003) describes differences between 10 0.49–0.85) than between the wild and domesticated gene pools (FST Argentinean and three French bean cultivars, in particu0.05). Within each population, most loci had achieved near-fixation. lar broad differences between the Andean and MesoAround 7% of individuals showed a lack of correlation between seed american gene pools. type and ISSR fingerprint. Furthermore, each population contained In the current research, the level of genetic diversity individuals with unusual markers but present in the other populations and differentiation was determined among one wild and (frequency 5 or 10%). Two nonmutually exclusive explanations were four domesticated sympatric populations of common discussed—incomplete lineage sorting and introgression—to account bean (Phaseolus vulgaris; 2n 2x 22) from the Sierra for the presence of these unusual individuals. Overall, ISSR markers were very useful to differentiate closely related populations. Further Norte de Puebla. Most studies of genetic diversity in research is necessary to quantify the actual level of outcrossing. common bean have been conducted in samples representing broad geographical ranges to identify major subdivisions in its germplasm, such as gene pools and races E management of genetic resources, whether (Singh et al., 1991; Gepts, 1998). Fewer studies have for conservation or for utilization in plant breeding been conducted to determine genetic relationships on programs, requires accurate and fast assessment of levsmaller geographic levels (Cattan-Toupance et al., 1998; els of genetic diversity and degrees of genetic relatPapa and Gepts, 2003). These studies are useful because edness. In the last decade, increasing use has been made they provide information on evolutionary factors that of molecular markers based on DNA analyses (Bretting can shape genetic diversity in common bean populaand Widrlechner, 1995; Gepts, 1995). An enduring contions, such as gene flow. For example, Cattan-Toupance cern with these markers is that they are fairly laborious et al. (1998) showed the importance of a disease pressure and costly. Hence, there has been a trend to markers that, in determining local population differentiation, in addiwhile highly polymorphic, are relatively easy and fast to tion to genetic drift. They also considered partial outanalyze. In common bean, these include randomly ambreeding to be a potential factor affecting association of traits. Papa and Gepts (2003) showed that, in sympatry, plified polymorphic DNA (RAPD) (e.g., Freyre et al., gene flow from domesticated to wild types is three times more important than in the opposite direction. FurtherA. González and P. Gepts, Dep. of Agronomy and Range Science, more, spatial autocorrelation studies showed that wild Univ. of California, 1 Shields Ave., Davis, CA 95616-8515, USA (A. beans exhibited a stronger local population structure González, current address: CSIRO Plant Industry, Horticulture Unit, than domesticated beans. PMB 44, Winnellie 0822, Darwin, NT, Australia); A. Wong and A. Delgado-Salinas, Inst. de Biologı́a, Univ. Nacional Autónoma de MéxIn addition to studying the level of genetic diversity ico, México, DF, México; R. Papa, Dipartimento di Scienze degli among sympatric populations of common bean, we sought Alimenti, Univ. Politecnicà delle Marche, Ancona, Italy. This research to determine the usefulness of ISSR markers in common was funded by the McKnight Foundation Collaborative Crop Research Program. Received 28 May 2003. Plant Genetic Resources. Abbreviations: AFLP, amplified fragment length polymorphism; *Corresponding author ([email protected]). ISSR, inter simple sequence repeat; PCR, polymerase chain reaction; RAPD, randomly amplified polymorphic DNA; RFLP, restriction Published in Crop Sci. 45:606–615 (2005). © Crop Science Society of America fragment length polymorphism; SAHN, sequential, agglomerative, hierarchical, and nested. 677 S. Segoe Rd., Madison, WI 53711 USA 606 Published online February 23, 2005