**6.1 Introduction**

The soybean genome is consisting of around 1115 Mbp, much smaller than the genomes of maize and barley, but larger than the genomes of rice and *Arabidopsis* (Arumuganathan & Earle, 1991). Soybean is a tetraploid plant, evolved from a diploid ancestor (n=11), went aneuploid loss (n=10), followed by polyploidization (n=20) and diploidization (chromosome pairing behavior) (Hymowitz, 2004). As a result of polyploidization soybean has a significant percentage of internal duplicated regions distributed among its chromosomes (Pagel *et al*., 2004). Sequence diversity in cultivated soybean is relatively low compared to other species leading to a major challenge in the improvement of this important crop. To efficiently broaden the genetic base of modern soybean cultivars, we have a detailed insight into genetic diversity of soybean germplasm. Such insight could be achieved through molecular characterization using DNA markers, which are more informative, stable and

Genetic Diversity and Allele Mining in Soybean Germplasm 9

soybean accessions from the Far East using RAPD profiles of mitochondrial and chloroplast DNA. Xu & Gai (2003), Pham Thi Be Tu *et al*. (2003), An *et al*. (2009) confirmed the results of Kanazawa *et al*. (1998) and Seitova *et al*. (2004) in terms of the high genetic variation between the wild and cultivated soybean accessions. They also found that the diversity of *G. soja* was higher than that of *G. max*; and environmental factors may play important roles in soybean evolution. Furthermore, they revealed that accessions within each species tend to form subclusters that are in agreement with their geographical origins, demonstrating that an extensive geographical genetic differentiation exists in both species. Consequently, it was indicated that geographical differentiation plays a key role in the genetic differentiation of both wild and cultivated soybeans. The relationship between geographical differentiation and genetic diversity appeared in the work of Chen & Nelson (2005) who identified significant genetic differences between soybean accessions collected from different provinces in China. Their data provided pronounced evidence that primitive cultivars of China were generally genetically isolated in relatively small geographical areas. Similar results were obtained by Li & Nelson (2001, 2002) in their study on soybean accessions from 8 provinces in China using a core set of RAPD primers with high polymorphism in soybean (Thompson *et al.*, 1998). On the contrary, Brown-Guedira *et al*. (2000) did not find an association between origin and RAPD markers among soybean lines of more modern origin. It is likely that these genotypes have been dispersed by human intervention from the areas

The relationship between genetic differentiation and origin of 120 soybean accessions from Japan, South Korea and China was evaluated with RAPDs (Li & Nelson, 2001). They found that the Japanese and South Korean populations were more similar to each other, whereas both were genetically distinct from the Chinese population, suggesting that the S. Korean and Japanese gene pools might be probably derived from a relatively few introductions from China. Li *et al*. (2001) compared the genetic diversity of ancestral cultivars of the N. American (18) as well as the Chinese soybean germplasm pools (32) using RAPD markers, the N. American ancestors have a slightly lower level of genetic diversity. Cluster analyses generally separated the two gene pools. In particular, a great genetic variability was detected between the ancestors of northern U.S. and Canadian soybeans and the Chinese

Chowdhury *et al*. (2002) examined the level of genetic similarity among forty-eight soybean cultivars imported out of their country Thailand using DNA (RAPD) markers. They found high level of genetic similarities between these cultivars. Cluster analysis of the obtained data classified the 48 cultivars into four groups at 0.57 similarity scale, even though the cultivars are morphologically or geographically very close. Comparing agronomic performance and RAPD analysis via dendrogram, a total of 11 cultivars can be useful to soybean breeders in Thailand who want to utilize genetically diverse introductions in soybean improvement. Baránek et *al*. (2002) evaluated the genetic diversity within 19 soybean genotypes included in the Czech National Collection of Soybean Genotypes by RAPD method. The polymorphism among the studied genotypes was 46%. Presented results enable the selection of genetically distinct individuals. Such information may be useful to breeders willing to use genetically diverse introductions in soybean improvement

SSRs molecular markers have been widely applied in the genetic diversity studies of the soybean germplasm (Abe *et al.*, 2003; Wang *et al*., 2006; Fu *et al*., 2007; Li *et al*., 2008; Wang &

of actual origin.

ancestors.

process.

**6.5 SSRs (Simple sequence repeats)** 

reliable, compared to pedigree analysis and traditionally used morphological markers. The genetic markers include RFLP, RAPD, SSR and AFLP markers were used to probe the genetic differences between wild and cultivated soybeans or for the origin and dissemination of soybeans (Brown-Guedira *et al*., 2000; Tian *et al*., 2000; Li & Nelson, 2001; Xu & Zhao, 2002; Abe *et al*., 2003). These studies have revealed higher levels of genetic diversity in wild soybean.
