**3. Genetic diversity of soybean germplasm based on morphological traits**

As we know, phenotypic traits are controlled by genes and affected by environment, but large numbers of accessions can adapt to environments. The phenotypic data has more polymorphism in genetic diversity and reveal genetic variation indirectly. On the contrary, the molecular data reveal genetic variation directly, but fewer markers have less polymorphism. It is very difficult to obtain molecular data for a large number of accessions that has enough polymorphism to show the genetic diversity of germplasm. So, the morphological traits are the suitable and practical tools for studying the genetic diversity on large numbers of accessions.

Variation in shape of plants has always been an important means of (1) distinguishing individuals; (2) controlling seed production; and (3) identifying the negative traits those

soybeans cultivated in different countries in the world were introduced directly or indirectly from China; and (5) the pronunciation of the word of soybean in many countries is about the same as the Chinese 'Shu'; for instance, it is pronounced 'soya' in England, 'soy' in the USA,

Although, the origin of soybean cultivation may be China, scholars have different viewpoints on the original areas of soybean domestication. One of these views is the theory that soybean originated from northeast China (Fukuda, 1933). This theory based on the observations that semi-natural wild soybeans are extensively distributed in northeast China, that is, there are large numbers of soybean varieties that possess 'primitive' characteristics, such as small black soybean germplasm that extensively distributed in the lower and middle reaches of the yellow river North provinces. The second theory is that soybean cultivation originated in South China. In this theory, it has been thought that south China could be the origin of soybean (Wang, 1947). The evidences for that are the wide distribution of wild soybean in this area, extensive presences of primitive soybean varieties such as Nidou, Maliao Dou, Xiao Huangdou and others that have (1) the short-day character, which is considered to be the initial physiological state of soybean, and (2) the primitive agronomic characteristics related to yield and quality of soybean varieties. The other evidence supporting this theory is the close relatedness between cultivated soybeans in southern China, to wild soybeans in genetic terms based on isoenzymes, and RFLP (Restriction Fragment Length Polymorphism) markers of chloroplast and mitochondrial DNA, SSR data and botanical traits (Ding *et al*., 2008; Guo *et al.,* 2010). In the third theory, it has been thought that the origin of soybean was the eastern part of northern China (i.e. the lower reaches the Yellow River) (Hymowitz, 1970). The evidences for his thought are the same blooming dates for both wild soybean and cultivated soybean at 35°N, confirming that cultivated soybean varieties may have been derived from local wild soybean at around 35°N. In addition, the protein content of cultivated soybean is close to that of wild soybean at 34–35°N. The fourth theory stated that the cultivated soybeans have multiple origins (Lü, 1978). The evidences for that postulation are (1) both South and North China have regions with early developed cultures, that is: the ancients in these regions used local wild soybean as food and did not domesticated wild soy-beans into cultivated ones; (2) the occurrence of wild soybean and cultivated soybean in the same regions and the similarities of both of them in morphological characters; (3) the successful cultivation of both wild and cultivated soybeans in different regions across China. In addition, the geographical distribution of the short-day character of wild soybean indicates the possibility of multiple origins of cultivated

**3. Genetic diversity of soybean germplasm based on morphological traits** 

As we know, phenotypic traits are controlled by genes and affected by environment, but large numbers of accessions can adapt to environments. The phenotypic data has more polymorphism in genetic diversity and reveal genetic variation indirectly. On the contrary, the molecular data reveal genetic variation directly, but fewer markers have less polymorphism. It is very difficult to obtain molecular data for a large number of accessions that has enough polymorphism to show the genetic diversity of germplasm. So, the morphological traits are the suitable and practical tools for studying the genetic diversity on

Variation in shape of plants has always been an important means of (1) distinguishing individuals; (2) controlling seed production; and (3) identifying the negative traits those

and in other languages.

soybean.

large numbers of accessions.

effects on yield, the genetic diversity centers of annual wild soybean and the soybean lines resistance to pod shatter, drought, pests or disease (Truong *et al.,* 2005; Malik *et al.,* 2006, 2007; Ngon *et a.,l* 2006). The studied soybean germplasm exhibited a wide range of phenotypic variation for pod number, seed number, and plant yield. It also showed that soybean developing stages had close association with agronomic traits as well as yield and yield components (Malik *et al.,* 2006, 2007; Ngon *et al.,* 2006).

Pod shape is one of the important descriptors for evaluating soybean genetic resources (IPGRI, 1998; USDA, 2001). Truong *et al.* (2005) tested the applicability of elliptic Fourier method for evaluating genetic diversity of pod shape in 20 soybean (*Glycine max* L. Merrill) genotypes. They concluded that principal component scores based on elliptic Fourier descriptors yield seemed to be useful in quantitative parameters not only for evaluating soybean pod shape in a soybean breeding program but also for describing pod shape for evaluating soybean germplasm.

The genetic diversity was evaluated for genotypes of soybean based on the yield-related traits (Rajanna *et al.,* 2000; Malik *et al.,* 2006, 2007; Ngon *et al*., 2006). It has been reported that differences among genotypes for all the characters were highly significant and the grain yield was positively and significantly correlated with number of pods per plant. The selection for the character had positive direct effect on yield. However, some traits had negative direct effects on yield, such as the leaf area, first pod height, days to 50% flowering, days to flowering completion, days to maturity, plant height, oil content and protein content.

The study of the genetic diversity of wild soybean is invaluable for efficient utilization, conservation and management of germplasm collections. Dong *et al*. (2001) statistically analyzed the agronomic traits of the data base from the National Germplasm Evaluation Program of China to study the geographical distribution of accessions, genetic diversity of characters and genetic diversity centers of annual wild soybean. The results showed that most annual wild soybeans are distributed in northeast China, and the number of accessions decreases from the northeast to other directions in China. They proposed three genetic diversity centers for annual soybean grown in China, the northeast, the Yellow River Valley and the Southeast Coasts of China. Based on these results and Vavilov's theory of crop origination, two opposing possible models for the formation of the three centers are proposed, either these centers are independent of each other and the annual wild soybeans in these centers originated separately, or the northeast center was the primary center for annual wild soybeans in China, while the Yellow River Valley center was derived from this primary center and served as the origin for the southeast Coast center.

The genetic variability in 131 accessions of edamame soybeans (the Japanese name for a type of vegetable soybean eaten at the immature R6 stage) was analyzed using phenotypic traits e. g. maturity information, testa color, and 100-seed weight for breeding new edamame lines resistance to pod shatter (Mimura, 2001). The 131 accessions include 108 Japanese edamame, 11 Chinese maodou, 8 WSU breeding lines, 2 US edamame and 2 US grain soybeans. The obtained results indicated that Edamame genetic diversity was generally clustered around maturity groups and testa color. It was also reported that the genetic diversity among the Japanese edamame cultivars was narrow, compared to Chinese maodou; Japanese edamame and Chinese maodou soybeans may have different genetic pools.

Soybean genotypes, which exhibit genetic diversity in root system developmental plasticity in response to water deficits in order to enable physiological and genetic analyses of the regulatory mechanisms involved, were identified (Young, 2008). These genotypes can

Genetic Diversity and Allele Mining in Soybean Germplasm 7

markers. SDS-PAGE is one of these techniques, widely used to describe seed protein diversity of crop germplasm (Sammour, 2007; Sammour *et al.,* 2007). Genetic diversity and the pattern of variation in soybean germplasm have been evaluated with seed proteins (Hirata *et al.,* 1999; Bushehri *et al*., 2000; Sihag *et al*., 2004; Malik *et al.,* 2009). SDS-PAGE (Bushehri *et al*., 2000) and discontinuous polyacrylamide slab gel electrophoresis (Sharma and Maloo, 2009) were used very successfully in evaluating the genetic diversity and identifying soybean (*Glycine max*) cultivars. Malik *et al*., (2009) evaluated the genetic variation in 92 accessions of soybean collected from five different geographical regions using the electrophoretic patterns of seed proteins. The accessions from various sources differed considerably, indicating that there is no definite relationship between genetic diversity and geographic diversity. Similar results were reported by (Ghafoor *et al.,* 2003). Based on the results of Ghafoor *et al.,* (2003) and Malik *et al*., (2009), SDS-PAGE cannot be used for identification of various genotypes of wild soybean at the intra-specific level, because some of the accessions that differed on the basis of characterization and evaluation exhibited similar banding patterns. However, it might be used successfully to study inter rather than intra-specific variation (Sammour, 1989; Sammour *et al*., 1993; Karam *et al*., 1999; Ghafoor *et al*., 2002). 2-D electrophoresis can be used to characterize the genotypes exhibited

Allozyme markers have been used in soybean to evaluate genetic diversity in accessions from diverse geographic regions (Yeeh *et al*., 1996; Chung *et al*., 2006), wild soybean in natural populations from China, Japan and South Korea (Pei *et al.*, 1996; Fujita *et al*., 1997), and Asian soybean populations (Hymowitz & Kaizuma, 1981; Hirata *et al*., 1999). From an analysis of the Kunitz trypsin inhibitor (*Ti*) and beta-amylase isozyme (*Sp1* = *Amy3*), Hymowitz & Kaizuma (1981) defined seven soybean germplasm pools in Asia: (1) northeast China and the USSR, (2) central and south China, (3) Korea, (4) Japan, (5) Taiwan and south Asia, (6) north India and Nepal and (7) central India. Hirata *et al.* (1999) compared the genetic variation at 16 isozyme of 781 Japanese accessions with the genetic variations of 158 Korean and 94 Chinese accessions, detecting a number of region-specific alleles that discriminated Japanese from Chinese accessions. The presence of alleles specific to the Japanese population suggested that the present Japanese soybean population was not solely

**6. Evaluation of genetic diversity in soybean germplasm using molecular** 

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

similar banding patterns (Sammour, 1985).

a subset of the Chinese population.

**markers** 

**6.1 Introduction** 

tolerate drought stress which is the major factor that limiting soybean yield. The results showed substantial genetic diversity in the capacity for increased lateral root development (number and total length of roots produced) and in the responses of overall root and shoot growth under water deficit conditions.

The extent of between- and within-species differences in the resistance of the four commonest species of Glycine (*G. canescens*, *G. clandestina* , *G. tabacina* and *G. tomentella*) to leaf rust caused by *Phakopsora pachyrhizi* was investigated by Burdon & Marshall (1981). The results of their study showed qualitative and quantitative resistance to leaf rust, and considerable variation in a number of disease characteristics both between and within populations of each species.
