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PLANT GENETIC RESOURCES

Molecular Genetic Analysis of U.S. and Chinese Soybean Ancestral Lines

^a Dep. of Crop Sciences, 1101 W. Peabody Dr., Univ. of Illinois, Urbana, IL 61801
^b Institute of Crop Germplasm Resources, Chinese Academy of Agricultural Sciences, Beijing, China
^c Pioneer Hi-Bred Intl., P.O. Box 328, Hamel, IL 62046
^d USDA-ARS, Plant Germplasm Introduction and Testing Research, Room 59 Johnson Hall, Washington State Univ., Pullman, WA 99164-6402
^e USDA-Agricultural Research Service, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, Dep. of Crop Sciences, 1101 W. Peabody Dr., Univ. of Illinois, Urbana, IL 61801

* Corresponding author (rlnelson{at}uiuc.edu)

	ABSTRACT

TOP NOTES ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION CONCLUSIONS REFERENCES

 
Most of the U.S. soybean [Glycine max (L.) Merr.] ancestral lines were introduced from China, but nothing is known of the genetic relationships among the ancestors of modern U.S. and Chinese cultivars. The objectives of this research were to measure the variation among the major ancestors of U.S. and Chinese cultivars, to establish the genetic relationships among these U.S. and Chinese soybean ancestral lines, and to determine the relationship between geographical origin and genetic diversity. Genomic DNA from these lines was characterized by random amplified polymorphic DNA (RAPD) with 35 selected decamer primers. On the basis of the presence or absence of amplified DNA fragments, simple matching coefficients were used to calculate genetic similarities between pairs of lines. Cluster analyses generally separated the ancestral gene pools of the USA and China. Clusters reflected the geographical origin of the lines. Large differences exist between northern U.S. and Chinese ancestral lines and central and southern Chinese ancestral lines. The pattern of diversity found within the U.S. and Chinese ancestors can aid breeders in selecting parental lines to more efficiently exploit the diversity found in these two major gene pools.

Abbreviations: AMOVA, Analysis of molecular variance • HHH, Huang Huai Hai region in China (east central) • MG, maturity group • NE, northeast region in China • PCR, polymerase chain reaction • RAPD, random amplified polymorphic DNA • SMC, simple matching coefficient • UPGMA, unweighted pair group method using arithmetic average

	INTRODUCTION

TOP NOTES ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION CONCLUSIONS REFERENCES

 
SOYBEAN ORIGINATED in China and is a crop of major importance in both China and the USA. Both countries have active soybean breeding programs. Over 650 cultivars were released in China from 1923 to 1995 (Cui et al., 1999). These cultivars were derived from 348 soybean ancestral lines including 302 Chinese landraces, 24 U.S. cultivars, 12 Japanese cultivars, and 10 cultivars from other countries (Cui et al., 1999). There have been over 400 publicly released cultivars in the USA, which were developed from approximately 80 soybean ancestral lines (Gizlice et al., 1994). Although most of the ancestors of U.S. soybean cultivars originally came from China in the early part of the 20th century, the genetic relationship between the two ancestral gene pools that produced the current cultivars of the USA and China is unknown. The genetic base of soybean breeding in North America is very limited (Gizlice et al., 1994; Sneller, 1994). Twenty-eight introductions and seven first progenies (U.S.-developed cultivars with uncertain pedigrees) have contributed over 95% of the genes in publicly released cultivars (Gizlice et al., 1994). The cultivars from China could be a potentially important resource for genetic diversity for many traits such as disease resistance, seed composition, and yield to improve U.S. cultivars. As more cultivars are exchanged between China and the USA, an understanding of the genetic diversity in the ancestral lines of these cultivars will aid plant breeders in selecting parents to enhance the performance of future soybean cultivars.

The objectives of this research were (i) to measure the variation among the major ancestors of the U.S. and Chinese cultivars; (ii) to establish the genetic relationships among these U.S. and Chinese soybean ancestral lines; and (iii) to determine the relationship between geographical origin and genetic diversity.

	MATERIALS AND METHODS

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Plant Materials
On the basis of ecological conditions and cropping systems, there are three major soybean production regions in China. They are the northeast (NE), the Huang Huai Hai region (HHH) in east central China, and the south (Zhang, 1985), which account for approximately 40, 35, and 20% of soybean planting area in China, respectively. On the basis of the contribution of ancestral lines to released cultivars, 32 important soybean ancestors (or selections from soybean ancestors) were chosen to represent these three major soybean production regions (Table 1). Seeds of the Chinese ancestral lines were not explicitly preserved. To identify extant lines that are most likely to be the same genotypes as those used in the original crosses, we consulted many sources in the Chinese literature to learn not only the history of Chinese cultivars but also the descriptions of parental lines. Since the names given to many of these ancestral lines are not unique, it is possible that in some cases the wrong genotype may have been included in this research even though the name matches that presented in the pedigree. The ancestral lines chosen for this research are in the pedigrees of more than 75% of all Chinese cultivars released during the past 75 yr (Anonymous, 1980; Zhang, 1985; Chang and Sun, 1991; Hu and Tian, 1993; Cui et al., 1999). More cultivars have been released in the northeast so more ancestors were selected from the northeast than from the HHH or the south (Table 1). The most important ancestors from the northeast occur in the pedigrees of more than 200 cultivars. In the HHH, none of the ancestors contributed to more than 61 cultivars, and in the south the greatest contributing ancestor occurs in the pedigree of only 20 cultivars (Table 1). The ancestors that originated in each region have made the greatest contribution to cultivars developed in that region. The ancestors from NE China occur in the pedigrees of 82% of the cultivars released in the northeast. The ancestors from the HHH and southern regions are in the pedigrees of approximately 57 and 42%, respectively, of the cultivars released in these regions (Table 2).

A combination of 18 soybean ancestors and first progenies, which were defined by Gizlice et al. (1994) and represent more than 85% of the genetic base of North American soybean cultivars, were selected to represent the U.S. ancestors in this research (Table 3). All accessions used in this research are in the USDA Soybean Germplasm Collection (Urbana, IL).

View this table: [in this window] [in a new window]   Table 3. Major contributing U.S. soybean ancestors or first progeny selected for diversity analysis and the percentage of genes theoretically contributed to U.S. cultivars.

Thirty-five decanucleotide primers obtained from Operon Technologies (Alameda, CA) and selected for high diversity scores among diverse soybean lines (Thompson and Nelson, 1998) were used in this research. The RAPD protocol reported by Kresovich et al. (1994) was followed with minor modifications, and the DNA was amplified in a Perkin-Elmer GeneAmp PCR System 9600. A 25 µL reaction volume was used with 50 ng of genomic DNA. The amplification program consisted of 2 min at 94°C followed by 45 cycles of 1 min at 94°C, 5 min at 38°C and 2 min ramp to 72°C, and 2 min at 72°C. A final cycle of 72°C for 7 min was completed before the reaction mixtures were held at 4°C. Amplified DNA products were electrophoresed on 1% (w/v) agarose gels in 1x TBE buffer at 96 V. A 100 bp DNA marker (GibcoBRL, Life Technologies, Rockville, MD) was used to estimate fragment size. The gels were stained with ethidium bromide, viewed under ultraviolet light, and photographed.

Data Collection and Analyses
To evaluate the degree of random amplified polymorphic DNA (RAPD) fragment variation within and between the U.S. and Chinese soybean ancestral gene pools, DNA fragments were scored as either present (1) or absent (0). Simple matching coefficients (SMC), S_ij = (a + d)/(a + b + c + d), were used to calculate the similarity coefficients between each pair of genotypes where a = number of fragments in common between lines; d = number of fragments absent in both lines, and b and c = number of fragments not in common between two lines. All scorable polymorphic and monomorphic fragments for each line were included to compute the similarity coefficients.

A SAS macro (Mumm and Dudley, 1995) was used to compute the similarity matrix on the basis of the SMC. Euclidean distances, D_ij = (1 - S_ij)^1/2, were calculated on the basis of the similarity coefficients, and used as input into the hierarchical cluster analysis methods of UPGMA (unweighted pair group method using arithmetic average) (SAS Institute, 1989a) and Ward's minimum variance method (Ward, 1963). The TREE procedure was used to generate dendrograms. A nonhierarchical cluster analysis, VARCLUS (SAS Institute, 1989b), was also used with the original data as input to calculate the covariance matrix. UPGMA and Ward's methods are common procedures used in clustering analysis. In UPGMA, the distance between two clusters is the average distance between pairs of observations and in Ward's method the distance between two clusters is the analysis of variance sum of squares between the two clusters summed over cluster members. VARCLUS performs the disjoining clustering of variables based on a covariance matrix. There is no way of determining which procedure most accurately represents the genetic reality so multiple procedures were used to analyze the data.

The average genetic distances and standard deviations between and within the two gene pools were obtained by the MEANS procedure in SAS (SAS Institute, 1989a). Pairwise F_st statistics for all pairs of populations for the two gene pools were calculated using the analysis of molecular variance (AMOVA) program (Schneider et al., 1997) in which the squared Euclidean distance from cluster analysis was used as input. The significance of pairwise F_st values was tested by permuting the individuals between the populations by a nonparametric permutation scheme (Schneider et al., 1997).

	RESULTS

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RAPD Data Profile
The 35 selected RAPD primers (Thompson and Nelson, 1998) produced 261 scorable fragments of which 145 fragments were found to be polymorphic (56%). In this research, each selected primer produced an average of 7.5 fragments. Nine fragments, OPE-11700, OPF-41100, OPH-13800, OPK-10500, OPL-9750, OPN-18480, OPP-9980, OPR-71350 and OPS-14580, were found to be present in the Chinese soybean ancestral lines only. These fragments were rare among Chinese lines and each occurred in 10 or fewer ancestral lines.

Genetic distances among the 2450 pairwise combinations of U.S. and Chinese soybean ancestors ranged from 0.26 to 0.52 with a standard deviation of 0.033 and a mean genetic distance of 0.43 (Table 4). ‘Arksoy’ and ‘Ralsoy’, a selection from Arksoy, had the smallest genetic distance. ‘Qin yang shui bai dou’, a Chinese ancestral line from Henan province, had the overall largest genetic distance from Arksoy. Within the U.S. gene pool, ‘Lincoln’, a major northern U.S. ancestor with unknown parents, and ‘Haberlandt’, a southern U.S. ancestor from N. Korea had the largest genetic distance (0.51). Within the Chinese gene pool, ‘58-161’ and ‘Pu dong da huang dou’, from the neighboring provinces of Jiangsu and Shanghai, had the least genetic distance (0.29) and ‘Hua xian da lu dou’ and ‘Ji ti No. 1’ from Henan and Liaoning provinces, respectively, had the largest genetic distance. Between the two gene pools, ‘Mukden’, a major northern U.S. ancestor originally from Liaoning, had the minimum genetic distance with ‘Tie jia si li huang’ from Jilin province.

Genetic Patterns of the U.S. and Chinese Soybean Ancestors
Each of the clustering procedures (UPGMA, Ward's and VARCLUS) assigned the U.S. and Chinese ancestral lines to ten clusters (Table 5). There were six clusters (3, 4, 5, 6, 9, and 10) that were consistently defined by all three procedures, three clusters (1, 7, and 8) that were consistently grouped by two of three procedures, and one cluster (2) that had a diverse pattern with the three procedures (Table 5). Two of these clusters (1 and 4) contained only U.S. ancestors. Cluster 1 was predominately northern U.S. soybean ancestors from the NE region of China, whereas Cluster 4 was predominately southern U.S. soybean ancestors. Lincoln and ‘Dunfield’, two important northern U.S. ancestors, were assigned to Cluster 1 by two of the procedures, UPGMA and VARCLUS, but were clustered with two Chinese ancestors, ‘Huang bao zhu’ from Jilin and Ji ti No. 1 from Liaoning, by Ward's method. Dunfield was originally from Jilin province in NE region of China; the parents of Lincoln are unknown. Although ‘S-100’ in Cluster 1 is a major southern U.S. soybean ancestor, it was derived from ‘Illini’, which is also in Cluster 1. Illini may be one of the parents of S-100 (Thompson et al., 1998). In Cluster 4, all lines but ‘Perry’ were originally from Jiangsu or had one parent from Jiangsu. Perry, ‘Jackson’, and ‘Ogden’ all had parents from Japan.

The other five clusters each contained Chinese and U.S. soybean ancestral lines. Cluster 3 was predominately Chinese ancestral lines from Heilongjiang, Liaoning, and Jilin in the NE region but also contained Mukden, a major ancestor in the northern U.S. that originally came from Liaoning. Cluster 9 has two relatively minor Chinese ancestral lines from the south and HHH regions and Arksoy and Ralsoy that were minor southern U.S. ancestral lines. Cluster 10 was also a mixture of two Chinese and three U.S. ancestral lines that originated from the NE region except for Haberlandt. Although the records show that Haberlandt originally came from North Korea, it is in MG VI and is mostly in the pedigrees of cultivars developed in the southern U.S. Cluster 7 included major ancestors for three of the five major soybean-producing regions of the USA and China. ‘Ai jiao zao’ and ‘Shanghai liu yue bei’ were two of the four top contributing ancestors of southern China. 58-161 is one of the three most important ancestors of the HHH region and CNS, originally from Jiangsu, is a major ancestral line of the southern USA. This cluster also included two other ancestors from the southern region of China. Both UPGMA and VARCLUS defined Cluster 7 identically, but with Ward's 58-161, Pu dong da huang dou, and CNS were assigned to Cluster 8.

Cluster 2 was the largest group defined by UPGMA, but it was divided into three clusters by each of the Ward's and VARCLUS procedures. However, since there was very little consistency among the groupings of Ward's and VARCLUS in Cluster 2, all of these lines were put into one cluster recognizing that it is a diverse group. This cluster included six Chinese ancestral lines from the NE region of China and one U.S. ancestor ‘Korean’, probably from North Korea. ‘Jin yuan’, Huang bao zhu, and ‘Zi hua No. 4’, included in this cluster, were the three most important ancestral lines of the NE region of China. These three lines were assigned to different clusters by both Ward's and VARCLUS.

‘Qi huang No. 1’ was one of the three most important ancestors in HHH region. It was classified as an outlier in UPGMA and was not consistently grouped with any other lines by the other two procedures, so we chose not to include it in any cluster.

Genetic Relationships among Regional Populations
The clusters formed by all procedures generally reflected the geographical origin of the lines. To explore the genetic relationships of these geographical subpopulations, F_st statistics for all pairs of populations among the two U.S. and three Chinese regions were computed by the AMOVA program (Schneider et al., 1997). On the basis of the relative contribution of ancestral lines to northern and southern U.S. cultivars, northern and southern U.S. ancestral groups were defined. Lincoln, ‘Mandarin (Ottawa)’, ‘Richland’, ‘A.K. (Harrow)’, Dunfield, Mukden, Illini, ‘Capital’, and Korean were included in the northern U.S. group, and the southern U.S. group consisted of CNS, S-100, Jackson, ‘Roanoke’, Ogden, Haberlandt, Perry, Ralsoy, and Arksoy. Because Dunfield was in MG III, it was included in the northern group although it made a slightly larger contribution to the southern cultivars than to northern cultivars. The analyses showed that although the ancestral lines of northern and southern U.S. cultivars were generally placed in different clusters, the average genetic distances between northern and southern U.S. ancestors, and between the northern U.S. and northern Chinese ancestors were not significantly different on the basis of a nonparametric permutation test (Table 6). A relatively small significant difference between the southern U.S. and northern Chinese ancestral lines (Table 6) was noted. Highly significant differences were found between ancestral lines of northern U.S. and northeast Chinese cultivars and the ancestral lines of central and southern China (Table 6).

	DISCUSSION

TOP NOTES ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION CONCLUSIONS REFERENCES

The cluster analyses can help to confirm origin information, refine genetic relationships that may be assumed through origin data, and assist in defining diverse gene pools for selecting parents in cultivar improvement programs. All of the U.S. ancestral lines came from China except for three first progenies that probably had parents from both China and Japan and four ancestral lines from North Korea. One MG I line Korean, presumably from North Korea, has consistently clustered with accessions from the NE region of China in this study and in the work by Thompson et al. (1998). The other three North Korean lines, Haberlandt, Ralsoy, and Arksoy, are in MG VI, which raises some doubts about their origin. In the work of Thompson et al. (1998), these three lines clustered together with Mukden, which indicated a northern origin. In this set of lines, Haberlandt clustered with the ancestors from the NE region of China but Arksoy and Ralsoy (derived from Arksoy) clustered with ancestors from southern China, which seems inconsistent with a North Korean origin. In the work of Thompson et al. (1998), the only lines which likely would have originally come from outside NE China were U.S. ancestral lines. In this research many lines came from the HHH and southern regions of China. This change in geographical representation between these two experiments could significantly alter the clustering patterns of lines included in both studies.

Thompson and Nelson (1998) found that in U.S. soybean breeding each of the most significant crosses involving major ancestors included parents from two different genetic groups as defined by analyses of RAPD fragments. To see if that were also true with the Chinese ancestors, the major ancestors from each region were identified. They were Jin yuan, Huang bao zhu, Zi hua No. 4, ‘Feng di huang’, and ‘Tie jia si li huang’ in the NE region; 58-161, ‘Tong shan tian e dan’, Qi huang No. 1, Ju xuan 23, Xin huang dou, ‘Tie jiao huang’, and ‘Pi xian ruan tiao zhi’ in the HHH region; and Feng xian sui dao huang, 493-1, Ai jiao zao, and Shanghai liu yue bai in the southern region. The pedigrees of released cultivars in the three regions of China (Zhang, 1985; Wang and Wang, 1992; Hu and Tian, 1993; Cui et al., 1999) indicate that the contributions that these major ancestors made were through a few significant crosses in the NE region and through many crosses in the HHH region and south region of China.

In the NE, the contributions of the most important ancestors, Jin yuan and Huang bao zhu, were made primarily through a cross between these two lines. The contributions of other major ancestors, Feng di huang, Zi hua No. 4, and Tie jia si li huang, were made through crosses with the progenies of Jin yuan and Huang bao zhu. Jin yuan and Huang bao zhu were both assigned to Cluster 2. UPGMA put them into the same group, but the other two procedures put them in separate groups. The same occurred with Zi hua No. 4 that was also in Cluster 2. Tie jiao si li huang and Feng di huang were placed into separate clusters by all procedures.

The contributions of two of the most important ancestors, 58-161 and Tong shan tian e dan, in the HHH region were made through a cross of 58-161 and Xu dou No. 1, a selection from Tong shan tian e dan. 58-161 and Tong shan tian e dan were placed in different clusters. Zhu xu 23 and Qi huang No. 1 (also in different clusters) made their genetic contributions through a direct cross and in crosses with many other lines. The six major ancestors of the HHH regions were distributed in four clusters.

In the south, contributions of the two major ancestors, Feng xian sui dao huang and 493-1, were mostly through crosses with other cultivars and they were both put in Cluster 8. Ai jiao zao and Shanghai liu yue bei were both put in Cluster 7. Both made their genetic contribution through a cross between these two lines, and in crosses with other lines.

The data from the Chinese ancestors were generally consistent with conclusions drawn from the U.S. ancestors. Within each of these major gene pools of soybean breeding in China, there were distinct genetic subgroups and the most significant ancestors in each gene pool were distributed in at least two different subgroups. These results provide additional evidence that the successful crosses in cultivar development often have genetically divergent parents as measured by diversity in DNA markers. Expanding genetic diversity in a breeding program could improve the performance of the resulting soybean cultivars.

The cluster analyses consistently grouped together lines with similar geographical origin and the pairwise F_st values obtained from the AMOVA procedure summarized these results by showing that, in general, genetic distance increased as geographical distance increased. The genetic diversities established by the cluster analyses can also define genetic divergence that exists within geographical regions and help to identify the divergent lines within gene pools. There were four clusters containing ancestors that originated from northeast China. Cluster 1 contained only U.S. ancestral lines and accounted for over 40% of the genes in northern U.S. cultivars. Cluster 10 had three U.S. ancestral cultivars that contributed nearly 30% of the genes in northern U.S. cultivars. Korean in Cluster 2 contributed less than 1% to the northern U.S. cultivars whereas this cluster had the major ancestors for the cultivars of the NE region in China. The complete separation of northern ancestors of both China and the USA. from ancestors from the HHH and south region of China indicated the large genetic differences among the lines from those regions.

This work is in general agreement with the conclusions of Cui et al. (2000b) but our data allows an actual comparison of the ancestral lines of the USA and China. Cui et al. (2000b) assumed that U.S. and Chinese ancestral lines were genetically distinct since none shared a common name. This may not be a valid assumption since all U.S. ancestral lines were named after importation into the USA and if they had a Chinese name it was generally not preserved. Our research supports the conclusion of Cui et al (2000b) that different regions of China have genetically independent gene pools but we also demonstrate the genetic relatedness of some U.S. and Chinese ancestral lines.

	CONCLUSIONS

TOP NOTES ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION CONCLUSIONS REFERENCES

 
RAPD fragments exhibited a high level of efficiency for detecting the DNA polymorphism among these soybean ancestors. Most U.S. soybean ancestral lines are genetically distinct from those used in soybean breeding in China. A low level of genetic diversity was detected between southern and northern U.S. soybean ancestral lines, but the U.S. soybean ancestral lines were genetically quite distinct from the ancestral lines from HHH or southern areas in China. DNA markers such as RAPDs, combined with appropriate statistical analyses are effective tools in identifying useful genetic relationships in the absence of pedigree information and are of great value in managing and utilizing germplasm.

	ACKNOWLEDGMENTS

 
Funding for this research was provided in part by the United Soybean Board and by the Illinois Soybean Program Operating Board.

	NOTES

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Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the USDA or the University of Illinois and does not imply its approval to the exclusion of other products or vendors that may also be suitable.

Received for publication June 5, 2000.

	REFERENCES

TOP NOTES ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION CONCLUSIONS REFERENCES

 

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