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PLANT GENETIC RESOURCES

Genetic Diversity Patterns in Japanese Soybean Cultivars Based on Coefficient of Parentage

^a Dep. of Crop Science, North Carolina State Univ., Raleigh, NC 27695-7631
^b USDA-ARS and Dep. of Crop Science, North Carolina State Univ., Raleigh, NC 27695-7631
^c National Institute of Agrobiological Resources, Tsukuba, Japan

* Corresponding author (tommy_carter{at}ncsu.edu)

	ABSTRACT

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS AND DISCUSSION REFERENCES

 
Japan is a historical center of genetic diversity for soybean [Glycine max (L.) Merr.], but diversity of modern Japanese cultivars is not well characterized. The objectives of this study were to quantify genetic diversity of Japanese cultivars via coefficient of parentage (CP), determine the relative importance of breeding factors in explaining that diversity, and incorporate results into a practical guide for management of diversity. All 86 public Japanese cultivars released and registered during 1950 to 1988 were subjected to CP and multivariate analysis. The mean CP for the 86 cultivars was low (0.04), indicating a potentially high degree of diversity in Japanese breeding. Eighty percent of all pairs of cultivars were completely unrelated by pedigree. The low mean CP for the cultivars was attributed to a continual incorporation of unique Japanese land races into the genetic base over time, to the introduction of foreign germplasm from China and the United States and Canada (US-CAN) as breeding stock, and to limited exchange of germplasm among Japanese breeding programs. Cluster analysis was an effective discriminator of diversity. Six clusters were identified which had a mean CP value equivalent to that of half-sibs or greater. These clusters encompassed a total of 54 cultivars, explained 57% of the variation in the CP relations, and had few ancestors in common. Each cluster was derived primarily from only a few programs. Backcrossing and full-sib matings were absent in Japanese pedigrees and, thus, clusters were formed primarily from parent-offspring, full-sib, and half-sib relations. Cultivar attributes such as growing region, release era, maturity designation, and developing institution did not elucidate strong patterns of pedigree diversity. In practical breeding, one may maximize the chances of finding good specific Japanese x Japanese or Japanese x US-CAN crosses by choosing Japanese cultivars from a wide array of Japanese clusters rather than sampling extensively within a cluster.

Abbreviations: CJ, central Japan • CP, coefficient of parentage • MDS, multidimensional scaling NJ, northern Japan • SJ, southern Japan • US-CAN, USA and Canada

	INTRODUCTION

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS AND DISCUSSION REFERENCES

 
CROP DIVERSITY IS ESSENTIAL to sustainable food production. The use of diversity in the form of resistance to diseases and insects, for example, has been a cornerstone of successful crop production in the past century (Campbell et al., 1999, p. 532). The primary developer of crop diversity for modern breeding was the ancient farmer. For millennia, farmers practiced on-farm breeding by noticing and saving beneficial genetic variants as they arose during production. Initial genetic variants derived from on-farm breeding facilitated the adaptation and spread of crops to a wide array of climates, soil types, and domestic uses, increased drastically the hectarage upon which subsequent on-farm breeding was practiced and resulted, ultimately, in a global reservoir of diversity. The thousands of genetic variants preserved in this way form the basis for modern cultivar improvement.

An important example of on-farm breeding success in soybean is cyst nematode (Heterodera glycines Ichinohe) resistance. Almost all cyst nematode resistance genes in modern U.S. cultivars trace their lineage directly from a few farmer-developed cultivars in China. These resistant cultivars were added to germplasm preservation banks after 1940, incorporated into modern breeding programs in the 1950s, and resulted in the release of the first resistant elite cultivars in the 1960s (Caviness, 1992). More than 30 000 accessions from on-farm soybean breeding are preserved in the germplasm collections of the USA, China, and Japan (Miyazaki et al., 1995a; Palmer et al., 1996; Xu et al., 1999).

While the importance of crop diversity is being recognized increasingly in agriculture, it is also true that diversity itself is being reduced in the farmer's field for many crops. A common scenario in agriculture is one where old cultivars and land races are replaced by new cultivars which are more closely related to each other than to the genetic materials they replaced (Ehrlich and Wilson, 1993). Soybean cultivars in the USA and Canada (US-CAN) provide a clear example of this trend, where cultivars today are more closely related than those grown 40 yr ago, and have an average pedigree relationship equivalent to that of half sib in the midwestern and southern growing regions (Gizlice et al., 1993). While this inbreeding in soybean has posed no obvious barrier to current sustainable soybean production in the USA (Specht et al., 1999), it is clear that the genetic diversity in applied breeding is much less than that available in the global germplasm collections. Reduced diversity is a potential problem for long-term soybean improvement and a concern with regard to genetic vulnerability.

In contrast to the trend in the USA, 75 yr of Chinese soybean breeding has not produced a sizable increase in the relationships of cultivars, even through yield gain has been substantial (1–2% per year) (Cui et al., 1998). On average, current Chinese cultivars share less than 2% of their genes in common, on the basis of CP analysis (Cui et al., 2000b). The CP between pairs of cultivars is the probability that a random allele at a random locus in one cultivar is identical by descent to a random allele at the same locus in another cultivar (Malécot, 1948; Kempthone, 1957). The successful maintenance of diversity in modern Chinese soybean breeding has been attributed to a continual infusion of new germplasm into applied programs and a strong tendency to avoid the mating of close relatives (Cui et al., 2000a,b).

In Japan, the relatedness of modern soybean cultivars and the changes in their CP relationships over recent decades is not quantified. However, researchers have noted the general distinctness of Japanese cultivars in comparison with those of the US-CAN and China. Zhou et al. (2000) reported that the Japanese genetic base was quite distinct from that of China or the US-CAN on the basis of pedigree analyses, and that cultivars from three major growing regions in Japan shared little ancestry in common with each other. The DNA marker analysis of modern cultivars from Japan has confirmed the distinctness of Japanese cultivars from those of China and the US-CAN (Thompson et al., 1997; Nelson et al., 1998; Carter et al., 2000).

Carter et al. (2000) proposed that modern cultivars from Japan, China, and the USA may serve as important contrasting and mutually beneficial reservoirs of genetic diversity for future applied breeding. Multi-year field tests in the USA indicated that modern Japanese cultivars may carry important agronomic genes for breeding (Carter et al., 2000). Elucidation of patterns of diversity among Japanese cultivars should aid the preservation and efficient use of Japanese cultivar diversity both within the Japanese soybean breeding pool and in its cross breeding with Chinese, US-CAN, and other elite materials. The objectives of this study were to quantify genetic diversity in Japanese cultivars, determine the relative importance of regions, release eras, maturity groups, and developing institutions (i.e., breeding programs) in explaining that diversity, and incorporate results into guidelines which promote efficient use of genetic diversity found in Japanese cultivars.

	MATERIALS AND METHODS

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS AND DISCUSSION REFERENCES

 
The origin, pedigree, year of release, Japanese maturity rating, and intended end use were compiled for all 86 public Japanese soybean cultivars released and registered during 1950 to 1988 (Fukui and Arai, 1951) (S. Miyazaki, personal communication, 1999). These cultivars were developed in 11 distinct breeding programs and represented up to five cycles of breeding in Japan since World War II. Cultivars were rated for maturity at Clayton, NC, in 1994 and 1995 in comparison to standard U.S. cultivars. Each cultivar was assigned to a primary growing region of Japan on the basis of the location of the developing institution, where regions were defined as northern Japan (NJ, Hokkaido Island), central Japan (CJ, Honshu Island), and southern Japan (SJ, Kyushu Island) (Table 1) (Zhou et al., 2000). Four release eras were defined as 1950s (1950–1959), 1960s (1960–1969), 1970s (1970–1979), and 1980s (1980 to 1988). The CP matrix for the 86 cultivars was computed by a FORTRAN program as described by Zhou et al. (2000). Briefly, pedigree information was compiled into a data base and checked exhaustively for errors. A first subroutine of the program assigned codes to ancestors and progeny. An overwrite file added CP relations that were not easily represented in the data base. The second subroutine used the output from the first subroutine and the overwrite file to calculate the CP matrix. The CP between individuals X and Y was calculated as CP_XY = pCP_XA + qCP_XB, where Y was the progeny of A and B, X was a second strain but not a descendent of Y, and p and q were the percentage contribution of A and B to Y. If two parents A and B contributed equally to Y, then the above formula was simplified to CP_XY = 1/2 (CP_XA + CP_XB) which was the usual case.

View larger version (28K): [in this window] [in a new window]   Fig. 1. Plot of coefficient of parentage (CP) relationship for 86 Japanese soybean cultivars released from 1950 to 1988. Coordinates for a cultivar were obtained from multidimensional scaling analysis employing two dimensions based on CP relations. The complement of the linear distances (1 - Distance) between any two cultivars estimates the coefficient of parentage between them. Distances 1 indicate no pedigree relationship between cultivars. For cultivar codes, see Table 1.

View larger version (34K): [in this window] [in a new window]   Fig. 2. Plot of coefficient of parentage (CP) relationship among six clusters representing 54 Japanese soybean cultivars released from 1950 to 1988. Coordinates for a cultivar were obtained from multidimensional scaling analysis employing two dimensions based on CP relations. The complement of the linear distances (1 - Distance) between any two cultivars estimates the coefficient of parentage between them. Distances 1 indicate no relationship. For cultivar codes, see Table 1.

The relation of various factors in explaining diversity patterns was computed through regression analyses of clusters, growing regions, release eras, maturity estimates, and breeding programs on the original CP matrix as described by Gizlice et al. (1996) and Cui et al. (2000b). Models with single and combinations of variables were fitted by the GLM procedure. The R² was used to assess the importance of each variable (SAS, 1985b). For regression analysis of the cluster factor, cultivars that were not part of an acceptable cluster were combined into one cluster for easy computation.

	RESULTS AND DISCUSSION

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS AND DISCUSSION REFERENCES

 
Genetic Diversity among Regions in Japan
The mean CP value for the 86 cultivars was low (0.04), indicating a potentially high degree of diversity in Japanese breeding. This value was slightly higher than that reported for Chinese soybean cultivars (0.02), but much lower than that for US-CAN cultivars (0.13–0.17) (Gizlice et al., 1993; Sneller, 1994; Cui et al., 2000b). The low mean CP for Japanese cultivars reflected the fact that 80% of all pairs of cultivars were completely unrelated within the boundaries of available pedigree data. Inspection of pedigrees showed that backcrossing and full-sib matings were completely absent in Japanese pedigrees, which contributed, in part, to the low relationship among cultivars.

Although Japanese cultivars exhibited a low overall CP of 0.04, the mean CP within each of the three regions was slightly higher (0.13, 0.07, and 0.07 for the NJ, CJ, and SJ regions, respectively) (Table 2). The mean CP between regions was near zero (<0.02). Cui et al. (2000b) found a similar trend for China, where the mean CP of Chinese cultivars within each of the three major growing regions varied from 0.02 to 0.06 but was essentially zero between regions. A similar trend was also observed for US-CAN soybean cultivars, where the mean CP within southern and midwestern growing regions was 0.23 and 0.18, respectively, while the mean CP between the two regions was only 0.04 (Gizlice et al., 1993).

The low CP relations between growing regions in Japan could be visualized graphically by means of coordinates from a two-dimensional MDS analysis (Fig. 1). The NJ cultivars were separated from others by dimension 1, and SJ cultivars were separated roughly from CJ cultivars by dimension 2. The cultivars from CJ occupied more space in the graph than the NJ and SJ cultivars together, even though the number of cultivars from NJ and SJ together is similar to that from CJ. This indicated that CJ cultivars were perhaps more diverse in terms of pedigree than those from the other two regions. This notion was supported, in part, by the fact that the CJ region had a lower mean CP than did the NJ region (Table 2).

Genetic Diversity among Contrasting Release Eras
Mean CP for Japanese cultivars would be expected to increase over cycles of breeding because breeders tend to use a limited number of elite lines from one cycle to generate the next. This practice tends to force the mating of relatives and drive CP upward (St. Martin, 1982). However, the mean CP for each release era was low and ranged only from 0.02 to 0.05. The CP between release eras was also low (0.01–0.04) (Table 3). The low mean CP of Japanese cultivars for all release eras reflected a continual expansion of the genetic base over approximately five cycles of breeding, through incorporation of new genetic materials. This trend for CP was similar to that found in China, but contrasted with the trend found for US-CAN release eras, where the mean CP for release eras increased steadily from 0.10 in the early 1950s to 0.17 in the early 1980s (Gizlice et al., 1993). The rising CP of US-CAN cultivars in succeeding eras reflected the almost closed nature of the US-CAN genetic base which was eroded over time through the mating of relatives (Gizlice et al., 1993). The contrasting trends in CP between U.S. and Japanese breeding can be described in population genetics terms, where US-CAN breeding had a relatively smaller effective population size and, thus, a faster rise in CP over time (St. Martin, 1982).

Cultivars with exotic ancestors in their pedigrees fell into distinct clusters. Eight of the twelve NJ cultivars with Chinese pedigree fell into cluster one. Four of six cultivars with elite U.S. materials in the pedigree fell into two clusters (three and four). No clear pattern was found with regard to the relationship between the intended end-use of cultivars and cluster assignments.

Genetic Diversity among Contrasting Maturity Groups
Exact U.S. maturity groupings are not well established for most Japanese cultivars. Maturity group estimates employed in this study, for example, were derived from only 2 yr of field observation in North Carolina. Thus, it is possible that some of the maturity group designations employed here were in error by as much as one full maturity group. To minimize the effect of this problem on analysis of maturity, genotypes from neighboring maturity groups were combined into larger maturity groupings prior to statistical analysis of maturity effects (Table 6). The mean CP for each combined maturity group ranged from 0.05 to 0.13 and CP between combined maturity groups ranged from 0.00 to 0.06 (Table 6). Thus, CP was lower and genetic diversity was greater within maturity groups than has been reported for U.S. cultivars, reflecting the general trend for Japanese breeders to avoid the mating of close relatives. (Gizlice et al., 1996).

Genetic Diversity among Breeding Institutions
Eleven breeding institutions developed the 86 cultivars used in this study. Among them, three breeding institutions were located in the NJ, five in the CJ, and three in the SJ regions. These breeding programs spanned a wide latitude (roughly from 31–45.5° N) equivalent in range to that of Toronto, Canada and Jacksonville, FL in North America. As a result, cultivars released from these programs contrasted greatly in mean maturity (from U.S. maturity group I–IX) (Table 7). Because of the wide range in maturity for the breeding programs, germplasm developed by one program was often unadapted for another and, thus, germplasm exchange among them was minimal. The low germplasm exchange was reflected statistically in a CP less than 0.1 between most programs. Only programs from the NJ region had CP relations slightly greater than 0.1 (0.15–0.18). The wide range in maturity among Japanese breeding programs also limited cooperative breeding trials among programs. Although formal regional cooperative yield tests among US-CAN breeders have been integral to breeding progress, no such practices developed in Japan except for the NJ region (S. Miyazaki, personal communication, 2001).

Relative Importance of the Diversity Patterns
To establish the relative importance of various factors in determining genetic diversity patterns in Japanese cultivars, we employed a series of regression analyses and compared R² values. Growing regions, although clearly distinct in pedigree, explained only 14% of the total variation in cultivar relationships. The four release eras, though quite distinct in terms of CP, accounted for only 1% of the variation in CP. Maturity group and breeding program effects explained more variation than did growing regions or release eras, but accounted for only 21 and 28% in the CP matrix, respectively. In contrast, the six clusters we identified accounted for 57% of the variation. Thus, cluster analysis identified the major diversity pattern in Japanese cultivars with respect to pedigree. Cluster analysis was also found to be the best discriminator of diversity patterns in CP for Chinese and US-CAN cultivars (Gizlice et al., 1996; Cui et al., 2000b). Regression of combinations of breeding factors against CP did not have an appreciable effect on R² values in comparison to single factor analyses. Regression of cluster plus breeding program, cluster plus region, cluster plus release era, and cluster plus maturity group against CP accounted for 72, 62, 65, and 68% of the variation, respectively. Other combinations accounted for less than 40% of the variation.

Use of Foreign Germplasm in Japanese Breeding
While Japanese breeders have relied extensively on Japanese landraces to infuse new genes into breeding, they also employed exotic materials from China, the US-CAN, and elsewhere (Zhou et al., 2000). Fourteen cultivars were derived from seven Chinese ancestors or old cultivars and six from US-CAN stocks (Table 8). Among those, seven Chinese ancestors or old cultivars, ‘Ouhoushu’, ‘Shika 4’, and ‘Mansoukin’ were widely grown cultivars in the Northeast of China before 1960 (Ouhoushu is also referred to as ‘Huang Bao Zhu’ in Chinese; Shika 4 is designated ‘Zi Hua 4 Hao’ in Chinese; and Mansoukin is designated ‘Man Cang Jin’ in Chinese) (Miyazaki et al., 1995b; Cui et al, 1999). Two other Chinese ancestors of Japanese cultivars, ‘Kingen’ (‘Jin Yuan’ in Chinese and a parent of Mansoukin) and ‘Si Li Huang’ (a parent of Ouhoushu) were also important ancestors in Chinese breeding, and together accounted for 11.6% of Chinese soybean genetic base (Cui et al., 2000a).

Japanese cultivars developed from US-CAN materials were all released after 1977, whereas most cultivars derived as first progeny from Chinese parents were released before 1960, indicating a change over time in the source of exotic germplasm for breeder use. If one assumes that a cross was made 10 yr before release of a cultivar and 8 yr before release (or use) of a breeding line from that cross, then almost all Chinese ancestors were used as parents before 1955 and all other exotic ancestors, except one, were used after 1965 (Table 8). This switch coincided with historical events. From 1931 to 1945, Japan occupied northeast China, providing Japanese breeders with access to Chinese germplasm. Commercial trade and presumably germplasm exchange continued between Japan and China until the Korean conflict in the early 1950s, but was minimal thereafter for some years (Schaller, 1985).

In contrast, the Japanese did not develop an apparent interest in U.S. germplasm until around 1958, when Japanese agronomists and horticulturists visited USDA germplasm collection maintenance facilities (J. Creech, personal communication, 2000). However, the trigger for Japanese breeders' use of US-CAN germplasm was the liberalization of soybean import in 1961 (S. Miyazaki, personal communication, 1999). As a result of this policy change, domestic soybean production lost competitiveness and decreased dramatically. Therefore, Japanese breeders were dispatched to the USA and Europe to study advanced soybean breeding programs. On the basis of their studies, Japanese programs were reorganized and strengthened. These developments, plus the availability and extensive characterization of U.S. germplasm for traits such as soybean cyst resistance, the more difficult access to Chinese germplasm after the Korean conflict of the 1950s, and the incomplete characterization of germplasm in the Chinese collection at that time induced Japanese soybean breeders to turn their attention to US-CAN germplasm.

It is interesting to note that germplasm flow from Japan to the USA began in the 1920s, when two USDA plant exploration groups were sent to Japan. Two soybean specialists, W.J. Morse and P.H. Dorsett joined one expedition (Creech, 2000). They traveled through Japan, Korea, and northeast China and brought back approximately 3000 soybean accessions. Among them, several became ancestors of US-CAN breeding, such as PI 80837 from Japan, ‘Kanro’ from South Korea, and PI 88788 from China.

Implications to Plant Breeding
Japanese soybean breeding has focused mainly on seed quality traits such as yellow hilum, large seed, high protein content, and cooking quality in addition to high yield. Some of these characters may be critically important not only to Japanese breeding, but to breeding efforts in the USA, China, and elsewhere. The results of the CP analysis reported here provide guidelines which should promote the efficient use of that genetic diversity which is present in Japanese cultivars. This information will be useful not only to Japan, but to China, the USA, and other countries which develop soybean cultivars.

The available data suggest that Japanese soybean breeding has remained robust in terms of genetic diversity. The close genetic relationships between modern cultivars have been minimized through avoidance of mating of close relatives and through continual additions of germplasm to the genetic base. Full sib and backcross matings were absent in Japanese pedigrees. Also, in contrast to soybean breeding in the USA, Japanese breeding had no land mark cultivars such as Lee, ‘Williams’, and Harosoy to dominate pedigrees of subsequent cultivars and drive CP upwards. The clearest patterns of diversity in Japanese cultivars were identified by cluster analysis. Breeding programs and maturity groupings were associated with CP to a lesser degree.

Breeding patterns identified here may assist the Japanese breeders in the efficient selection of parental stock for making selections. Avoidance of matings within clusters would be a practical approach to continued maintenance of diversity in Japanese breeding. Manjarrez-Sandoval et al. (1997) found that a CP between parents greater than that of half sibs (0.25, the average relation of Japanese clusters identified here) often means small genetic variance for yield in their progeny and, thus, slow breeding progress. Also, increased exchange among breeding programs would be a desirable breeding approach in the maintenance of diversity. Elite breeding lines from contrasting Japanese breeding programs often have CP relations much lower than 0.25, affording breeders the opportunity to capitalize upon gains made in each program, without sacrificing diversity.

For soybean breeding in the US-CAN, the original genetic base was narrow, and new cultivars were developed through intensive selection upon what has remained a narrow base. Introduction of exotic germplasm to broaden diversity has been slow in U.S. breeding because of a focus on short-term breeding gains rather than maintenance of diversity. Also, it is not clear to most breeders how best to select germplasm to broaden their programs. A benefit of the present study is in the assistance of US-CAN breeders in the selection of Asian cultivars with which to broaden the US-CAN genetic base. Clusters identified in this study may represent successful breeding endeavors in Japan, and thus, they may offer good choices for parental stock. We suggest that breeders may maximize their chances of finding good specific US-CAN by Japanese crosses by (i) choosing a wide range of U.S. parental stock, (ii) choosing Japanese parental stock from multiple clusters, multiple breeding programs, or otherwise from diverse pedigrees, (iii) avoidance of Japanese cultivars with U.S. pedigree, and (iv) by selecting Japanese cultivars with a desirable phenotype such as high yield.

Extensive evaluation of Japanese cultivars in the USA via the SAVE (Soybean Asian Variety Evaluation) project revealed that several Japanese cultivars were relatively higher yielding, with no clear pattern to high yielding ability in terms of regional origin, release era, or cluster assignment (Carter et al., 2000). Cultivars from the SJ region were slightly higher yielding, relative to controls, than those from other regions. Surprisingly, older cultivars were often as high yielding as more recently released Japanese cultivars. Japanese soybean breeding objectives and/or interaction between genotype and environment may have caused this result.

The CP analysis provided here is not the only guide available to breeders for preservation or increase of genetic diversity in applied programs. Analysis of DNA marker populations may shed light on the most efficient use of desirable Japanese cultivars in future breeding. However, the low pedigree relation among Japanese cultivars, the low pedigree relation of Japanese cultivars to U.S. and Chinese cultivars, the large number of ancestors in the genetic base of Japanese breeding, and the lengthy pedigree history of soybean breeding in Japan (since World War II) all suggest that the reservoir of genetic diversity represented by Japanese cultivars is a promising area for future breeding research.

Received for publication March 22, 2001.

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