|
|
||||||||
a Dep. of Crop Science, North Carolina State Univ., Raleigh, NC 27695-7631 USA
b USDA-ARS and Dep. of Crop Science, North Carolina State Univ., Raleigh, NC 27695-7631 USA
c National Institute of Agrobiological Resources, Tsukuba, Japan
tommy_carter{at}ncsu.edu
| ABSTRACT |
|---|
|
|
|---|
Abbreviations: CP, coefficient of parentage CJ, central Japan NJ, northern Japan SJ, southern Japan
| INTRODUCTION |
|---|
|
|
|---|
To address this problem, breeders have developed the concept of genetic base to compare, in a relative way, the diversity of contrasting applied breeding programs (Delannay et al., 1983; Gizlice et al., 1994; Song et al., 2000). Genetic base has been defined as all genetic stocks that have contributed to cultivar development (Cui et al., 2000). Quantification of genetic base (i.e., calculation of the proportional contributions of ancestors to the base) has been achieved to date primarily through pedigree analysis of cultivars by means of coefficient of parentage (CP), a form of numerical taxonomy (Cox et al., 1985a,b; Murphy et al., 1986; Knauft and Gorbet, 1989; Souza and Sorrells, 1989; Dilday, 1990; Smith et al., 1990; Smith and Smith, 1992; Martin et al., 1991; Cuevas-Perez et al., 1992; McClean et al., 1993; Gizlice et al., 1994; Hintum and Haalman, 1994; Voysest et al., 1994; Cui et al., 2000).
In soybean, the genetic base of Chinese soybean breeding has been described as broad and that of USA and Canadian (US-CAN) breeding as narrow (Gizlice et al., 1994; Cui et al., 2000). Coefficient of parentage analysis revealed that 35 and 339 ancestors contributed 50 and 90% of the genes in Chinese cultivars while only five and 26 ancestors contributed similar amounts to the US-CAN base. Each of the three major growing regions in China were almost independent in terms of genetic base and each had more contributing ancestors than did the whole of the US-CAN. The midwestern and southern growing regions of the US-CAN were quite distinct, on the basis of pedigrees, but less so than the major growing regions of China. Although most of the U.S. breeding base is derived from Chinese landraces, China and US-CAN cultivars share only a small degree of common ancestry based upon pedigree, and thus, have remained relatively isolated from each other in the 20th century.
The genetic base of modern Japanese soybean cultivars is not well characterized. Elucidation of this genetic base and its relation to Chinese and US-CAN breeding should facilitate the efficient use of Japanese cultivars in breeding and aid in determining the current status of genetic diversity in the crop. The objective of this study is to quantify the genetic base of Japanese soybean cultivars registered by the Ministry of Agriculture, Forestry and Fisheries between 1950 to 1988 by determining (i) the genetic contribution of each ancestor to the genetic base of Japanese soybean cultivars using CP analysis; (ii) the relative genetic diversity and relatedness of three major growing regions of Japan; (iii) the changes in the genetic base of Japanese cultivars over time; and (iv) the genetic structure of the Japanese base in comparison to those of the US-CAN and China.
| Materials and methods |
|---|
|
|
|---|
|
Genetic Contribution of Ancestors to Genetic Base and Assumptions
The genetic contribution of an ancestor to a modern cultivar was determined as the fraction of genes in the modern cultivar that could be traced to that ancestor through pedigree analysis (Gizlice et al., 1994; Cui et al., 2000). Coefficient of parentage was used to estimate this contribution. Coefficient of parentage between two individuals is defined as the probability that a random allele at a random locus in one individual is identical by descent to a random allele at the same locus in another individual (Malécot, 1948; Kempthorne, 1957). The average CP between an ancestor and all 86 cultivars in the study was taken as the overall genetic contribution of an ancestor to the genetic base of Japanese soybean (Gizlice et al., 1994). The ancestors did not have recorded common antecedents, and thus, total contributions of all ancestors to the genetic base summed to unity.
In the calculation of CP, we assumed the following: (i) all ancestors, cultivars, and parental breeding lines were homozygous and homogeneous; (ii) a cultivar or a breeding line derived from manual hybridization or natural outcrossing obtained 50% of its genes from each parent; (iii) the CP value between a naturally occurring or mutagen-induced mutation and its antecedent was 1.0; and (iv) the CP value between two full-sib inbreds from a cross of two unrelated parents was 0.5 if the two inbreds shared no common F2 plant, 0.75 if two inbreds were derived from a common F2 plant, or 1.0 if the two inbreds were derived from the same F5 plant.
Ancestors with Multiple Phenotypic Types in the Japanese Collection
Five ancestors (`Akasaya', `Ani', `Shirasaya', `Tamanishiki', `Tsuru No Ko') appeared as multiple phenotypic sources with identical names in the Japanese Germplasm Storage Center of the National Institute of Agrobiological Resources (Miyazaki et al., 1995b). Genetic relations among the multiple phenotypic sources were not clear from passport data. Multiple phenotypic sources for a single ancestor raised the possibility that more than one source of an ancestor was used as a parent in breeding and added a degree of uncertainty to pedigree relations. For two of the ancestors above (Ani, Tsuru No Ko), contrasting phenotypic sources of the single ancestor were collected from breeding stations. The ancestor Ani, for example, was collected at two different breeding stations while a third station actually developed a cultivar from it (source not specified). We adopted the following rules and assumptions for such cases. The multiple phenotypic types with a common ancestral name were assigned a CP value of 0.75 for all pairs to reflect an assumed similarity among the types. If a breeding station was the site of collection for an ancestral phenotype, we assumed that the station also used that same source in breeding. A breeding station which was not a collection site, but employed one of the multiple phenotypes in breeding, was assumed to use the source collected nearest to it. We further assumed that only one phenotypic ancestral source was used for breeding at any one station. We then counted each ancestral name as a single ancestor in the calculation of the genetic base.
Off-Type Variants Which Arose from Preexisting Strains
Twenty-three genotypes in the pedigree data base arose as selections from preexisting strains. Because of the uncertain pedigree associated with their development, these 23 genotypes could have arisen from mutation, natural outcrossing (via unknown male parents), or through mechanical mixing with the expected CP relation between selection and antecedent of 1.0, 0.5, or 0.0, respectively. Where phenotypic data were available, we examined conventional descriptive traits (flower, pubescence, maturity, and 100-seed weight) of the selection and its antecedent to help resolve pedigree uncertainties. Six of the 23 selections were compared with antecedents in this way. Phenotypic data were obtained from field evaluation of Japanese cultivars and available ancestors in 1994 and 1995 at Clayton, NC, from seed sources identified by Miyazaki et al. (1995a,b) from the Japanese Germplasm Storage Center of the National Institute of Agrobiological Resources (data not shown). Because of the rarity of multiple mutations in a single plant, we assumed an outcrossing event to be the origin of the variant if it differed from the preexisting strain by two or more of the four conventional descriptor traits and assigned a CP relation of 0.5 between the two in such cases. In the absence of evidence for outcrossing (i.e., no or only one phenotypic difference), a mutational event was assumed and a CP value of 1.0 was assigned. Employing this rationale, five selections were assigned a CP relation of 0.5 with their respective antecedents, and one selection was assigned a CP relation of 1.0. Four genotypes developed through irradiation were also compared phenotypically against their antecedents with no differences detected except for maturity dates.
In the absence of phenotypic data to clarify the origin of an off-type selection, we arbitrarily ignored the possibility of seed mixing and assigned a CP relation of 0.75 between the remaining 17 off-type genotypes and their preexisting source. The value 0.75 is the midpoint of the CP values associated with mutation or natural outcrossing as the origin of a selection. Murphy et al. (1986) assigned the identical value in a CP analysis of wheat (Triticum aestivum L.), and Cui et al. (2000) assigned a similar value of 0.87 for Chinese soybean on the basis of case studies of phenotypic difference between genotypes. For the five off-type selections deemed to have arisen from natural outcrossing and the 17 off-type selections with uncertain male pedigree, the category of assumed, but unknown, male parent (called pseudo ancestor hereafter) was employed to aid computational analysis of CP.
Analysis of Coefficient of Parentage
The pedigree information was recorded into a pedigree data base file with four column headings: progeny name, female and male parent, and a six or fewer letter abbreviation of progeny name. This file was checked extensively for typing errors against a hard copy. The CP matrix for ancestors and cultivars was computed by a FORTRAN program following the same procedures described in detail by Cui et al. (2000). Briefly, a first subroutine of the program assigned codes to ancestors and progeny. All ancestor codes were numerically smaller than all progeny codes, and the total number of ancestors was consistent with that derived via visual inspection of the original pedigree information. An overwrite file added pseudo ancestor relations and other relations not easily represented in the data base. The second subroutine took the output from the first subroutine and the overwrite file as input to calculate the CP matrix. Subsequently, the CP between Individuals X and Y was calculated as CPXY = pxCPXA + qxCPXB, 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 above formula was simplified to CPXY = 1/2(CPXA + CPXB) which was the usual case. The average CP of each ancestor with all cultivars was then calculated.
| Results and discussion |
|---|
|
|
|---|
|
|
The CJ region released twice as many cultivars as other regions and had a correspondingly larger base than the other regions of Japan. This larger genetic base for CJ is reflected in the total number of ancestors for the region and in the number of ancestors contributing 50% of the genetic base (twice as many as for the other two regions, Table 1). The NJ and SJ regions were similar in terms of number of releases and size of genetic base. However, exotic ancestors contributed 18% of the NJ base but only 2% of the SJ base (Table 3). The CJ region was intermediate in the use of exotic germplasm with 7% derived from exotic sources. The U.S. ancestors only contributed genes to the CJ and SJ base, while Chinese strains only contributed genes to the NJ and CJ bases. The ratio of ancestors employed to cultivars released and average number of ancestors used for each individual cultivar were relatively constant across regions, despite the larger number of releases in the CJ region (Table 1). These findings support the view that breeders from the contrasting regions tended to share a common philosophy which promoted the inclusion of a broad range of diversity in breeding.
Changes over Time in Japanese, Chinese, and US-CAN Genetic Bases
New Japanese cultivars were released in every decade since 1950, and the genetic base of Japanese soybean breeding expanded in a corresponding way (Tables 1 and 4)
. The expansion of the base was exemplified by the relatively large percentage contribution of new ancestors added to the base in successive decades from 1950 (15, 12, 18, and 27%) and by the relatively stable ratio of ancestors used to cultivars released across decades (Tables 1 and 5) . There were only three ancestors that made sizable contribution to the genetic base for at least three of the four decades studied (Ani, Geden Shirazu, and Daizu Hon 326).
|
|
|
The three genetic bases of Japan, China, and the US-CAN were largely independent based upon pedigree analysis (Gizlice et al., 1994; Cui et al., 2000). Approximately 6% of the US-CAN and 3% of the Chinese genetic bases traced to Japanese stock. Only 5 and 2% of the Japanese base traced to China and the US-CAN, respectively. The genetic separateness of Japan cultivars from those in China and the US-CAN was confirmed recently by DNA-based genetic distance measures (Thompson et al., 1997; Nelson et al., 1998; Carter et al., 2000). The elite Japanese cultivars were the most distinct group as indicated by four types of molecular markers.
Implications to Breeding
The relative independence of applied breeding programs in Japan, China, and the USA suggests that each of these three breeding pools may serve as important reservoirs of genetic diversity for the others. Carter et al. (2000) proposed the use of foreign cultivars as sources of new yield genes for applied breeding in the USA, because applied soybean breeding was based primarily on a narrow genetic base of one dozen founding ancestors (source of 80% of genes) introduced prior to 1930 (Gizlice et al., 1994; Sneller, 1994). Gizlice et al. (1993a) reported that intensive selection upon this narrow base caused a decline in genetic diversity, noting that newer cultivars from the USA were as highly related as half sibs on the average. Some breeders have suggested that this decline could threaten future yield advances in U.S. breeding if left unchecked (Zhou et al., 1998). Because cultivars are usually more productive than random plant introductions from germplasm collections, Japanese and Chinese cultivars may be attractive potential sources of yield genes and other agronomically important diversity (Bernard et al., 1998; Carter et al., 2000). At present, however, Japanese cultivars are viewed by many U.S. breeders only as useful sources of desirable food processing traits for niche markets.
In China, there is not an apparent threat to genetic diversity in applied breeding because of the large genetic base and the tendency of Chinese breeders to avoid the mating of close relatives (Cui et al., 2000). However, Chinese breeders have demonstrated the ability to develop high-yielding, popular cultivars in recent years from the hybridization of traditional Chinese cultivars with cultivars from the USA. More than 20 cultivars with at least 25% U.S. cultivar pedigree are currently grown in China (J. Gai, 1999, personal communication). This important success story suggests that the U.S. and Chinese cultivars are mutually important to each other as a source of yield genes for breeding. In Japan, a narrow genetic base does not appear to be a serious hindrance to breeding progress, yet 12 cultivars have been released with 25% or greater U.S. or Chinese pedigree. These Japanese breeding successes indicate that all three contrasting gene pools may be economically important in applied breeding. Many Chinese, Japanese, and publicly derived U.S. cultivars are available freely as breeding stock from the USDA-ARS National Soybean Germplasm Collection.
At present, modern Japanese and Chinese cultivars have not made a great impact in U.S. soybean breeding. Duvick (1984) indicated that most U.S. soybean breeders preferred to use only elite U.S. cultivars as donor sources for pest resistance and stress tolerance, even though most of these same breeders supported the concept of expanding the soybean genetic base through germplasm introgression. A later survey by Frey (1996) indicated that 104 science-person years were devoted to U.S. soybean cultivar development, with only 26 responsible for germplasm enhancement. A more recent survey revealed that less than 1% of U.S. field breeding involves breeding lines using introductions not already part of the genetic base (T.E. Carter, 1998, unpublished data).
Marshall (1989) identified an important reason why exotic germplasm such as Japanese cultivars are seldomly used in mainstream U.S. breeding: unknown relations between the exotic germplasm and adapted cultivars. Breeders are reluctant to spend breeding capital on exotic germplasm unless there is a clear rationale. Providing a clear rationale for selecting one plant introduction over another has proven elusive in terms of yield improvement (Goodman, 1985). Recent development of molecular marker techniques in conjunction with detailed pedigree analysis, such as provided here, may provide breeders with useful tools to measure genetic diversity among cultivars. These techniques may enhance the use of exotic material in practical soybean breeding (Nelson et al., 1998; Thompson et al., 1998; Li 1999; Boerma and Rouf Mian, 1999; Carter et al., 2000).
Received for publication February 14, 2000.
| REFERENCES |
|---|
|
|
|---|
This article has been cited by other articles:
![]() |
J. S. C. Smith, D. N. Duvick, O. S. Smith, M. Cooper, and L. Feng Changes in Pedigree Backgrounds of Pioneer Brand Maize Hybrids Widely Grown from 1930 to 1999 Crop Sci., November 1, 2004; 44(6): 1935 - 1946. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. N. Ude, W. J. Kenworthy, J. M. Costa, P. B. Cregan, and J. Alvernaz Genetic Diversity of Soybean Cultivars from China, Japan, North America, and North American Ancestral Lines Determined by Amplified Fragment Length Polymorphism Crop Sci., September 1, 2003; 43(5): 1858 - 1867. [Abstract] [Full Text] [PDF] |
||||
![]() |
X. Zhou, T. E. Carter Jr., Z. Cui, S. Miyazaki, and J. W. Burton Genetic Diversity Patterns in Japanese Soybean Cultivars Based on Coefficient of Parentage Crop Sci., July 1, 2002; 42(4): 1331 - 1342. [Abstract] [Full Text] [PDF] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| The SCI Journals | Agronomy Journal | Vadose Zone Journal | |||
| Journal of Natural Resources and Life Sciences Education |
Soil Science Society of America Journal | ||||
| Journal of Plant Registrations | Journal of Environmental Quality |
The Plant Genome | |||