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a Dep. of Natural Resource Sciences and Landscape Architecture, Univ. of Maryland, College Park, MD 20742
b USDA-ARS, Soybean Genomics and Improvement Lab., Beltsville, MD 20705
c Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA 30602
* Corresponding author (wk7{at}umail.umd.edu).
| ABSTRACT |
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0.30. Genetic distance (GD) between pairs of genotypes was calculated on the basis of the similarity indices determined by the 332 AFLP fragments. Within each of the cultivar groups, the average GD between pairs of genotypes was 6.3% among the Japanese cultivars, 7.1% among the NASC, 7.3% among the NASA, and 7.5% among the Chinese cultivars. The average GD between the NASC and the Chinese cultivars was 8.5% and between the NASC and the Japanese cultivars was 8.9%. Although these distances were not significantly different, they were greater than the average GD between all pairs of NASC (7.1%). Clustering and principal coordinate analysis using all 332 fragments showed a separation of the cultivars into three major groups according to their geographic origin. North American soybean ancestors overlapped with all three cultivar groups. The Japanese cultivars were more removed from NASA and NASC than the Chinese cultivars and may constitute a genetically distinct source of useful genes for yield improvement of NASC.
Abbreviations: AFLP, amplified fragment length polymorphism GD, genetic distance NASA, North American soybean ancestors NASC, North American soybean cultivars PIC, polymorphic information content RAPD, random amplified polymorphic DNA RFLP, restriction fragment length polymorphism
| INTRODUCTION |
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The genetic similarity among NASC has reached a level that could limit continued breeding success. Introduction of new sources of germplasm into the breeding pool may provide the genetic variability to permit continued progress in developing high yielding cultivars. Though plant introductions (PIs) provide genetic variability, they are less frequently used as sources of new yield genes than current cultivars and elite lines because they often yield less. Populations developed from crossing cultivars with PIs, which have been selected for good phenotypic traits, generally have a lower mean yield and lower frequency of desirable lines than those populations developed from crossing elite parents (Vello et al., 1984; Ininda et al., 1996). Recent studies have used molecular markers to help identify genetically diverse PIs to use in crosses in cultivar improvement programs (Thompson and Nelson, 1998a, b; Thompson et al., 1998; Narvel et al., 2000). These studies have had more success than conventional selection programs in producing productive lines from PI crosses with elite genotypes. Modern Asian cultivars, which share no ancestors with NASC, represent a potential reservoir of new alleles available for improving U.S. soybean yield, and is a different approach than using other germplasm in crosses with NASC.
Acquisition of soybean germplasm from Asia has increased over time, though not all the introduced cultivars or germplasm have been assessed for their usefulness in soybean improvement. There is a need for extensive evaluation of new germplasm from Asia to determine its genetic diversity and to identify Asian lines to serve as sources of unique genes for U.S. soybean yield improvement.
Conventional molecular marker analysis using restriction fragment length polymorphism (RFLP) (Apuya et al., 1988), ribosomal DNA (Doyle and Beachy, 1985), and random amplified polymorphic DNAs (RAPDs) (Williams et al., 1990) have identified only low levels of genetic diversity in cultivated soybean. Microsatellite markers can detect higher levels of genetic diversity among soybean cultivars but this marker system requires the synthesis of primers and construction of genomic libraries (Maughan et al., 1996). AFLP is a PCR-based, molecular technique that detects high numbers of polymorphic bands (Powell et al., 1996). AFLPs are detected frequently in soybean, are inherited in a stable Mendelian fashion, and exhibit high levels of diversity (Maughan et al., 1996). The objectives of this study were to determine the level of genetic diversity within and between Asian and NASC by AFLP analysis and to identify Asian cultivars with significant genetic difference from NASC.
| MATERIALS AND METHODS |
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The 10-fold diluted ligation mixture was preamplified by 20 PCR cycles. The PCR reaction was performed in a thermal cycler with the following temperature profile: 94°C for 30 s, 56°C for 60 s, and 72°C for 60 s using EcoRI+A(5'GACTGCGTACCAATTC+A3') and MseI+C(5'GATGAGTCCTGAGTAA+C3') primers (provided in the kit) described by Vos et al. (1995). Five primer combinations, E-ACT/M-CAT, E-ACC/M-CAA, E-AAG/M-CTT, E-ACA/M-CAC, and E-AGC/M-CTC, were chosen from a pool of primer combinations that produced seven or more polymorphic bands among the parents of the cross PI290136 x BARC-2 (Rj4) (Ude et al., 1999) and were used for fingerprinting the 190 genotypes in this study.
One hundred-twenty microliters of distilled water was added to 5 µL of each of the preamplified DNA to make a 1:24 dilution from which 5 µL was used for selective amplification. Selective amplification was conducted in 5 µL-aliquots of the diluted preamplified fragments with 32P-ATP labeled EcoRI+3 primer with an unlabeled MseI+3 primer. Amplification was done by PCR with one temperature cycle at 94°C for 30 s, 65°C for 30 s, and 72°C for 60 s, followed by lowering the annealing temperature each cycle 0.7°C for 12 cycles. At the end of the 12 cycles, the reaction was programmed to amplify for 23 cycles at 94°C for 30 s, 56°C for 30 s, and 72°C for 60 s. The reaction products were loaded on a 5% (w/v) polyacrylamide DNA sequencing gel containing 7.5 M urea. Ten base pair (bp) DNA ladder (Cat. No. 10821-015) purchased from Life Technologies Inc., Gaithersburg, MD, was used as a molecular weight standard in every gel. Autoradiography was performed by exposing Kodak Bio-Max MR-2 film (Eastman Kodak Co., Rochester, NY) to the dried gel at room temperature for 48 h.
The gel autoradiographs were scored visually for polymorphism. A band was considered polymorphic if it was present in at least one soybean genotype and absent in others. A matrix was generated in which each band was scored as "1" if present and as "0" if absent for each genotype. Polymorphic information content (PIC); the fraction of polymorphic loci (ß); the arithmetic mean heterozygosity (Hav); the effective multiplex ratio (ER); the marker index (MI), and the average expected heterozygosity for polymorphic markers [Hav(p)] for each of the primer combinations were estimated according to Powell et al. (1996).
The sum of polymorphic heterozygosity (
Hp) is the sum of the polymorphic information content for all loci for each primer pair (
Hp =
PIC) and the fraction of polymorphic loci (ß) is the number of polymorphic loci (np) divided by the sum of polymorphic (np) and nonpolymorphic loci (nnp) [ß = np/(np + nnp)]. The arithmetic mean heterozygosity (Hav) is the product of the fraction of polymorphic loci (ß) and the polymorphic heterozygosity (Hp) divided by the number of polymorphic loci (np) (Hav = ß
Hp/np).
The effective multiplex ratio (E) is defined as the product of the total number of loci per primer (n) and the fraction of polymorphic loci (ß) (E = nß). The marker index (MI) is the product of the total number of loci per primer pair (n) and the arithmetic mean heterozygosity (Hav) (MI = nHav). The marker index (MI) can also be defined as the product of effective multiplex ratio (E) and the average expected heterozygosity [Hav(p)] for the polymorphic markers [MI = EHav(p) where Hav(p) = MI/(n x ß) and Hav(p) = MI/E].
Genetic similarities between pairs of genotypes were estimated with 332 monomorphic and polymorphic bands by means of simple matching coefficients (Powell et al., 1996) in the NTSYS-pc software package version 2.02f (Rohlf, 1998). Genetic distances were calculated by subtracting the similarity indices from 1 and multiplying the result by 100. Student's t tests (P = 0.05) were used to compare the average genetic distances within and among the groups of soybeans studied. A dendrogram based on the similarity coefficient matrix and unweighted pair group method of the arithmetic average clustering was produced. Principal coordinate analysis was also done to show multiple dimensions of the distribution of the genotypes in a scatter-plot (Keim et al., 1992). Genetic distances calculated with monomorphic and polymorphic markers are about one third that calculated with only polymorphic bands (Becker et al., 1995).
| RESULTS AND DISCUSSION |
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0.30 indicating that only 16% of the 332 AFLP bands contributed significantly to the genetic discrimination of the 190 soybean genotypes studied. A PIC score
0.30 has been used previously by Keim et al. (1992) and Lorenzen et al. (1995) with RFLP probes and by Thompson and Nelson (1998b) with RAPD fragments to determine usefulness in other soybean germplasm diversity studies.
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Marker index (MI) is the statistic used to calculate the overall utility of a marker system and is the product of expected heterozygosity and multiplex ratio. The primers E-AGC/M-CTC and E-ACA/M-CAC had low marker indices (2.16 and 1.11, respectively), while the other primers [E-AAG/M-CTT (9.14), E-ACC/M-CAA (8.24), and E-ACT/M-CAT (6.12)] showed high MI values. Just as the Hav(p) analysis indicated, these primers were more useful than E-AGC/M-CTC and E-ACA/M-CAC in discriminating between the soybean genotypes in this study. Average MI for the five-primer pairs used in this study was 5.35, and it was similar to the MI reported by Powell et al. (1996) for the AFLP marker system.
Genetic Relationships
Average genetic distance among the 190 soybean genotypes was 8.1%, and the range of genetic distance (GD) was 0.9 to 15.0% (Table 3). There were no significant differences between the genetic distance means of any of the four genotype groupings. The average GD was lowest among Japanese cultivars (6.3%) whereas the Chinese cultivars had the highest average GD estimate (7.5%). The average GD of NASA and NASC were also not significantly different. The average GD for all possible pairings of the 66 NASC with Chinese cultivars and with Japanese cultivars were 8.5 (GD range 3.6 to 13.9) and 8.9% (range 4.8 to 14.5), respectively. The most diverse cross between a NASC and an Asian cultivar would have a genetic distance of 14.5%.
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The UPGMA-derived dendrogram assigned the 190 genotypes into four major clusters (Fig. 1) designated as a, b, c, and d. The NASA were primarily in cluster a, the NASC in cluster b, the Japanese cultivars in cluster c, and the Chinese cultivars in cluster d (Fig. 1). In general, 85% of the 190 soybean lines clustered between 90 and 95% similarity distance.
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The soybean ancestors Arksoy, Ralsoy, Mejiro, and Mukden were grouped and they clustered with seven NASC in subgroup 4 of cluster a. Arksoy and Ralsoy were always grouped together in studies by Brown-Guedira et al. (2000) and give an additional example of how these groupings agree with previous studies.
Mandarin (Ottawa) was the only NASA in subgroup 5 of cluster a. Also contained in subgroup 5 were eight Canadian cultivars, three Chinese cultivars, and two Japanese cultivars. The grouping of Mandarin (Ottawa) with other cultivars from North America, China, and Japan suggests that it has a broad genetic base that has some similarity to elite cultivars from both Asian regions. It has been reported that Mandarin (Ottawa), which was originally introduced from China, is a major ancestor of the Canadian and North American cultivars having contributed between 18 and 55% of their genomes (Lohnes and Bernard, 1991; Kisha et al., 1998).
Cluster b consisted of four subgroups made of three NASA, 49 North American, and three Chinese cultivars. In this cluster, the NASC Hutcheson (Buss et al., 1988) and Narow (Caviness et al., 1985) grouped very closely. Although they are both in maturity group V and they have several common ancestors in their pedigree, this level of similarity was unexpected. Carter et al. (1993) reported a genetic similarity estimate of 0.529 between Hutcheson and Narow where 1.0 is defined as genetic identity. Since these cultivars also differ for several morphological traits, it seems unlikely that the observed level of similarity is correct and a more likely explanation is that the original DNA samples were mislabeled.
Cluster c was composed of eight Chinese and 26 Japanese cultivars. This suggests that the Asian cultivars in cluster c were derived from soybean ancestors that are very different from the ancestors of the NASC. A recent report by Cui et al. (2000) identified a very minor NASA (Mamotan) in the pedigrees of three of the Chinese cultivars in subgroup 1 of cluster c (Yu dou 11, Zheng 77249, and Zhong dou 19), but essentially this cluster has no NASC or NASA.
The fourth cluster d consisted of three NASA (Peking, PI88788, and Korean), two NASC, 45 Chinese, and two Japanese cultivars. The three soybean ancestors Peking, PI88788, (both collected from China), and Korean (collected from North Korea) were very different from the other NASA. Gizlice et al. (1993) also observed Peking to be very different from other NASA based on the 10 metric traits they measured on plants grown in a phytotron. In general, PI88788 and Peking [two sources of soybean cyst nematode (Heterodera glycines Ichinohe) resistance genes], Manokin, Jin dou 14, Kitakomachi, and Yuuhime constituted the most divergent group from all the soybean accessions used in our study.
It is not clear on the basis of their pedigrees why Manokin (Kenworthy et al., 1996) and Harlon would be in cluster d. Manokin (maturity group IV) was the most genetically different within the NASC, with an average GD of 8.8% from other NASC. A previous pedigree analysis by Sneller (1994) did not identify Manokin as having a unique coefficient of parentage. Manokin was derived from a cross of parents representing northern U.S. by southern U.S. germplasm. Manokin has cyst nematode resistance that was derived from Peking, an ancestor also in this cluster. Pedigree information (Lohnes and Bernard, 1991) on Harlon (maturity group I) indicates that it was selected from the cross of Blackhawk x Harosoy 63 and has four ancestors from China-Mandarin (Ottawa), Mukden, Richland, and A.K. (Harrow) which contributed 37, 25, 25, and 13% of its genome, respectively. However, Harlon's pedigree would be similar to other NASC grown in the northern USA and has no obvious uniqueness.
Principal coordinate analysis (PCO) was used to identify multidimensional relationships that describe portions of the genetic variance in a data set. The first two principal coordinates of the AFLP data explained 15.4% of the total variance (Fig. 2). Principal coordinate analysis separated the germplasm into four broad groups corresponding to the UPGMA clusters (a, b, c, and d) on the basis of the geographical origin of the accessions. The PCO scatter plot, however, showed overlap between accessions from different geographic origins. The NASA lines occupied a central position among North American, Chinese, and Japanese cultivars and overlapped each of them (Fig. 2). With the exception of Kitakomachi and Yuuhime, the rest of the Japanese cultivars were well separated from the North American cultivars and ancestors. The Chinese cultivars were widely scattered in all clusters and they also appeared as a bridge between the North American accessions (cultivar and ancestor) and the Japanese cultivars.
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Agronomic data and yield for all of the Asian cultivars in this study are available from the Soybean Asian Variety Evaluation Project (Project SAVE) report by Manjarrez-Sandoval et al. (1997). Seven of the Asian cultivars yielded at least 80% of the NASC checks of similar maturity in at least 1 yr of the 2-yr SAVE project. Those cultivars and their yield as a percentage of the NASC checks (2-yr average) are Akishirome (76%), Hyuuga (83%), Misuzu Daizu (83%), Nakasennari (87%), Nasu Shirome (68%), Otsuru (75%), and Tachinagaha (70%) (Manjarrez-Sandoval et al., 1997).
The U.S. soybean breeders have been slow to utilize diverse genetic material in cultivar improvement programs. Gizlice et al. (1993) found that many recent U.S. cultivars were as closely related as half-sibs. Asian breeders have utilized a different strategy in their breeding programs. Cui et al. (2000) reported that Chinese breeders avoid mating related parents, and continue to introduce new germplasm in cultivar development programs. Chinese breeders have successfully introgressed U.S. germplasm into Chinese cultivars, but U.S. germplasm contributes only about 7% of the total genetic base of Chinese cultivars. Similarly, Zhou et al. (2000) reported that U.S. and Chinese cultivars have been utilized by Japanese breeders in their cultivar development programs. Intermating cultivars from these three major gene pools should provide new genetic recombinations to exploit in cultivar development programs. The information presented here should assist breeders in the selection of sources of new genes for the yield improvement of NASC.
| ACKNOWLEDGMENTS |
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| NOTES |
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Received for publication February 5, 2002.
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