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a USDA-ARS, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300 USA
b USDOD-ACE, Cold Regions Research and Engineering Laboratory, 72 Lyme Road, Hanover, NH 03755-1290 USA
stlarson{at}cc.usu.edu
| ABSTRACT |
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± SE (x1000)] estimated for P-7, Goldar, and Whitmar was 100.2 ± 7.1, 80.1 ± 6.6, and 79.4 ± 6.7, respectively. By all measures, genetic variation within P-7 is significantly higher than genetic variation within cultivars. However, the estimated number of inter-population nucleotide differences per site [dX ± SE (x1000)] between Goldar and Whitmar, e.g., 36.6 ± 1.6, is only slightly higher than
within these cultivars, therefore the net nucleotide-sequence divergence [dA ± SE (x 1000)] between these cultivars is relatively small, e.g. 2.5 ± 0.3. These results indicate that selectively neutral genetic diversity has not been dramatically reduced or inadvertently lost via genetic drift that may have occurred since the divergence of Goldar and Whitmar. No AFLP markers completely distinguish Goldar and Whitmar, therefore discrete morphological differences between these cultivars (e.g., the presence and absence of awns) most likely result from natural or artificial selection.
Abbreviations: AFLP, amplified fragment length polymorphism bp, (nucleotide) base pair B, intrapopulation nucleotide-sequence diversity dA, interpopulation net nucleotide-sequence divergence dXY, interpopulation nucleotide-sequence differences F, proportion of shared AFLP bands for a pair of haploid genomes MOPX, multiple-origin polycross PCR, polymerase chain reaction RAPD, random amplified polymorphic DNA RFLP, restriction fragment length polymorphism OTUs, operational taxonomic units UPGMA, unweighted pair-group method by arithmetic average
| INTRODUCTION |
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Only two bluebunch wheatgrass cultivars, Goldar and Whitmar, are currently available despite the increasing standards and demand for native plant materials that will be used for many rangeland seedings in the western USA (Shaw and Roundy, 1997; Richards et al., 1998; Holzworth and Brown, 1999). These diploid cultivars were selected from an evaluation of approximately 500 natural bluebunch wheatgrass collections representing six putative ecotypes from the Pacific Northwest. A third cultivar, Secar (Morrison, 1981), was also released from this collection. However, Secar actually belongs to a distinct allotetraploid species known as Snake River wheatgrass (Elymus wawawaiensis J. Carlson and Barkw.) (Jones et al., 1991; Carlson and Barkworth, 1997). Whitmar, released in 1946 (Hein, 1958), was derived from an awnless collection originating from a prairie grassland near Colton, WA, in an area of 500 mm annual precipitation on a Palouse silt-loam soil. Goldar, released in 1989 (Gibbs et al., 1991), was derived from a collection with strongly divergent awns originating from an open Pinus ponderosa Douglas ex Lawson & C. Lawson woodland on Mallory Ridge, Umatilla National Forest near Anatone, WA. Therefore, Goldar and Whitmar are morphologically distinct (i.e., awned versus awnless) and originate from different plant communities (e.g., mountain woodland versus Palouse grassland) less than 83 km apart.
Supplemental funding and free-market seed availability are factors that limit implementation of native plant species in large-scale fire rehabilitation efforts, the overwhelming revegetation effort on public rangelands in the western USA (Richards et al., 1998). Cultivars have the potential to provide a readily available, abundant source of high-quality native grass seed. However, some ecologists are concerned that the agronomic approach typically used in cultivar development has been to select or breed plants with specific characteristics, which reduces genetic diversity (Roundy et al., 1997; Roundy, 1999). They assert that such plant materials may lack the genetic diversity to maintain adaptation in dynamic environments, non-local seed sources may not have adapted genomes, or that non-local sources may result in genetic pollution (Roundy et al., 1997; Roundy, 1999). However, gene flow in cross-pollinated species may reduce the capacity of natural selection to create locally adapted populations even across strong environmental gradients (Rice and Knapp, 1997). A better scientific understanding of how genetic variation is partitioned and maintained through this process of cultivar development in cross-pollinating native grasses will help plant breeders and natural resource managers develop and implement these plant materials.
The AFLP technique (Vos et al., 1995), a relatively new method of genomic DNA fingerprinting, is highly informative in biosystematic studies of closely related grass species (Aggarwal et al., 1999; Massa et al., 1999) or cultivars (Pakniyat et al., 1997; Pejic et al., 1998; Zhu et al., 1998; Burkhamer et al., 1998). This technique also offers the opportunity to measure analytically selectively neutral genetic variation within and among heterogeneous populations of cross-pollinated grasses. The extent of DNA polymorphism within a heterogeneous population is often measured by
, defined as the average number of either nucleotide differences or substitutions per site for a group of DNA sequences (alleles) sampled (Nei, 1987). Likewise, a standard measure of divergence between two heterogeneous populations is dA, where the average
within populations has been subtracted from dXY, the average number of nucleotide differences or substitutions per site between populations (Nei, 1987). Together, these three parameters (i.e.,
, dXY, and dA) can be used to dissect interpopulation and intrapopulation variation at the DNA level (Nei, 1987). One possible method of estimating
and dA is by DNA sequencing. However, Nei and Li (1979) developed methods for estimating
and dA from restriction fragment length polymorphism (RFLP) data and Clark and Lanigan (1993) adapted similar methods for estimating
and dA from random amplified polymorphic DNA (RAPD) data. More recently, Innan et al. (1999) developed a method for estimating
from AFLP data. These methods enable researchers to estimate and directly compare the same intrinsic parameters of genetic diversity (e.g.,
, dXY, and dA) within and between species by different methods.
This study employs the AFLP method to quantify and compare
, dXY, dA, and other measures of genetic variation within and between Goldar, Whitmar, and Generation 2 of P-7, a multiple-origin polycross (MOPX2) developed by intermating collections from 25 geographically dispersed source populations. A primary objective of this study was to quantify and test the pertinent hypothesis that P-7 is genetically more diverse than Goldar or Whitmar. Another major objective of this study is to test the hypothesis that genetic variation has been lost via genetic drift since the divergence of Goldar and Whitmar. One reference value for the upper limit of genetic diversity in the natural source population(s) of these cultivars is
within P-7, a highly diverse reference population. A second reference value for genetic diversity in the natural source population(s) of these cultivars is dXY between Goldar and Whitmar. The value of dXY between these cultivars is unaffected by bottlenecks that may have occurred since the divergence of these cultivars. Assuming that relatively few novel mutations have accrued since the divergence of Goldar and Whitmar, dA between cultivars is an accurate, if not liberal, measure of genetic diversity lost via allele frequency drift since the divergence of Goldar and Whitmar populations.
In the context of this study, we assume that AFLP variation, for the most part, is a selectively neutral measure of genetic drift within and between populations. By examining allele frequency differences between Goldar and Whitmar across a large number of AFLP loci we will test the hypothesis that natural or artificial selection may have contributed to the true-breeding morphological differences between cultivars (e.g., the presence and absence of awns). If allele frequency differences for these AFLP loci are not sufficient to account for true-breeding polymorphisms between Goldar and Whitmar, then we may conclude that diaspore selection may have occurred during source population divergence and/or cultivar development. We do not believe that
, dXY, dA, or any other estimates of genetic diversity within or between Goldar and Whitmar were inadvertently "broadened" in the process of cultivar development, since these cultivars remain very uniform with regard to the presence or absence of awns, respectively.
| Materials and methods |
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1-bp intervals by Genographer (Benham et al., 1999).
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and dXY from F, the estimated proportion of shared AFLP products for a pair of haploid genomes, was kindly provided by Hideki Innan (University of Tokyo, Japan). This method is based on the fact that each AFLP product represents a 16-bp sequence assay when using the EcoRI and MseI restriction enzymes, which have 6 and 4 bp recognition sequences, respectively, and three selective nucleotides on each of the two AFLP selective amplification primers. Therefore, each shared AFLP product indicates 0/16 nucleotide differences, whereas polymorphisms indicate >1/16 nucleotide differences. The actual number of differences that contribute to each polymorphism is a function of F, which can be used to determine the overall number of nucleotide substitutions per site as describe by Innan et al. (1999). We used equations 25, 25, and 27 (Innan et al., 1999) to estimate the F values used in calculating
within a diploid population in Hardy-Weinberg equilibrium. To estimate F for dXY, we summed over loci (i) the expected frequency of the xth AFLP product in Population 1 (f1x) multiplied by the expected frequency of the xth AFLP product in Population 2 (f2x) to estimate hx, the probability that the AFLP product is shared by two haploid genomes as the numerator of F, and (ii) the average frequency of each AFLP product per haploid individual, (f1x+f2x)/2, as the denominator of F (H. Innan, 1999, personal communication). Finally, dA is determined as the average diversity, i.e., (
X+
Y)/2, subtracted from dXY (Nei, 1987). These methods for estimating the number of nucleotide differences based on the proportion of shared AFLP products are good when GC content is near 0.5 and the when number of differences are not too large (Innan et al., 1999). This assumption seems acceptable for bluebunch wheatgrass because the GC contents of wheat (Triticum aestivum L.) and maize (Zea mays L.), two other divergent Poaceae species, are estimated to be 45.5 and 46.0%, respectively (Salinas et al., 1988; Montero et al., 1992). Nei and Miller (1990) described how to use the jackknife method (Efron, 1982) to compute variances of
, dXY, and dA. Phenograms developed by unweighted pair-group method by arithmetic average (UPGMA) analyses, based on Jaccard's similarity coefficients (the proportion of matching AFLP products between pairwise comparisons of genotypes), were developed with NTSYS-pc, Version 2.0 (Rohlf, 1992). | Results and discussion |
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By all measures, the P-7 MOPX2 population displayed more genetic variation than Goldar or Whitmar. Compared with the averages for Goldar and Whitmar, P-7 displayed about 15% more polymorphic loci (nearly twice as many unique polymorphisms) and about 34% fewer fixed loci (Table 3)
. Moreover,
within P-7 was about 13.5% greater than
within either cultivar (Table 3). The UPGMA phenograms, based on Jaccard's similarity coefficients, also suggest that cultivars (Fig. 1A)
are less diverse than P-7 (Fig. 1B). However, the magnitude of
within cultivars is actually quite large (Table 3) and is only about 7% less than dXY between Goldar and Whitmar (Table 4)
, a useful reference value for the upper limits of genetic diversity in the source populations of these cultivars. Therefore, dA between Goldar and Whitmar, a liberal estimate of genetic diversity lost via genetic drift since the divergence of these cultivars, is correspondingly small (Table 4), and the UPGMA analysis does not even completely separate Goldar and Whitmar (Fig. 1A). Only six loci showed allele frequency differences greater than 0.5 (maximum difference = 0.65) between Goldar and Whitmar. Two thirds of the AFLP loci (743 out of 1131) showed allele frequency differences less than 0.1 and nearly 95% of the loci (1072 out of 1131) displayed allele frequency differences less than 0.3. Therefore, the magnitude of these allele frequency differences is not likely to account for true-breeding differences between Goldar and Whitmar. Although P-7 displayed more genetic variation than Goldar or Whitmar, these results suggest that genetic drift has been minimal and high levels of genetic diversity have been maintained during source population divergence and cultivar development of Goldar and Whitmar.
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within P-7 (Table 3) and dA between P-7 and either cultivar was nearly negligible (Table 4). Less than 5% (99 out of 2174) of the alleles were unique to P-7 (Table 3), whereas over 6% (143) of the alleles were unique to cultivars (Table 3).
Goldar displayed more polymorphic loci and fewer fixed loci, compared to Whitmar, even though F and
were similar within these cultivars (Table 3). Allele frequencies within each population also contribute to F and
, which may explain why the numbers of polymorphic or fixed alleles generally show relatively more variability than
(Table 3). Careful examination of the cultivar phenogram (Fig. 1A) also suggests that that awnless Whitmar may be a sub-population of the more typical awned forms of bluebunch wheatgrass. Therefore, Goldar may be slightly more diverse than Whitmar even though F and
were similar within these cultivars.
| Conclusions |
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, dXY, or dA among cross-pollinating, heterogeneous grass populations. In part, this may be attributed to a lack of efficient methods. Eight AFLP primer pairs produced 1131 different products (i.e., loci) in this bluebunch wheatgrass study, an effective survey of 18096 nucleotide bp from each of 66 plants using eight electrophoresis gels. By a more conservative account, this study assayed an average of 6119 nucleotide bp from each plant, as determined by the number of AFLP products actually amplified. Although the latter amount of information could also be obtained from eight fluorescent DNA sequencing gels, this approach requires two series of reactions (PCR and sequencing) and is conditional on the availability of conserved PCR primer-annealing sites. Moreover, DNA sequencing results would be confounded by heterozygosity in cross-pollinated grasses unless each template was cloned and reamplified. A comparable amount of information would also be difficult to obtain with RFLP or RAPD methods. Moreover, RFLP methods require DNA clones that are not readily available in most plant species and molecular sizing of RFLP or RAPD products are typically not performed with single-bp resolution. The AFLP technique provides a robust method for estimating
, dXY, or dA within and between heterogeneous plant populations. With single base resolution and appropriate DNA size standards, it should be possible for researchers to compare AFLP profiles from different studies of similar germplasm groups.
Results of this study provide limited support for the hypothesis that selectively neutral genetic diversity has been reduced or inadvertently lost via genetic drift that may have occurred since the divergence of Goldar and Whitmar. Our results indicated that
within Goldar and Whitmar was only (i) 7% less than dXY between individuals of Goldar and Whitmar, an accurate if not liberal estimate of genetic diversity in the source populations of these cultivars, and (ii) only 13.5% less than
within P-7, a highly diverse reference population of bluebunch wheatgrass. Although RFLP and AFLP methods for estimating genomic nucleotide differences may be somewhat biased, our estimates of
remaining within Goldar or Whitmar are actually higher than dXY among some tetraploid wheat species, 69.8, estimated by RFLP analysis. The dXY values between 13 wheat species ranged from 6.3 (x1000) between Triticum abyssinicum Vav. and T. pyramidale Perc. to 90.4 (x1000) between T. orientale Perc. and T. araraticum Jakubz, with an average of 69.8 (x1000) (Mori et al., 1997).
No true breeding AFLP differences between Goldar and Whitmar were detected, and the vast majority of AFLP loci showed subtle changes in allele frequencies since the divergence of these cultivars. Therefore, genetic drift is not sufficient to account for any true-breeding differences between Goldar and Whitmar or source populations of these cultivars. Natural or artificial selection is a more likely explanation for the presence of awns in Goldar and the absence of awns in Whitmar. However, it is difficult to discern how much selection and genetic drift occurred through source population divergence versus cultivar development, without directly comparing these cultivars to their source populations. This may be difficult considering that these collections were made more than 50 yr ago. Nevertheless, results of this study support the hypothesis that natural or artificial selection may have contributed to the true-breeding morphological differences between cultivars (e.g., the presence and absence of awns).
Results of this study support our hypothesis that P-7 is more genetically diverse than Goldar or Whitmar. Moreover, allele frequencies have remained remarkably stable since the divergence of Goldar and Whitmar, indicating that it should also be possible to maintain genetic diversity, in P-7, over the typical lifetime of cross-pollinating cultivars. A more extensive survey of trait differences and nucleotide variation among widely dispersed natural bluebunch wheatgrass populations may help ecologists better understand the impact of gene flow, genetic drift, and local adaptations among natural grass populations. This, in turn, will enable plant breeders and natural resource managers develop and implement the most appropriate plant materials for these areas.Holzworth Brown comps. 1999; Shaw Roundy comps. 1997
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| REFERENCES |
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