Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP.

Cost reduction in plant breeding and conservation programs depends largely on correctly defining the minimal sample size required for the trustworthy assessment of intra- and inter-cultivar genetic variation. White clover, an important pasture legume, was chosen for studying this aspect. In clonal plants, such as the aforementioned, an appropriate sampling scheme eliminates the redundant analysis of identical genotypes. The aim was to define an optimal sampling strategy, i.e., the minimum sample size and appropriate sampling scheme for white clover cultivars, by using AFLP data (283 loci) from three popular types. A grid-based sampling scheme, with an interplant distance of at least 40 cm, was sufficient to avoid any excess in replicates. Simulations revealed that the number of samples substantially influenced genetic diversity parameters. When using less than 15 per cultivar, the expected heterozygosity (He) and Shannon diversity index (I) were greatly underestimated, whereas with 20, more than 95% of total intra-cultivar genetic variation was covered. Based on AMOVA, a 20-cultivar sample was apparently sufficient to accurately quantify individual genetic structuring. The recommended sampling strategy facilitates the efficient characterization of diversity in white clover, for both conservation and exploitation.

Introduction

The characterization of genetic variation, and its partitioning within and among populations, is important for plant breeding and conservation research focused on the management of genetic resources (Herrmann ; Nybom and Bartish, 2000). Prior to the mid 1960’s, genetic variation was estimated by using morphological and physiological characters (phenotypic characterization). However, with this approach, and apart from the bias arising from environmental variability, estimates of diversity were based on a limited set of loci. Subsequently, molecular marker techniques have come to offer an attractive alternative to such a limited scope (Kölliker ), through facilitating the rapid estimation of genome-wide intra- and inter-cultivar genetic variation at the DNA level. Molecular marker techniques are therefore preferred to phenotypic characterization if they are reasonably cost-effective.

Among the variety of molecular marker techniques available, the amplified fragment length polymorphism (AFLP) technique, first described by Vos , has proved to be the most suitable for assessing intra-species diversity (Bonin ). It has been successfully applied for determining genetic diversity in a multitude of legume forages including red clover (Trifolium pratense L.; Herrmann ), alfalfa (Medicago sativa L.; Segovia-Lerma ), bird’s foot trefoil (Lotus corniculatus L.; Sardaro ), sulla (Hedysarium coronarium L.; Marghali ), and white clover (Trifolium repens L.; Kölliker ). This technique requires no sequence knowledge for developing species-specific primers, such as SSR (simple sequence repeat) markers (Peakall ). Nevertheless, the cost of using AFLP genetic markers depends greatly on the number of samples to be analyzed.

White clover (2n = 4x = 32) is one of the most important pasture legumes in temperate climates, worldwide. As its gametophytic self-incompatibility system requires outbreeding (Williams, 1987) to thus maintain high levels of diversity in natural (ecotype) and synthetic (cultivar) populations (Gustine and Sanderson, 2001), apparently there is the need for a relatively large number of samples to detect the prevailing genetic variation. An optimal sampling strategy is further complicated by lateral clonal spread via stolons (Brink ; Chapman, 1983). As both clonal propagation and recruitment from seeds are the rule, white clover populations are comprised of many genetically different individuals (genets), each consisting of several identical individuals (ramets) (Welham ). The effectiveness of a sampling scheme thus depends on avoiding the redundant genotyping of clones. One way to avoid this is to place the samples sufficiently apart in a grid-based sampling approach.

Numerous parameters have been developed to better understand and estimate inter- and intra-population genetic diversity. Genetic differentiation (Φst) is a widely used parameter for investigating diversity at the inter-population level. As to the intra- level, diversity parameters can be classified into two groups.

The first group consists of parameters based on allele richness. One popular parameter based on allele richness is the mean number of alleles per locus (A), estimated by the Ewens sampling formula (Ewens, 1972). This formula was based on an ideal population with a random matting population of constant size, without either migration or selection. As natural populations rarely comply with formula assumptions, accuracy in this case was later questioned. Several attempts were then made to develop novel approaches to standardize estimation of A, such as rarefaction (Petit ), repeat random subsampling (Leberg, 2002), the Bayesian method (Belkhir ) and non-linear regression (Bashalkhanov ). The use of A, when estimating genetic diversity, is restricted to studies with codominant genetic markers. The Shannon index (I) is another diversity parameter based on allele richness, and which is extensively used in genetic diversity studies relying on dominant genetic markers, as AFLPs (Ward and Jasieniuk, 2009). According to its mathematical formula, the Shannon index (I) is associated with the number of alleles and their frequency. This index gives the same weight to both the number and frequency of alleles, without emphasizing which are common or rare (Zhao ). One reason for its popular use is that it does not rely on Hardy-Weinberg equilibrium. This makes the Shannon index comparable across studies (Bussell, 1999). The second group are heterozygosity-based diversity parameters, including expected heterozygosity (He), which is the most commonly used parameter for estimating intra-population genetic diversity. As with the Shannon index (I), the expected heterozygosity (He) formula is associated with the number and frequency of alleles. Nevertheless, alleles with high frequencies (common alleles) contribute more to He values than those with low ones (rare alleles) (Zhao ).

An inappropriate sampling strategy can severely bias genetic diversity parameters, whereas excessive sampling inflates costs (Suzuki ). Even so, studies of white clover genetic diversity have been inapt at explicitly optimizing sample sizes or verifying sampling effectiveness (Kölliker ; Gustine and Elwinger, 2003; Van Treuren ; Bortolini ; Rizza ). Herein, an investigation was undertaken of the impact of both sample size and the sampling scheme, on assessing genetic diversity within and among white clover cultivars. Three commercially available clover-cultivars were grown in experimental plots mimicking the prevailing conditions in pastures. Several samples per cultivar were collected and genotyped using genome-wide AFLP markers. The main aim was to infer the minimal sample size required to accurately assess genetic variation within and among cultivars, based on widely used parameters, viz., the Shannon index (I), expected heterozygosity (He) and genetic differentiation (Φst). In addition, we tested whether the applied grid-based sampling scheme avoided the inclusion of clones.

Materials and Methods

Plant material and sampling scheme

Three varieties of white clover, diverse in phenotypic characteristics and origin, were used. These were the Aberherald (medium-leaf type) from the UK, the Riesling (large-leaf type) from the Netherlands, and the Rivendel (small-leaf type) from Denmark. In 2005, seeds of each variety were sown in an experimental plot, together with perennial ryegrass (0,5 g of white clover seeds and 2,5 g ryegrass seeds per square meter), at the Institute for Agriculture and Fisheries Research (ILVO), Merelbeke, Belgium. In 2008, 45 samples per plot were collected and subdivided into a 0.4 x 0.4 m grid pattern. Sampling was carried out at the center of each square, to so maintain fixed distances (40 cm) between sampling points in both dimensions. The spatial coordinates of each collected sample were recorded. The sampling distance itself was set at 40 cm based on previous reports of clone sizes in wild clover populations, as well as visual assessment of the field studied. In addition to the 45 field samples, leaf samples were collected from 30 greenhouse-sown seedlings of each cultivar. Up to that time, the 75 samples of each variety used to investigate appropriate sample size was more than the norm in studies of genetic diversity in white clover (Kölliker ; Gustine and Elwinger, 2003; Van Treuren ; Bortolini ; Rizza ).

AFLP analyses

Prior to DNA extraction, leaf material was freeze-dried for 48 h,and then homogenized and ground (Tissue Lyser, QIAGEN) to a fine powder. Total DNA was extracted from 20 mg of freeze-dried leaf material by applying the modified Cetyltrimethylammonium Bromide (CTAB) method, as described by Doyle and Doyle (1990). DNA concentration was estimated with NanoDrop ND-1000 spectrophotometer software v. 3.0.1 (NanoDrop Technologies). AFLP analysis was according to Vos , with minor modifications. The enzymes EcoRI and MseI were used for DNA digestion. Each individual plant was fingerprinted with six primer combinations (Table 1). Fragment separation and detection were with an ABI Prism 3130xl capillary sequencer. GeneScan 500 Rox-labelled size standard (Perkin Elmer) was loaded into each sample. Fluorescent AFLP patterns between 50 and 500 bp were scored using a version 4.0 Genemapper (Applied Biosystems).

Table 1

AFLP primer combinations used for selective amplification and the number of polymorphic loci.

Primer combinations	Number of polymorphic loci
E1+ACA / M2+CAG	51
E+AGG / M+CTT	61
E+ACC / M+CAT	57
E+ACT / M+CAT	47
E+AAC / M+CAT	45
E+AAC / M+CTG	22

E indicates EcoRI primer.

M indicates MseI primer.

Data analysis

The extent of clonality among the collected samples was quantified, in order to evaluate the effectiveness of the applied sampling scheme. A histogram of pairwise Dice genetic similarity coefficients was calculated to account for minor, but potential, differences within genets, due to somatic mutation and scoring errors (Meirmans and Van Tienderen, 2004). Based on the bimodal distribution of this histogram, a threshold was set up, as outlined by Meirmans and Van Tienderen (2004), as a means of assigning individuals to genets (Figure 1).

Figure 1

Frequency distribution of the number of pairwise genetic distances among 45 individuals of the white clover varieties Aberherald (I), Rivendel (II) and Riesling (III). Pairwise distances were calculated using GENOTYPE/GENODIVE software.

The evolution of intra- and inter-population genetic diversity parameters over an increasing sample size was investigated, in order to determine the minimal sampling size. Hence, a computer simulation method was employed to generate randomly selected subsets with 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70 and 74 individuals, drawn from the total sample (n = 75).

Next, for each sample size, intra- and inter-cultivar genetic diversity parameters were calculated for each of 50 randomly drawn subsamples per sample size using GenAlEx v.6 (Peakall and Smouse, 2006). Intra-cultivar genetic diversity was calculated as the expected heterozygosity (He) and the Shannon diversity index (I), the two most widely used genetic-diversity parameters (Suzuki ). The analysis of molecular variance (AMOVA) was applied for estimating the Φst parameter representing the proportion of genetic variation among the three cultivars. Significance of Φst was tested using 9999 random permutations.

Finally, the intra-cultivar genetic diversity estimate for a given sample-size was divided by the value for the total sample of 75 individuals, and then multiplied by 100. Thus, mean values were converted into index percentages of total variation (Zhu ). The inter-cultivar genetic diversity parameter (Φst) and the index percentages of the intra-cultivar genetic diversity parameters (He and I), were then regressed against sample sizes, by the following formula: ln(Y) = b0 + (b1/t), where b0 and b1 are parameters, t sample size, and Y index percentages or Φst.

Results

The six EcoRI/MseI primer pair combination generated 283 clearly identifiable loci. The number of AFLP polymorphic bands detected by each primer pair, across three cultivars, ranged from 22 to 61 (Table 1). Very few samples were assigned to the same genet upon applying a Dice similarity threshold of 0.97, and all belonged to neighboring grids (intersample distance 40 cm) (Figure 1). The largest genet consisted of 4 samples and was found in the Aberherald plot. Only 3 samples in the Rivendel plot and 2 in the Riesling plot were replicates. As replication could thus be considered negligible, replicates were not removed from the dataset in subsequent analysis.

Intra-cultivar genetic diversity was comparable for the three cultivars. The mean expected heterozygosity (He) per cultivar for total sample size (n = 75) was 0.319, 0.289 and 0.272 for Aberherald, Rivendel and Riesling, respectively, and the mean Shannon diversity index (I) 0.487, 0.459 and 0.421, respectively. Regression of He and I across different sample sizes (from 5 to 74), showed that sample size had a profound impact on estimating intra-cultivar genetic diversity (Figure 2). As regards the first three sample sizes (5, 10 and 15 individuals), the curve ascended steeply and then flattened out at around 20 samples for both He and I. A sample size of 20 individuals accounted for 97%, 96% and 97% for He, and 97%, 96% and 97% for I, of the total genetic diversity measured in all the 75 samples of Aberherald, Rivendel and Riesling white clover cultivars, respectively. A sample size of 30 came extremely close to total genetic diversity, with 98.8%, 98.5% and 98.8% for He, and 98.7%, 98.6% and 98.5% for I.

Figure 2

The influence of sample size on intra-cultivar genetic diversity parameters. Dots represent either the amount of expected heterozygosity (He) or the Shannon diversity index (I) of total variation. The regression formula applied was ln(Y) = b0 + (b1/t), where b0 and b1 are parameters, t represents sample size, and Y refers to the index of percentage of each sample. Samples in various subsets were subtracted 50 times from the total sample.

By AMOVA based on all 75 samples per cultivar, most genetic variation was shown to be among varieties (78.8%), whereas 21.2% was among cultivars (Table 2).

Table 2-

Analysis of molecular variance (AMOVA) in three white clover varieties. P values were obtained by 9,999 permutations.

Source	df	SS	MS	Est. Var.	%D
Variance among varieties	2	2259.74	1129.87	14.35	21.2 *
Variance within varieties	222	11851.04	53.38	53.38	78.8
Total	224	14110.78		67.74	100

Statistics include: df, degrees of freedom; SS, sum of squares; MS, mean squares; Est. var., estimated variance; and %D, distribution of total variance.

p = 0.0001.

The overall and highly significant (p = 0.0001) genetic differentiation index (Φst) was 0.212. Resampling analysis of Φst showed an overestimation of Φst when using 5 to 15 samples (Figure 3). Although Φst remained stable at 20 samples, variance among subsamples diminished still further.

Figure 3

The influence of sample size on estimated Φst among cultivars. Dots show the calculated genetic differentiation index (Φst) of each subset. Samples in various subsets were drawn 50 times from a total of 75 individuals. The regression formula applied was ln(Y) = b0 + (b1/t), where b0 and b1 are regression parameters, t the sample size and Y the genetic differentiation index (Φ st) of each subset.

Discussion

The main aim was to present an optimal sampling strategy for studying genetic diversity in white clover cultivars. Hence, 75 samples from three cultivars, mutually different in phenotypic characteristics and geographical origins, were genotyped at a large number of AFLP loci (n = 283). These proved to be sufficient for the sure assessment of population genetic parameters (Mohapatra ).

Influence of the applied sampling scheme

The grid-based sampling method has already been successfully applied when investigating genetic diversity in white clover. However, the reported width of clonal patches varied from several centimeters to several meters (Harberd, 1963; Cahn and Harper, 1976; Gustine and Elwinger, 2003). As an adequate sampling interval was unavailable, the determination of a grid-sampling scheme, with suitable spatial intervals, became necessary to avoid collecting spatially correlated samples and to maximize the information obtained. On using a grid-based sampling approach with a 40 cm intersample distance, very few clonal replicates were encountered, after growing clover plants for three years in plots mimicking common clover-pasture conditions (Figure 1). In other words, patch-sizes were less than 40 cm. Although an intersample distance of 40 cm was found suitable for studying diversity, this should be further investigated before recommending it. Further investigation including census sampling (harvesting all individuals within the frame) or using a higher density sampling grid are indicated. In natural populations, very old and large genets can occur (Harberd, 1963). Differences in clone-size are also likely to be magnified by environmental heterogeneity (Vandepitte ), which is less prominent in pastures.

The influence of sample size

Based on the lack of considerable change in genetic diversity beyond 30 samples (Figures 2 and 3), a total sample-size of 75 individuals should adequately represent the real AFLP variation within and among the cultivars studied. It is very unlikely that genetic diversity would once again increase after reaching a plateau. Furthermore, the intra-genetic diversity parameters obtained, as well as AMOVA results, are in accordance with reports of higher levels of variation within than among clover cultivars (Kölliker ). The noted intra-cultivar variation of 78% was close to the 84% reported by Kölliker . This result is commonly attributed to obligate outcrossing (Hamrick and Godt, 1996), and the breeding system of white clover (Annicchiarico and Piano, 1995).

Sample size was important when estimating both intra- and inter-genetic parameters (Figures 2 and 3). In subsets of less than 20 samples per cultivar, inter-genetic diversity (Φst) was overestimated and intra-genetic diversity (He and I) was severely underestimated. In subsets of 20 or more individuals, the intra-genetic diversity parameters obtained (He and I) covered, on an average, more than 95% of the total genetic diversity, the threshold proposed by Sedcole (1977). Furthermore, the influence of sample-size did not greatly differ among the three cultivars and the two intra-cultivar genetic diversity parameters used (Figure 3).

Such patterns of biased discordance in small sample-sizes have also been observed in previous studies (Isabel ; Wu ). On using simulations, Berg and Hamrick (1995) showed that, on reducing sample sizes to below 20 per population, estimates of inter-genetic diversity (Φst) became increasingly inflated. They also forewarned that this may cause severe misinterpretation, based on the observation that population genetic parameters calculated using 15 individuals or less, often generated higher estimates than when using larger sample sizes. Likewise, a sample-size of 20 was found to be adequate for studying the level of genetic diversity within and among cultivars of open-pollinating species, this including red clover (Trifolium pretense L.; Kongkiatngam ) and tall fescue (Festuca arundinacea Schreb.; Xu ). In accordance with these studies, we recommend a sample size between 20 and 30 samples to quantify the genetic diversity within and among white clover cultivars. Although the use of 20 samples maximizes cost-effectiveness, the use of 30 attains utmost precision, whereby its adequacy, for example, in detecting minor differences at the level of intra-cultivar genetic variation.

The study of genetic diversity in genetic resources could provide significant information as to its potential for breeding purposes (Singh ). The proposed sampling strategy (sampling scheme and sample-size) should facilitate the efficient management and exploitation of white clover germplasm in breeding and conservation programs.