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PLANT GENETIC RESOURCES

Multivariate Analysis of Genetic Relationships between Italian Pepper Landraces

^a Dep. of Exploitation and Protection of the Agricultural and Forestry Resources (Di.Va.P.R.A.), Plant Genetics and Breeding, Univ. of Turin, via L. da Vinci 44, 10095 Grugliasco, Turin, Italy
^b Research Institute for Vegetable Crops, via Paullese 28, 26836 Montanaso Lombardo, Lodi, Italy

^* Corresponding author (sergio.lanteri{at}unito.it)

	ABSTRACT

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION REFERENCES

 
The heterogeneity of pedoclimatic conditions and the farmer selection for adaptation to local tastes and uses have favored the maintenance in cultivation in Italy of numerous pepper (Capsicum annuum L.) landraces. We have used amplified fragment length polymorphism (AFLP) fingerprinting and morphological variation in fruit type to assess the diversity of 19 pepper ecotypes representative of the autochthonous germplasm. Principal component analysis grouped together triangular and blocky fruited types, while elongate types were subdivided into long and half long, differing mainly with respect to the length/diameter ratio. The half-long types were divided into two further clusters on the basis of overall dimension, weight, and flesh thickness. Genetic similarities between the ecotypes were calculated from AFLP data and this allowed the separation of the accessions into two major and three minor clusters. One major cluster comprised five ecotypes with blocky or triangular fruits, while the other contained nine ecotypes with long or half-long fruits. AFLP markers were successful in both detecting genetic diversity and determining genetic relationships in Italian pepper germplasm. They also made it possible to distinguish most of the provenances within a given landrace, and to identify pairs of genetically similar ecotypes carrying different names. We believe that our analyses will help in the identification of rational strategies for the preservation of Italian pepper genetic resources.

Abbreviations: AFLP, amplified fragment length polymorphism • AMOVA, analysis of molecular variance • DI, distance index • EDC, Euclidean distance coefficient • EMR, effective multiplex ratio • JSI, Jaccard's similarity index • MI, marker index • PC, primer combination • PCA, principal component analysis • PIC, polymorphic information content • RAPD, random amplified polymorphic DNA • UPGMA, unweighted pair-group arithmetic mean method

	INTRODUCTION

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THE CAPSICUM GENUS originates from the New World; after its introduction to Europe by C. Columbus at the end of the 15th century, it was later on dispersed to Mediterranean countries, then to Africa, India, China, and at last returned to Oriental Europe through Asia (Lefebvre, 2004). The Capsicum genus includes 27 species, of which five (annuum, chinense, frutescens, baccatum, and pubescens) have been domesticated (Pickersgill, 1997) and used worldwide as spices, condiments, and vegetables. The major cultivated pepper is C. annuum L., an herbaceous diploid (2n = 2x = 24) which includes most of the Mexican chili peppers, most of the hot peppers of Africa and Asia, and various cultivars of sweet (nonpungent) peppers grown in the temperate regions of Europe and North America (Pickersgill, 1997). The species is considered to be self-pollinating (Allard, 1960); the flowers are hermaphrodites, flowering starts with one or two flowers at the first branching node, then a flower forms at each additional node in geometrical progression. Indeed, in C. annuum, different rates of outcrossing (2–90%), associated with natural insect pollinators as well as environmental conditions, have been recorded (Franceschetti, 1971; Pickersgill, 1997; Tanksley, 1984). Carotenoids and capsaicinoids are responsible for much of the variation in taste, color, and aroma of cultivated C. annuum germplasm. The former contribute to fruit color and nutritional value, while the latter are responsible for pungency (Bosland and Votava, 2000). On the basis of the content of these compounds, pepper genotypes can be classified as sweet, intermediate, or hot (highly pungent). A further classification defines fruit shape: almost round, blocky (7–10 cm long and wide), triangular or heart shaped, and elongated (Pochard, 1966).

Molecular markers provide complementary descriptors to conventional morphological variation, particularly when used to assess genetic diversity at both the inter- and intraspecific level (Prince et al., 1995; Rodriguez et al., 1999; Tam et al., 2005). Because they are independent of any environmental interference, DNA markers are particularly favored. Restriction fragment length polymorphisms (RFLPs) have detected substantial polymorphism between small- and large-fruited C. annuum cultivars, but have been largely ineffective in discriminating between large-fruited inbred lines. When RAPD (random amplified polymorphic DNA) and AFLP fingerprinting was applied by Paran et al. (1998) to assess genetic variation among cultivars of various types, large-fruited sweet cultivars were distinguishable from the small-fruited pungent types, with the former group being less diverse than the latter. More recently, Lefebvre et al. (2001) split the large-fruited group into blocky and long types, with the intermediate half-long types presumed to represent the outcome of a hybrid between blocky and long types.

In Italy, pepper is cultivated over 11000 ha, producing about 2500 Mg yr^–1 (ISTAT, 2005). In several regions, the heterogeneity of the land, climate, and soil favors the use of varieties and landraces specifically adapted to local conditions. Thanks to European and national institutions promoting the sustainable use of agricultural resources, there is a growing incentive to both grow and preserve this germplasm. Accurate characterization, at both the morphological and molecular level, is thus timely and of interest both for the enhancement and protection of landrace materials, and for future exploitation in breeding. We report here the assessment of AFLP and fruit morphological variation in 19 pepper accessions representative of the autochthonous germplasm presently in cultivation in Italy.

	MATERIALS AND METHODS

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Plant Material and Morphological Characterization of the Fruits
Nineteen local varieties were sampled. For nine of these, samples from two separate locations were assayed, as reported in Table 1.

DNA Extraction and AFLP Analysis
Three plants, sampled from the same farmer, were analyzed for each of the thirty accession in study; a Bolivian accession of C. chinense was included as a reference (Accession CH18-PEA373, from the Genebank of the DiVaPRA–Plant Genetics and Breeding, University of Turin). The DNA was extracted from 0.15 g fresh young leaves by the CTAB (cetyltrimethylammoniumbromide) method (Doyle and Doyle, 1990). The AFLP protocol was adapted from Vos et al. (1995), as described by Lanteri et al. (2003). On the basis of previous studies (Lanteri et al., 2003; Portis et al., 2004a), the following nine primer combinations (PCs) were applied: E32/M48 (AAC/CAC), E32/M59 (AAC/CTA), E33/M59 (AAG/CTA), E35/M59 (ACA/CTA), E35/M61 (ACA/CTG), E36/M48 (ACC/CAC), E36/M59 (ACC/CTA), E36/M61 (ACC/CTG), and E37/M60 (ACG/CTC). Amplified fragments were separated on 5% denaturing polyacrylamide gels, and silver stained as described by Bassam et al. (1991). Each amplified fragment (60–650 bp) was assumed to represent a single biallelic locus, so that data were scored as the presence (1) or absence (0) of each polymorphic band.

Data Analysis
Quantitative data were subjected to ANOVA followed by LSD mean comparison. Z-transformation was applied to mean values of all quantitative traits to meet the requirements of independence and normal distribution with zero mean (Sneath and Sokal, 1973). Standardized trait values were subjected to principal component analysis (PCA) to determine the traits most effective in discriminating between accessions. Common components coefficients, eigenvalues, and relative and cumulative proportions of the total variance expressed by single traits were calculated. The first two components explaining the maximum variance were selected for the ordination analysis, and the correlation between the original traits and the respective principal component was calculated. Characters with a correlation > 0.6 were considered as relevant for that component, as recommended by Matus et al. (1996). In addition, a dissimilarity matrix based on Euclidean distance coefficient (EDC) was generated to assess the level of dissimilarity between accessions. All calculations and analyses were made using the appropriate options of SPSS version 12.0 (Apache Software Foundation, Chicago, IL) and NTSYS-pc version 1.80 (Rohlf, 1993).

The AFLP data were evaluated by means of polymorphic information content (PIC) and marker index (MI). The PIC was calculated by applying the simplified formula of the expected heterozygosity 2f (1-f), were f is the percentage of plants where the marker is present (Anderson et al., 1993). The MI was calculated as the product of PIC and effective multiplex ratio (EMR), following Powell et al. (1996). The EMR of a PC was defined as ßn, were ß is the percentage of polymorphic bands and n is the number of bands detected per PC (Milbourne et al., 1997). A binary matrix was imported into NTSYS-pc software for cluster analysis. Genetic similarity among all individuals was calculated according to Jaccard's similarity index (JSI; Jaccard, 1908) using the SIMQUAL routine, and the similarity coefficients were used to construct a dendrogram using the unweighted pair-group arithmetic mean method (UPGMA). To evaluate the relative strength of the tree nodes, 1000 bootstrap replicate matrices were generated with RAPDPLOT 2.3 package (Black, 1998); dendrograms and bootstrap values were then obtained by means of the NEIGHBOR and CONSENSE programs from PHYLIP 3.5 package, respectively (Felsenstein, 1993; http://evolution.genetics.washington.edu/phylip.html, verified 10 Aug. 2006).

A cophenetic matrix was produced using the hierarchical cluster system by means of the COPH routine and correlated with the original distance matrices to test for any association between the cluster in the dendrogram and the JSI matrix. Relationships among the accessions were evaluated by comparing mean genetic similarity values.

An analysis of molecular variance (AMOVA; Excoffier et al., 1992) was performed to partition the genetic variation into within and among accessions. A hierarchical analysis then allocated the total variance into various covariance components, and the significance of these was tested using 1000 permutations at different levels. Only values 0.05 were considered significant. The AMOVA and significance tests were performed using Arlequin version 2000 (Schneider et al., 2000).

	RESULTS

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Morphological Characterization
Means, standard deviations and LSDs among the 30 pepper accessions are reported in Table 1. No significant block effects were detected. Fruit color was either yellow or red, although in four cases (‘Quadrato d'Asti’, ‘Quadrato di Carmagnola’, ‘Cuneo’ and ‘Corno pescarese’) this varied between the two provenances of a given landrace. Most of the materials produced half-long (10) or long (3) fruits. Six landraces had a length/diameter ratio < 2, but with different shape of the fruit: blocky (3), triangular (2), and almost round (1). Mean weight and flesh thickness of the fruit was highly variable, the former ranging from 12.9 g in ‘Ciliegia’ to 275.4 g in one accession of Quadrato d'Asti, the latter from 1.2 mm in one accession of ‘Corno calabrese’ to 6.8 mm in one accession of Cuneo. As expected, the number of fruits produced per plant was inversely related to fruit weight, ranging from >200 in the highly pungent Corno calabrese to 9 in the sweet ‘Braidese’.

AFLP Fingerprinting
The nine PCs defined 807 fragments, of which 107 (13.3%) were polymorphic across the set of C. annuum accessions (Table 2). Table 2 also reports the mean number of polymorphic bands per PC (11.9, range 10–14), and the PIC and MI values for each PC. E32/M48 was the most informative PC, showing the highest values for PIC and MI. The lowest PIC values were obtained using E32/M59 and E36/M61, while the lowest MI was produced by E33/M59 as a result of its low level of PIC (11.5%). Seven PCs detected, in all, 12 unique–distinctive bands (i.e., present in only one accession), ranging from 1 to 3 per PC. Seven landraces were characterized by distinctive bands, while ‘Friarè’ and Friariello shared two otherwise unique bands (Table 3). Capsicum annuum and C. chinense differed by 126 polymorphisms (mean per PC 14.0, range 11–16; Table 2).

View larger version (20K): [in this window] [in a new window]   Fig. 1. Principal component analysis based on quantitative fruit traits. (A) Whole set of plants in study. (B) Centroids of the 30 accessions in study.

View larger version (20K): [in this window] [in a new window]   Fig. 2. Dendrogram based on the Jaccard's Similarity Index and UPGMA clustering of AFLP data. The percentages at the forks indicate the number of times the group consisting of the accessions which are to the right of that fork occurred among the 1000 trees constructed after bootstrap analysis.

	DISCUSSION

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That cultivated pepper shows little polymorphism at the molecular level (Lefebvre et al., 1993; Prince et al., 1995; Paran et al., 1998; Rodriguez et al., 1999) is not surprising, since following its domestication in Mesoamerica (Smith and Heiser, 1957) it was only introduced to Europe post-Columbus and thus the progenitor gene pool of European landraces must have been rather limited. Nevertheless, RFLP, RAPD, and AFLP data have all been shown to be informative for the discrimination of closely related cultivars (Lefebvre et al., 1993; Prince et al., 1995; Lefebvre et al., 2001; Lanteri et al., 2003; Portis et al., 2004a), with AFLP being more efficient than RAPD (Paran et al., 1998; Kochieva et al., 2004). The C. chinense accession selected as an outlier was well differentiated from the C. annuum genotypes. Both species belong, along with C. frutescens, to the C. annuum complex, which is characterized by a common ancestral gene pool. Although this suggests that species designation based on morphological descriptors could be difficult (Pickersgill et al., 1979; Pickersgill, 1988), the three species are readily distinguishable at the molecular level with whatever marker system is applied (Rodriguez et al., 1999; Kochieva et al., 2004). In the present study, we have been able to define 107 polymorphic AFLP fragments out of a total of 807 (13.3% per PC), consistent with the rate reported by Paran et al. (1998). Lefebvre et al. (2001) detected a somewhat higher level of polymorphism in a study of 47 inbred lines of diverse geographical origin. The number of markers necessary for cultivar discrimination depends on the required precision of the estimate of genetic distance, and the estimation accuracy increases with the square root of the number of markers deployed, although above 100 the marginal increase in precision is low (Dillmann et al., 1997). We have based our conclusions on a sample of about 107 polymorphic bands, which should allow a sufficiently accurate estimate of genetic relationships; the cophenetic correlations indicate that the genetic clusters accurately represent the estimates of genetic similarity.

The AFLP profiles identified two main groups of pepper, along with three minor clusters. One major group consists of sweet blocky or triangular types, characterized by large and thick fruits and a length/diameter ratio < 2. The four local varieties in this group (i.e., Cuneo, Quadrato d'Asti, Quadrato di Carmagnola, and Braidese) are grown in close proximity to one another within Northwestern Italy, so that gene flow between them might have occurred. The two commercial accessions of California wonder and, at an higher level of genetic differentiation, the landrace ‘Nocera’ were also comprised in this group. The latter is originating from Campania (South Italy) but is considered one of the progenitors of the Cuneo type (Bassi, 1969), with which it shares the triangular shape of the berry. Within the second major group, we have identified two subclusters. One of these includes three half-long and sweet types, of which one (‘Corno di toro’) has rather smaller fruits and is somewhat genetically differentiated from the others. The second subcluster groups accessions from Southern Italy, specifically half-long types with small and thin fruits, and the long, highly pungent Corno calabrese. The two accessions of ‘Senise’ (a half-long sweet type from Southern Italy), and the almost-round small-fruited, somewhat pungent Ciliegia cluster with this group at a higher degree of differentiation. No genetic differentiation (JSI = 1.00) was found between three plants of Corno calabrese A and two plants of Corno di Carmagnola A. On the other hand, range of genetic differentiation < 2% were detected among plants belonging to the accessions Corno di toro, Corno calabrese A and B, and Lombardo A. By comparing the AFLP profiles of identical clones and replicate samples, we previously estimated that the scoring error in our analyses was about 2% (Portis et al., 2004b), which is consistent with that estimated in other studies (Mueller and Wolfenbarger, 1999; Hodkinson et al., 2002); lower values can thus be attributed to genotyping errors.

The hierarchical AMOVA approach confirms that most of the detected variability is due to variation among morphological types (23.1%) and among accessions within them (66.2%); only the 10.7% of variation observed could be attributed, at a different extent, to differences among plants within accessions (Table 5). Both the EDC calculated from the morphological data and the JSI derived from the AFLP fingerprinting show that blocky types are less diverse than the half-long and long types, as also concluded by Lefebvre et al. (2001). The agreement between the EDC and JSI does not, however, extend to the half-long and long types, since at the AFLP level the long types appear to be the more diverse, while at the morphological level the half-long types seem the more diverse.

Amplified fragment length polymorphism profiling shows that each pepper type can be uniquely fingerprinted and, except for the two accessions of Cancaricchio, accessions within a given landrace were always distinguishable from one another. Thus, adaptation to local conditions and farmer selection appear to have generated a significant degree of genetic differentiation. Farmer selection is generally directed at fruit morphology, but not all farmers apply the same criteria; thus it is possible that independent selection pressure applied across a number of crop generations to a restricted gene pool can result in genetic divergence within a particular landrace. The lowest JSI (0.760) between provenances of the same local cultivar was found in Senise, and a lower—but still high—genetic differentiation separates the two provenances of Cuneo. We have previously shown in an AFLP-based analysis of five populations of Cuneo ecotype that there is a substantial level of within-landrace polymorphism (Lanteri et al., 2003). If the mean JSI between provenances of the same landrace (JSI = 0.83 ± 0.04) is taken as a threshold to identify material sharing the same genetic background, the landraces Friariello and Friarè, both originating from the Campania region in Southern Italy, should not be considered as separate entities (JSI = 0.84). Indeed, these two accessions were found to share two unique–distinctive AFLP fragments, and they were largely indistinguishable with respect to their fruit morphologies.

To date, there has been no systematic molecular description of pepper genetic resources in Italy. The present results should serve as a reference point for both the future development of pepper breeding, and for the development of ex situ and in situ conservation strategies. We have shown that AFLP profiling can be used to identify synonymous landraces. We have uncovered landrace-specific AFLP fragments in about half of the landraces studied, and these, if confirmed in a representative sample of genotypes, could potentially be converted into simple diagnostic assays allowing for the facile identification of germplasm. The genetic definition of a cultivated crop type is of particular importance for the stabilization of its commercial value, and for the promotion of its status as protected geographical indication or protected designation of origin.

Received for publication April 4, 2006.

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