Genetic diversity assessment in cultivated cardoon by AFLP (amplified fragment length polymorphism) and microsatellite markers

Cultivated cardoon (Cynara cardunculus L. var. altilis DC) belongs, together with globe artichoke (C. (cardunculus L. var. sylvestris L.) and wild cardoon (C. cardunculus L. var., sylvestris (Lamk) Fiori). to the family Asteraceae (Compositae). Cultivated cardoon is of regional importance in Italy. Spain and southern France, where it is used for the preparation of traditional dishes. It has been shown to have potential as a source of oil from its seeds, inulin from its roots and various biopharmaceuticals from its leaves. Levels of genetic diversity and relatedness between eleven Italian and 10 Spanish accessions were assessed by DNA profiling with eight AFLP primer combinations and at five microsatellite loci. The AFLP analysis of genetic similarities showed that the Spanish and Italian accessions represent two distinct gene pools; substantial variation was present within each accession. On the other hand a limited variation was detectable by applying SSR markers.     

Genetic diversity in apricot cultivars based on AFLP markers

A set of cultivars used as genitors in apricot breeding programs aimed at introducing sharka resistance were examined by AFLP molecular marker analysis. The markers obtained indicated that apricot cultivars resistant to sharka were related to the European cultivars, but they potentially share a common ancestor donor of sharka outside of the European group. Segregation of AFLP and RAPD markers has been tested in two progenies of two crosses, one between a resistant and a susceptible cultivar and one between two susceptible accessions. The heterozygozity of families obtained from crosses between resistant and susceptible cultivars is similar to those obtained from other self-incompatible Prunus species. On the other hand, heterozygosity of a progeny obtained from a cross between European susceptible cultivars was very low. The usefulness of the information provided by AFLPs for apricot breeding programs is discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic relationships of macadamia cultivars and species revealed by AFLP markers

World production of macadamia nuts is based on two species, the smooth shell Macadamia integrifolia Maiden and Betche, and the rough shell Macadamiatetraphylla L.A.S. Johnson, and their hybrids. One hundred and five AFLP markers were used to analyze 26 macadamia accessions representing four species: M. integrifolia, M. tetraphylla,M. ternifolia, and M. hildebrandii as well as a wild relative,Hicksbeachia pinnatifolia (rose nut).Each macadamia accession showed distinct AFLP fingerprints indicating a significant level of genetic variation in this macadamia germplasm collection. The fourMacadamia species included in this study were clearly separated using cluster analysis with AFLP marker data. Based on a single accession, the separation of M. ternifolia from M. integrifoliasuggested the relatively distant genetic relationship between these two species and casts doubts on the notion that the M. ternifolia may be a variant of M. integrifolia. Within the major cluster ofM. integrifolia, nine established smooth shell cultivars were separated into two sub-clusters, suggesting the heterozygous nature of the original gene pool that had contributed to macadamia variety improvement programs. M. hildebrandii and H. pinnatifoliaformed a distinct cluster and share dramatically less genetic similarity with the other Macadamia species. Additional data would be needed to clarify the phylogenetic nature and status of M. hildebrandii in the genus Macadamia. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity in cornsalad (Valerianella locusta) and related species as determined by AFLP markers

Fifteen amplified fragment length polymorphism (AFLP) EcoRI/MseI‐based primer combinations with five selective bases (Eco RI‐ANN, MseI‐CN) were used to estimate genetic diversity among 45 line varieties of cultivated cornsalad and 19 genebank accessions classified into nine different species related to cornsalad. Polymorphic fragments were scored for calculation of Jaccard's coefficient of genetic similarity (GS). The average GS estimate in elite germplasm (GS = 0.90) was substantially higher than in exotic germplasm (GS = 0.47). UPGMA‐cluster analysis revealed genetic relationships among recently bred varieties, old varieties and genebank accessions. Analysis of molecular variance indicated almost threefold variability within sets compared with between sets due to a high level of polymorphism among wild species. Sources for increasing genetic diversity in elite germplasm of cornsalad were suggested and a duplicate among the genebank accessions was detected. AFLPs could be considered a powerful tool for genetic diversity estimation in cornsalad germplasm and are recommended for systematic fingerprinting of remaining cornsalad species.     

Relationship between heterosis and genetic distance based on morphological traits and AFLP markers in pepper

Genetic diversity is considered as one of the criteria for the selection of parents for hybrid breeding. The present study was undertaken to evaluate genetic divergence among seven pepper cultivars and to assess the relationship between heterosis and parental genetic distance. Twenty‐one F₁ hybrids and seven parents were evaluated for 15 morphological characters in a greenhouse and in the field. The parents were examined for DNA polymorphisms using six amplified fragment length polymorphism (AFLP) primer combinations. Cluster analysis using two genetic distance measures grouped the seven parents differently. Mid‐parent and high‐parent heterosis was observed for most characters. Most hybrids outperformed the parental lines for fruit yield, earliness and plant height. Morphological and AFLP‐based distance measurements were efficient enough to allocate pepper genotypes into heterotic groups. The correlations of morphological distances with mid‐parent heterosis were significant for days to flowering and maturity, suggesting earliness can be predicted from morphological distances of parental lines. However, the correlations of AFLP‐measured genetic distances with mid‐ and high‐parent heterosis were non‐significant for all characters, except for fruit diameter, and proved to be of no predictive value.     

Phenotypic variation in local populations and cultivars of meadow fescue – potential for improving cultivars by utilizing wild germplasm

The utilization of gene bank accessions for breeding purposes is generally hampered by a lack of sufficient genetic and phenotypic characterization. Results are given here of a phenotypic analysis of 30 Norwegian local populations and 10 Nordic cultivars of meadow fescue, and a combined analysis of phenotypic data with previously published molecular data based on 95 amplified fragment length polymorphic markers. Seventeen phenological and morphological, and two derived characters, were assessed on 2264 individual plants. Previous molecular diversity analyses have shown that the Norwegian local populations can be divided into three groups based on a likely history of the introduction of the species into Norway. A similar pattern was evident from relationships between the mean phenotypic values of populations and cultivars. Such a combined phenotypic and genetic characterization of germplasm can facilitate the use of gene bank material in breeding, as breeders can use these data to select populations with extreme values of a field trait, along with markers which represent potential predictors of phenotypic value.     

Genetic diversity among populations and breeding lines from recurrent selection in Brassica napus as revealed by RAPD markers

Recurrent selection facilitated by dominant male sterility has been conducted to broaden the genetic basis for cultivar development in Brassica napus. This study aimed to evaluate the genetic variation in four base populations (C0‐C3) and breeding lines from two of the populations produced during recurrent selection by random amplified polymorphic DNA (Rapd) markers. Genetic variation in four populations declined gradually with the advance of selection cycles as measured by expected genetic heterozygosity (from 0.2058 in C0 to 0.1536 in C3) but the decline was not statistically significant. When compared with the average genetic distances for 21 germplasm collections with wide geographical and genetic origins (0.4712) and seven breeding lines from pedigree selection (0.2059), seven breeding lines selected from the C1 population and 11 from the C3 population had a larger average genetic distance (0.5339 and 0.5486, respectively). Clustering analysis indicated that the lines from recurrent selection had a much lower genetic similarity than lines from pedigree selection. Our results suggest that base populations derived from recurrent selection could provide a wider genetic variation for selection of breeding lines with more broad genetic bases.     

Genetic diversity of late blight resistant and susceptible Indian potato cultivars revealed by RAPD markers

Twenty-four tetraploid Indian potato cultivars were characterized by using RAPD markers to assess diversity within and between late blight resistant and susceptible cultivars. Sixty-four random decamer primers generated802 fragments, ranging in size from 60–3200 bp, with 96.4% fragment polymorphism. Shannon's index of diversity was used to quantify the degree of variability present within and between the variety types. Most of the diversity was detected within variety types, with 88% of variation being within and 12% being between the resistant and susceptible cultivars. No clear groupings based on late blight resistance and susceptibility or kinship was reflected on the dendogram. The late blight resistant cultivars exhibited higher variability compared to susceptible cultivars and they were more dispersed on the PCO plot. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity of hexaploid wheat cultivars estimated by RAPD markers, morphological traits and coefficients of parentage

Estimates of genetic diversity can be based on different types of data. The aim of this research were to study genetic diversity among Croatian wheat cultivars by random amplified polymorphic DNA (RAPD) markers, morphological traits and pedigree records; to analyse differences between wheat cultivars from two breeding centres; and to evaluate usability of RAPD markers for estimation of genetic diversity among wheat cultivars in comparison with morphological traits and pedigree record data. Studies were conducted on 14 wheat cultivars and breeding lines from two breeding centres in Croatia. For the RAPD analysis 36 primers were screened and the 14 most polymorphic ones yielded 341 polymorphic bands. Twelve morphological traits were used for morphological analysis. Pedigrees were composed of seven generations of ancestors. RAPD markers showed a high level of polymorphism among the cultivars examined and the breeding lines. No significant correlations were observed among the methods tested.     

Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes

Tea plant [Camellia sinensis (L.) O. Kuntze] is an important beverage crop in the world. In recent years many clonal tea cultivars have been released, and they play major roles in improving the production and quality of tea. It is important to understand the genetic diversity and relatedness of these cultivars to avoid inbreeding and narrow genetic basis in future tea breeding. In the present study, genetic diversity and relationship of 48 tea cultivars from China, Japan and Kenya were evaluated by inter‐simple sequence repeat (ISSR) markers. A total of 382 ISSR bands were scored, of which 381 (99.7%) were polymorphic. The ISSR primers showed high ability to distinguish between tea cultivars according to their high Resolving Power (R_P) with an average of 7.4. The mean of Nei’s gene diversity (H) and Shannon’s information index (I) were 0.22 and 0.35, respectively. More abundant diversity was revealed among cultivars in China than those in Japan and Kenya. Within Chinese populations, the level of diversity in east China was higher than that in other regions. The coefficient of genetic differentiation (G_ST) was 0.202, which indicates a high degree of genetic variation within populations. This result was further confirmed by analysis of molecular variance, which revealed the variance component within the populations (92.07%) was obviously larger than that among populations (7.93%). The level of gene flow (N_m) was estimated to be 2.0. This could be explained by frequent natural cross‐pollination and seed dispersal among tea populations. The pairwise similarity coefficient between the cultivars varied from 0.162 to 0.538. A dendrogram of 48 tea cultivars was constructed where all the tested cultivars were divided into two groups. Our data show that the genetic relationship among tea cultivars can be determined by the ISSR markers. This will provide valuable information to assist parental selection in current and future tea breeding programmes.     

Genetic diversity and differentiation of Chinese wild soybean germplasm (G. soja Sieb. & Zucc.) in geographical scale revealed by SSR markers

Wild soybean (Glycine soja), as the progenitor of soybeans (G. max), is widely distributed in China and has been collected as a supplementary germplasm pool of soybeans. In this study, 375 wild soybean accessions from a set of genebank core collection were analysed for genetic diversity by using 42 simple sequence repeat primer pairs. The mean allele number per locus was 19.62. Ten‐percent unique alleles involving 35 or 83.33% loci differentiated among the geographical regions. The mean gene diversity (h) per locus was 0.89. A very low mean coefficient of gene differentiation (G_ST = 0.08) for geographical regions and a high mean within‐region gene diversity (H_S = 0.81) were observed, indicating that most genetic diversity existed within the regions. There was an obvious relationship between genetic distance and geographical distance. The results showed multiple centers of genetic diversity for Chinese wild soybean in North China, the Huanghe River Valley, and Central China as well as the Changjiang River Valley, implicating multiple site origins of soybeans within China.     

Genetic diversity of garlic (Allium sativum L.) germplasm from China by fluorescent‐based AFLP,SSR and InDel markers

Garlic (Allium sativum L.), an asexually propagated crop, is an important vegetable and medicinal plant. China is the biggest garlic producer in the world; however, the genetic background of garlic from China is not well understood. In this study, population structure and clustering analysis of garlic germplasm was performed using amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and insertion–deletion (InDel) markers. Among 212 accessions of garlic, genetic diversity analysis identified 546 alleles amplified by AFLP, SSR and InDel primers, and 492 of these were polymorphic. All accessions were divided into five groups by structure analysis and neighbor‐joining clustering. Most traits, including allicin content, were only slightly affected by population structure, which indicated that this germplasm can be used as populations for association mapping. The results provide a molecular basis for understanding the genetic diversity of the garlic germplasm preserved in China.     

Genetic diversity in soybean genotypes from north‐eastern China and identification of candidate markers associated with maturity rating

Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to estimate the genetic relationships among 101 soybean cultivars developed in north‐eastern China. Fifty‐three fragments of the 100 RAPD markers and 35 SSR markers tested were polymorphic across the 101 soybean cultivars. Similarity values among these soybean cultivars ranged from 45.2% to 100% for RAPD data, and ranged from 36.1% to 100% for SSR data. The similarity matrices for SSR data and RAPD data were moderately correlated (r = 0.31, P < 0.05). Cluster analyses indicated that the cultivars released from the same seed company were mostly grouped together. A principal component analysis, based on the combined RAPD and SSR data, yielded a good separation of soybean varieties with different maturity ratings [represented by soybean Heat Unit (HU)]. The varieties with HU < 2200 were well separated from those with HU > 2200. Four RAPD markers and eight SSR markers were significantly associated with the maturity ratings of soybean.     

Genetic diversity and structure of landrace of lablab (Lablab purpureus (L.) Sweet) cultivars in Thailand revealed by SSR markers

Lablab (Lablab purpureus (L.) Sweet) is a legume crop widely cultivated in tropical and subtropical regions of Africa and Asia. In this study, we assessed genetic diversity and population structure of 299 individuals of subspecies purpureus and bengalensis of lablab from Thailand using 13 simple sequence repeat (SSR) markers. The SSR markers detected only 34 alleles in total with a mean of 2.6 alleles per locus. Overall gene diversity was 0.360. Gene diversity (H_E) and allelic richness (A_R) in different geographic regions was comparable. Similarly, both H_E and A_R between subspecies purpureus and bengalensis were similar. STRUCTURE and neighbor-joining (NJ) analyses revealed that the 299 individuals were clustered into two major groups. In contrast, principal coordinate analysis (PCoA) revealed admixture of the lablab germplasm. STRUCTURE, NJ and PCoA analyses also revealed that the subspecies purpureus and bengalensis are not genetically differentiated. Although the number of individuals from the west of Thailand was small and all of them were collected from the same province, they possessed comparable gene diversity with those from the other geographic regions. These results demonstrated that there is moderately low genetic diversity of lablab in Thailand and the west of the country possesses high diversity of lablab.     

Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi,Indonesia revealed by microsatellite markers

Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi.     

Genetic diversity in bread wheat, as revealed by coefficient of parentage and molecular markers, and its relationship to hybrid performance

Variable results have been obtained in different crop species using geneticsimilarity (GS) estimates based on molecular markers and coefficient ofparentage (COP) to predict heterosis.This study was designed: i) to assess the level of GS among 40 breadwheat (Triticum aestivum L.) cultivars selected in Central and SouthEurope; ii) to compare GS with COP; iii) to correlate the estimates ofparental diversity with the heterotic effects detected on 149 F₁hybrids obtained by crossing the 40 cultivars according to three matingdesigns.The parental cultivars and the F₁ hybrids were grown in severallocations at normal seed density. Significant heterotic effects were detectedfor grain yield and other traits including quality attributes. The parentalcultivars were assayed for DNA polymorphisms using two classes ofmarkers: 338 RFLP and 200 AFLP^® bands were scored. GS estimates werecomputed considering each molecular marker set separately (GS_RFLP,GS_AFLP) and together (GS_TOT). Ample differentiation amongthe parental cultivars was detected with the two marker sets. Although theaverage GS_TOT (0.43) was higher than COP (0.10), the twomeasurements were significantly correlated (r = 0.36, p < 0.01).Correlations between the different estimates of genetic diversity andF₁ performance or mid parent heterosis for grain yield and otherrelated traits were in general low although statistically significant.A more detailed analysis was conducted on 28 F₁ hybridsproduced in a half diallel cross of eight parental cultivars characterized byhigh heterotic effects for grain yield. The GS estimates based on RFLP,AFLP^® markers and also on RAPD were partitioned into general andspecific components. Correlations with general and specific combiningability effects for the measured traits were in several cases statisticallysignificant but too low to be predictive and therefore exploitable in practicalbreeding.     

Genetic diversity in tropical maize inbred lines: heterotic group assignment and hybrid performance determined by RFLP markers

Tropical maize inbred lines, eight derived from a Thai synthetic population (BR‐105) and 10 from a Brazilian composite population (BR‐106), were assayed for restriction fragment length polymorphisms with 185 clone‐enzyme combinations. The aim of this study was to investigate genetic distances among tropical maize material and their relationship to heterotic group allocation and hybrid performance. Genetic distances (GDs) were on average greater for BR‐105×BR‐106 lines (0.77) than for BR‐106×BR‐106 (0.71) and for BR‐105×BR‐105 (0.69) lines. Cluster analysis resulted in a clear separation of BR‐105 and BR‐106 populations and was according to pedigree information. Correlations of parental GDs with single crosses and their heterosis for grain yield were high for line crosses from the same heterotic group and low for line combinations from different heterotic groups. Our results suggest that RFLP‐based GDs are efficient and reliable to assess and allocate genotypes from tropical maize populations into heterotic groups. However, RFLP‐based GDs are not suitable for predicting the performance of line crosses from genetically different heterotic groups.     

Genetic diversity in landrace populations of Hordeum vulgare L. from Sardinia, Italy, as revealed by RAPDs, isozymes and morphophenological traits

Barley is the second most widely cultivated cereal on the island of Sardinia. It is grown for green fodder, grain and straw, all of which are used for animal feet. The cultivation of modem varieties is limited and many farmers grow local populations of the six-row landrace ‘S'orgiu sardu’. Twelve local populations (20 strains per population) were evaluated for 13 random amplified polymorphic DNA (RAPD) markers, sisisozyme loci and five morphophenological traits. Results showed that Sardinian barley is characterized by a lax six-row spike and is. in general, a spring type. Isozyme polymorphism was delected for only two esterase loci (Est and Est 4). The genetic variation for all types of murkers, was found located mostly within population (about 84%, for isozymes aud morphaphenological traits and 89%, for RAPDs). This finding appears to confirm the hypothesis that the populations studied belong to the same land race called ‘S'orgiu sardu’ by farmers. A geographical differential ion between southern and northern populations was foand in relation to distinct environmental characteristics. Taking into account all types of marker 209 (90.5%) different genotypes were identified out of 231 individuals. The overall results confirm the high variability that can be found within landrace populations, underlining the value of landraccs as a source of genetic variation.