Genetic diversity and population structure of an endangered Orchid (Dendrobium loddigesii Rolfe) from China revealed by SRAP markers

Dendrobium loddigesii Rolfe is an endangered perennial herb with ornamental and medicinal value. Due to habitat deterioration and human over-exploitation, it has suffered a significant decline in abundance. Determining the level of genetic diversity and pattern of population genetic structure of this species would be helpful for its conservation and management. In this paper, sequence-related amplified polymorphism (SRAP) markers were applied to assess the level and pattern of genetic diversity in seven populations of D. loddigesii. Seventeen SRAP primer combinations generated a total of 231 clear amplification bands encompassing 187 (80.95%) polymorphic bands. A high level of genetic diversity was detected (PPB = 80.52%, H = 0.2743, I = 0.4113) at the species level. There was a moderate genetic differentiation (G_st = 0.304) among populations. Two main clusters were detected by cluster analysis using the unweighted pair-group method with arithmetic average (UPGMA). Mantel test revealed that no significant positive correlation was found between genetic distances and geographic distances (r = 0.2302; P > 0.05). Recommendations for conservation of the endangered species resources are proposed.     

Genetic diversity in Apium graveolens and related species revealed by SRAP and SSR markers

Genetic diversity is essential to crop improvement. However, lack of molecular markers prevents the understanding of genetic diversity in celery and related species. In this study, SRAP and SSR markers was firstly used to evaluate genetic variation in 68 accessions of Apium graveolens and related species. A total of 888 bands were generated by 40 primer combinations of SRAP and 32 bands were produced by eight SSR markers. Of the 920 bands, 95.1% were polymorphic between A. graveolens and related species, and 49.2% were polymorphic within A. graveolens. Cluster and structure analysis could distinguish local celery, celery, and related species. These results suggested that both SRAP and SSR technologies can be efficiently used to characterize genetic variation and analyze genetic relationship in celery and related species.     

Genetic diversity of apricot revealed by a set of SSR markers from linkage group G1

Eight polymorphic simple sequence repeat (SSR) markers located in the G1 linkage group of apricot (Prunus armeniaca L.) were previously developed and evaluated in a small set of cultivars. Those primers were used for studying variability in 77 apricot cultivars belonging to five different geographical groups, such as Chinese, Asian (Irano-Caucasian and Central Asian), North American, Mediterranean and Western European as well as Middle European cultivars. Six of the markers were polymorphic and revealed a total of 71 alleles ranging from 5 (aprigms11) to 20 (aprigms1) alleles per locus with a mean value of 11.83 alleles per locus. In conclusion, the SSR loci located in the G1 linkage group show a level of polymorphism which is similar to loci dispersed throughout the entire genome. The total number of alleles and the number of unique alleles were the highest in Chinese apricots and the lowest in Middle European cultivars. Heterozygosity also showed a decrease from Asia and China to Middle Europe. No association could have been observed between any SSR markers tested and plum pox virus (PPV) resistant phenotype of cultivars. PPV resistant cultivars did not form a separate clade on the dendrogram obtained by UPGMA cluster analysis. Middle European and Chinese cultivars formed separate clusters while other genotypes formed smaller multiple sub-groups or scattered among different clusters. Our results support previous hypotheses on the origin of PPV resistance in North American apricots. The allele data was also presented in a form that allowed the easy observation of allele frequencies in each geographical group at each locus. Using this data field, differences and similarities between cultivar groups can be easily assessed. The analysis demonstrated the links between the North American and Mediterranean apricot germplasm and confirmed that the Chinese and Eastern European cultivars are distantly related.     

Genetic assessment of apple germplasm in Bosnia and Herzegovina using microsatellite and morphologic markers

Traditional apple cultivars from Bosnia and Herzegovina (B&H), potentially diverse due to specific geographic location and history of the country, represent a possible source of valuable traits for future breeding efforts and sustainable fruit growing. A total of 39 accessions, 24 traditional B&H cultivars and 15 modern international cultivars, maintained at the ex situ apple collection “Srebrenik” in Northeast Bosnia were, investigated using 10 SSR (simple sequence repeats) markers and 23 morphologic characteristics. All the used primer pairs manage to amplify clearly distinguishable and highly polymorphic SSR alleles, in average 10.4 alleles per locus. More than two different alleles per locus were detected for seven accessions (five traditional B&H cultivars and two international cultivars). Forty one unique alleles were exclusively present within the B&H cultivars, while seven unique alleles were only detected within international cultivars. The differentiation between traditional B&H and international cultivars (Fst = 0.060; P < 0.0001) was significant, also confirmed by analyses of molecular variance (AMOVA) (f_CT = 0.092; P < 0.001). Cluster analyses of 39 apple accessions, based on 10 SSR loci, revealed that only two traditional B&H cultivars grouped tightly with international cultivars (Ljepocvjetka and Bobovec Jon), while the rest formed separate clusters. Multivariate analyses of variance (MANOVA), nonparametric multivariate analyses of variance (NPMANOVA) and analyses of similarity (ANOSIM) showed statistically significant difference in morphologic characteristics between traditional B&H cultivars and the international cultivars. Cluster analyses of 39 apple accessions, based on the morphologic data, displayed less differentiation between traditional and international accessions, in comparison to the cluster analyses based on molecular data. No correlation between the molecular and morphologic data set was detected using the Mantel test. Many of the morphologic characteristics which have been analyzed in this study have significant commercial importance, we can assume that unlike the microsatellites these traits have been under agronomic selection pressure.     

Use of ISSR,SRAP, and RAPD markers to assess genetic diversity in Turkish melons

The genetic relationships among 63 melon (Cucumis melo L.) genotypes collected from various regions of Turkey were determined by comparing their molecular ISSR, SRAP, and RAPD markers with those of 19 foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish melon germplasm. Total 162 polymorphic markers (69, 18, and 75 obtained from ISSR, SRAP, and RAPD primers, respectively) were used to define the genetic similarity among the melon genotypes by dendrogram or two and three dimensional scalings. The average similarity (SM coefficient) between any two pairs of accessions examined as estimated by molecular variation was 0.73 ± 0.48. Within-group genetic similarities ranged between 0.46 and 0.96. Related genotypes or genotypes collected from similar regions were partitioned to similar clusters. Southeastern Anatolian genotypes were distinctly apart from group inodorus and group cantalupensis (sweet) genotypes. This reinforced the position of Turkey in the secondary genetic diversity center of melon. The genetic diversity among Turkish genotypes (H = 0.28 and I = 0.42) was only a little less than that of the world accessions (H = 0.30 and I = 0.45). On the other hand, the percentage of polymorphic loci among Turkish melon genotypes (90.7%) was even higher than that of the world accessions (87.6%).