The present study generates information related to the molecular divergence between turcicum leaf blight (TLB)-resistant and -susceptible lines. During molecular diversity studies, a total of 212 alleles were detected at 75 marker loci and ranged from two to five with an average of 2.83 alleles per locus. A direct correlation for the number of alleles and polymorphism information content (PIC) values was ascertained. For instance, marker phi123 produced high number of alleles (5) with PIC values of 0.77. Using the DARwin 6.0 programme, the UPGMA dendrogram grouped 40 maize inbreds into two distinct clusters, cluster-I (36 inbreds) and cluster-II (4 inbreds). Cluster-I contained two subclusters; the first subcluster contained 28 inbreds and the second subcluster contained eight inbreds whereas cluster-II contained four inbreds. This major cluster-II was further classified into two subclusters which contained two inbreds each. Most of the inbred lines except V-25 from cluster-II were highly resistant to TLB disease. These inbred lines can be used in crossing programmes to develop TLB-resistant hybrids by using divergent parents. In this study, allelic diversity and PIC values indicated a good efficiency of markers for studying the polymorphism level available in studied inbred lines. High level of diversity among the inbreds detected with simple sequence repeat markers indicated their suitability for the further breeding programme.

In the fields of agricultural, food and medical research, the potential impacts of tea on human health are of special interest because tea (Camellia sinensis (L.) Kuntze) is continuously consumed by many people in the world. The evaluation of the diversity of genotypes found in tea germplasm can aid in the improvement of the breeding programme. In this study, the genetic diversity of 30 tea genotypes from two commercial sites of tea production in Iran was investigated by using morphological and 12 ISSR markers. Morphological analysis showed that the diversity between samples of tea was limited, and the narrow matching range was calculated. In cluster analysis at level 0.63, samples were divided into four groups. The application of 12 ISSR primers produced 91 polymorphic bands. PIC test showed a range of 0.41–0.48. Based on the ISSR data, the matching range was obtained in the range of 0.24–0.93. In cluster analysis, samples at level 0.58 were divided into five groups. According to the results, it can be understood that these series of traits and primers can very well recognize genetic differences. Using these markers, genetic diversity was observed among tea genotypes, but this diversity was not such as to be able to separate genotypes of various regions from each other. The results showed that the tea genotypes in Iran had high genetic diversity. As a consequence, the findings of our study will help the development of tea germplasm conservation strategies and their sustainable use in breeding programmes.

Haemoparasites represent a diverse group of vector-borne parasites that infect a wide range of vertebrate hosts. In birds, haemoparasite infection rates may be associated with various ecological and life history traits, including habitat choice, colony size and migration distance. Here, we molecularly assessed the prevalence of 3 main haemoparasite genera (Plasmodium, Haemoproteus and Leucocytozoon) in 2 bird species with different habitat preferences and migratory behaviour: black-headed gulls (Chroicocephalus ridibundus) and common terns (Sterna hirundo). We found that gulls showed a much higher prevalence and diversity of Plasmodium or Haemoproteus (ca. 60% of individuals infected) than terns (zero prevalence). The prevalence of Leucocytozoon was low in both species (<3%). The differences in haemoparasite prevalences may be primarily driven by varying vector encounter rate resulting from different habitat preferences, as black-headed gulls mainly use vector-rich vegetated freshwater habitats, whereas common terns often use vector-poor coastal and brackish habitats. Since common terns migrate further than black-headed gulls, our results did not provide support for an association between haemoparasite prevalence and migratory distance. In gulls, we found a negative association between colony size and infection rates, suggestive of an ideal despotic distribution, and phylogenetic analyses of detected haemoparasite lineages provided evidence for higher host specificity in Haemoproteus than Plasmodium. Our results suggest that the preference for coastal areas and less vegetated habitats in terns may reduce haemoparasite infection rates compared to other larids, regardless of their migratory distance, emphasizing the role of ecological niches in parasite exposure.

European dry-wood termites belong to the genus Kalotermes (Kalotermitidae), one of the two termite genera in Europe. Until the recent description of two new species, Kalotermes italicus in Italy and Kalotermes phoenicae in the eastern Mediterranean area, Kalotermes flavicollis was the only taxon known in this region. The presence of additional entities, suggested by morphological and physiological variation observed in K. flavicollis, was supported by molecular studies revealing four distinct genetic lineages: lineage A, K. flavicollis sensu strictu, from the Aegean area to Italy; lineage B, in Tuscany; lineage SC, in Sardinia and Corsica; lineage SF, in southern France. Lineages A and B may form mixed colonies, suggesting hybridization. To draw a more detailed picture of Kalotermes evolution and biogeography in Europe, we analyzed samples from previously unsampled areas, such as Spain and southern Italy, by means of the highly informative cox1/trnL/cox2 mitochondrial DNA marker. Overall, phylogenetic analyses confirmed previously identified lineages and taxa, but widened the distribution of the lineage SC to the mainland and of the lineage SF to Spain and Portugal. Results further provided evidence for the synonymy between lineage B and K. italicus. Species delimitation analysis suggested that the three K. flavicollis lineages, as well as K. italicus, can be separate taxa. Data also suggest a possible interspecific hybridization between K. italicus and both K. flavicollis lineages A and SC.

To address the molecular diversity and occurrence of pathogenic species of the genus Entamoeba spp. in wild non-human primates (NHP) we conducted molecular-phylogenetic analyses on Entamoeba from wild chimpanzees living in the Issa Valley, Tanzania. We compared the sensitivity of molecular [using a genus-specific polymerase chain reaction (PCR)] and coproscopic detection (merthiolate-iodine-formaldehyde concentration) of Entamoeba spp. We identified Entamoeba spp. in 72 chimpanzee fecal samples (79%) subjected to species-specific PCRs for six Entamoeba species/groups (Entamoeba histolytica, Entamoeba nuttalli, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba coli and Entamoeba polecki ST2). We recorded three Entamoeba species: E. coli (47%), E. dispar (16%), Entamoeba hartmanni (51%). Coproscopically, we could only distinguish the cysts of complex E. histolytica/dispar/moshkovskii/nuttalli and E. coli. Molecular prevalence of entamoebas was higher than the prevalence based on the coproscopic examination. Our molecular phylogenies showed that sequences of E. dispar and E. coli from Issa chimpanzees are closely related to sequences from humans and other NHP from GenBank. The results showed that wild chimpanzees harbour Entamoeba species similar to those occurring in humans; however, no pathogenic species were detected. Molecular-phylogenetic methods are critical to improve diagnostics of entamoebas in wild NHP and for determining an accurate prevalence of Entamoeba species.

Old germplasm is an important genetic resource for enhancing modern crops with new alleles. In the present study, the genetic diversity of 52 historic varieties and landraces of bread wheat originated from the Western (Bulgaria) and Northeastern (Ukraine, Russia and Georgia) regions of the Black Sea basin was assessed based on microsatellite markers and agronomic characteristics. A set of 24 markers detected a total of 263 alleles at 25 microsatellite loci, with an average number of 10.5 alleles per locus and an average polymorphic information content (PIC) of 0.74. A total of 63 alleles at 22 loci were unique, being specific to a particular accession. Half of the alleles (132) were regionally specific, and the rest were common between the Western and Northeastern accessions. The latter group was characterized with greater total and private allelic richness, a higher number of unique alleles and a higher average PIC. The population was found to be very heterogeneous (average heterogeneity 41%), with the Northeastern pool (52.8%) being more diverse than the Western pool (30.9%). Most of the accessions of the Western group clustered together, and the rest were distributed among the subclusters of the Northeastern germplasm. Large inter-group differences in the frequencies of alleles ranging from 3.1 at Xgwm294-2A to 16.7 at Xgwm333-7B were observed. This variation might partly account for the differences in certain yield-related traits. The Northeastern accessions had significantly longer spikes with more number of spikelets. Some issues related to germplasm preservation in seed genebanks are discussed herein. The large molecular variation observed could be utilized by breeders for the selection of diverse parents, or by researchers for the production of mapping populations.

Diverse agroecosystems offer phytophagous insects a wide choice of host plants. Myzus persicae is a polyphagous aphid common in moderate climates. During its life cycle it alternates between primary and secondary hosts. A spatial genetic population structure may arise due to environmental factors and reproduction modes. The aim of this work was to determine the spatial and temporal genetic population structure of M. persicae in relation to host plants and climatic conditions. For this, 923 individuals of M. persicae collected from six plant families between 2005 and 2008 in south-eastern Spain were genotyped for eight microsatellite loci. The population structure was inferred by neighbour-joining, analysis of molecular variance (AMOVA) and Bayesian analyses. Moderate polymorphism was observed for the eight loci in almost all the samples. No differences in the number of alleles were observed between primary and secondary hosts or between geographical areas. The proportion of unique genotypes found in the primary host was similar in the north (0.961 ± 0.036) and the south (0.987 ± 0.013), while in the secondary host it was higher in the north (0.801 ± 0.159) than in the south (0.318 ± 0.063). Heterozygosity excess and linkage disequilibrium suggest a high representation of obligate parthenogens in areas with warmer climate and in the secondary hosts. The FST-values pointed to no genetic differentiation of M. persicae on the different plant families. FST-values, AMOVA and Bayesian model-based cluster analyses pointed to a significant population structure that was related to primary and secondary hosts. Differences between primary and secondary hosts could be due to the overrepresentation of parthenogens on herbaceous plants.

Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climate and food habits of peoples due to its short duration, high photosynthetic efficiency, nutritional richness and fair resistance to pest and diseases. However, foxtail millet yields are low mainly due to the lack of effort for its improvement and the lack of proper utilization of existing genetic variability. To enhance the use of diverse germplasm in breeding programmes, a core collection in foxtail millet consisting of 155 accessions was established. Core collection accessions were fingerprinted using 84 markers (81 simple sequence repeats (SSRs) and three Expressed Sequence Tag (EST)-SSRs). Our results showed the presence of greater molecular diversity in the foxtail millet core collection. The 84 markers detected a total of 1356 alleles with an average of 16.14 alleles (4–35) per locus. Of these, 368 were rare alleles, 906 common alleles and 82 the most frequent alleles. Sixty-one unique alleles that were specific to a particular accession and useful for germplasm identification were also detected. In this study, the genetic diversity of foxtail millet was fairly correlated well with racial classification, and the race Indica showed a greater genetic distance from the races Maxima and Moharia. The pairwise estimate of dissimilarity was >0.50 except in 123 out of 11,935 pairs which indicated a greater genetic variability. Two hundred and fifty pairs of genetically most diverse accessions were identified. This large molecular variation observed in the core collection could be utilized effectively by breeders or researchers for the selection of diverse parents for breeding cultivars and the development of mapping populations.

Three methanogen 16S rRNA gene clone libraries were constructed from liquid (LM), solid (SM) and epithelium (EM) fractions taken from the rumen of Jinnan cattle in China. After the amplification by PCR using methanogen-specific primers Met86F and Met1340R, equal quantities of PCR products from the same fractions from each of the four cattle were mixed together and used to construct the three libraries. Sequence analysis showed that the 268 LM clones were divided into 35 phylotypes with 18 sequences of phylotypes affiliated with the genus Methanobrevibacter (84.3% of clones). The 135 SM clones were divided into 19 phylotypes with 11 phylotypes affiliated with the genus Methanobrevibacter (77.8%). The 267 EM clones were divided into 33 phylotypes with 15 phylotypes affiliated with the genus Methanobrevibacter (77.2%). Clones closely related to Methanomicrobium mobile and Methanobrevibacter wolinii were only found in the LM library, and those to Methanobrevibacter ruminantium and Methanobrevibacter gottschalkii only in the SM library. LM library comprised 12.4% unidentified euryarchaeal clones, SM library 23.7% and EM library 25.5%, respectively. Five phylotypes (accession number: EF055528 and EF055531–EF055534) did not belong to the Euryarchaeota sequences we had known. One possible new genus (represented by phylotype E17, accession number EF055528) belonging to Methanobacteriaceae was identified from EM library. Quantitative real-time PCR for the first time revealed that epithelium fraction had significantly higher density of methanogens, with methanogenic mcrA gene copies (9.95 log 10 (copies per gram of wet weight)) than solid (9.26, P < 0.01) and the liquid (8.44, P < 0.001). The three clone libraries also appeared different in Shannon index (EM library 2.12, LM library 2.05 and SM library 1.73). Our results showed that there were apparent differences in the methanogenic diversity and abundance in the three different fractions within the rumen of Jinnan cattle, with Methanobrevibacter species predominant in all the three libraries and with epithelium fraction having more unknown species and higher density of methanogens.

Two recognized strains of Schistosoma intercalatum, one from the Democratic Republic of Congo (DRC), formerly Zaire, and the other from Cameroon, have been investigated using DNA sequences from 3 mitochondrial genes, cytochrome oxidase subunit 1 (cox1), NADH dehydrogenase subunit 6 (nad6) and the small ribosomal RNA gene (rrnS). In addition, partial DNA sequences from the nuclear large subunit ribosomal RNA gene (lsrDNA) were included within the study. Although partial lsrDNA alone reveals little taxonomic information, phylogenetic analysis of the mitochondrial data demonstrates a clear dichotomy between the 2 purported strains and it is proposed that they should be treated as distinct taxa. The ‘original’ S. intercalatum now falls relatively basal in the S. haematobium group, while the proposed new species is more derived and sister taxon to S. bovis and S. curassoni.