A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

The Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.     

Species-specific primers for Fusarium redolens and a PCR-RFLP technique to distinguish among three clades of Fusarium oxysporum

The currently available morphological and molecular diagnostic techniques for Fusarium redolens and the three phylogenetic clades of Fusarium oxysporum are problematic. Aligned translation elongation factor 1 alpha (TEF-1 alpha) gene sequences from these species and their close relatives were used to design F. redolens-specific primers, and to identify restriction sites that discriminate among the three clades of F. oxysporum. The F. redolens-specific primers distinguished this species from all others included in the study. There were three TEF-1 alpha-RFLP patterns among formae speciales of F. oxysporum. These PCR-RFLP patterns corresponded with the three clades. These techniques provide simple and inexpensive diagnostic methods for the identification of F. redolens and members of the three clades of F. oxysporum.     

A new species of Heliocephala from Mexico with an assessment of the systematic positions of the anamorph genera Heliocephala and Holubovaniella

During a study of the microfungi on decaying leaves collected in México we encountered a fungus sharing features of the anamorph genera Heliocephala and Holubovaniella. This hyphomycete resembled Hol. elegans in possessing obclavate to fusiform, three-septate, rostrate phragmoconidia, but it can be distinguished by its much shorter, branched, determinate conidiophores. Unlike members of genus Heliocephala, which also possess determinant conidiophores, the phragmoconidia of this taxon are short-rostrate and have not been observed to germinate iteratively. Prompted by the discovery of this hyphomycete, we investigated the phylogenetic relationships among species of Heliocephala and Holubovaniella. Analysis of large subunit rDNA gene sequences positioned species of Heliocephala and Holubovaniella in the Dothideomycetes and identified Stomiopeltis betulae (Micropeltididaceae) as their closest relative. These results also indicated that Heliocephala and Holubovaniella are closely related taxa. Based on these findings and the similarity of the developmental and morphological characters of species of Heliocephala and Holubovaniella, we recognize these genera as synonymous and describe a new species, Heliocephala triseptata. A dichotomous key to the species of Heliocephala is provided.     

Categorical learning between 'male' and 'female' photographic human faces in jungle crows (Corvus macrorhynchos)

We trained jungle crows to discriminate among photographs of human face according to their sex in a simultaneous two-alternative task to study their categorical learning ability. Once the crows reached a discrimination criterion (greater than or equal to 80% correct choices in two consecutive sessions; binomial probability test, p < .05), they next received generalization and transfer tests (i.e., greyscale, contour, and ‘full’ occlusion) in Experiment 1 followed by a ‘partial’ occlusion test in Experiment 2 and random stimuli pair test in Experiment 3. Jungle crows learned the discrimination task in a few trials and successfully generalized to novel stimuli sets. However, all crows failed the greyscale test and half of them the contour test. Neither occlusion of internal features of the face, nor randomly pairing of exemplars affected discrimination performance of most, if not all crows. We suggest that jungle crows categorize human face photographs based on perceptual similarities as other non-human animals do, and colour appears to be the most salient feature controlling discriminative behaviour. However, the variability in the use of facial contours among individuals suggests an exploitation of multiple features and individual differences in visual information processing among jungle crows.     

Molecular characterization of Mycobacterium bovis isolates from Ethiopian cattle

Background

Bovine Tuberculosis (BTB) is a widespread and endemic disease of cattle in Ethiopia. Information relating to genotypic characteristics of Mycobacterium bovis strains affecting the cattle population in Ethiopia is limited. We carried out molecular characterization of M. bovis strains isolated from BTB infected cattle using the spoligotyping technique. The relationship between distribution of spoligotypes and recorded variables was also investigated. A new approach that can numerically reflect the degree of genetic polymorphism in a M. bovis population was also developed. The study was conducted from July 2006 to January 2007 in cattle slaughtered at five representative abattoirs in Ethiopia.

Results

Forty-five M. bovis isolates were obtained from 406 pathologic tissue specimens collected from 337 carcasses with lesions compatible with BTB. Twelve spoligotypes were identified from 34 distinct strains; with SB1176 as a dominant spoligotype (41.2% of the isolates) followed by SB0133 (14.7%). Comparison of spoligotypes with an M. bovis global database http://www.mbovis.org revealed six new spoligotypes which were subsequently registered in the database with international identification codes of SB1517, SB1518, SB1519, SB1520, SB1521 and SB1522. The majority of strains were obtained from cattle slaughtered at Addis Ababa abattoir. On the basis of the Spoligotype Evolutionary Index, SEI (a numeric expression approach to make standardized comparison of spoligotype evolution), M. bovis isolates from Ethiopia were relatively more heterogeneous (SEI = 3.2) compared to isolates from other countries. This might be attributed to extensive livestock movement linked to trading or seasonal migration, high degree of livestock mingling, and also diversities of the country's agricultural and livestock ecosystems, in addition to lack of disease control measures that led to high infection prevalence. Multiple spoligotype infection was recorded in nine (50%) of infected carcasses and this may indicate the prevailing high degree of super infection.

Conclusions

This study provided molecular evidence for the widespread distribution of M. bovis in the cattle population in Ethiopia. It also demonstrated a relatively high degree of genetic polymorphism of the isolates. Further molecular investigation of M. bovis strains in humans and other domestic animals is recommended in order to elucidate the zoonotic importance as well as reservoirs and pattern of transmission among various hosts.     

Systematics of Catenulifera (anamorphic Hyaloscyphaceae) with an assessment of the phylogenetic position of Phialophora hyalina

Catenulifera, typified by C. rhodogena (=Scopulariopsis rhodogena), was established to accommodate the anamorphs of Hyphodiscus (Ascomycota, Helotiales) and to delimit these taxa from members of Phialophora section Catenulatae. Catenulifera rhodogena has been inferred as monophyletic, but its relationship to ascomycetes with poorly differentiated phialidic anamorphs remains enigmatic. To test the hypothesis that C. rhodogena is closely related to morphologically similar species of Phialophora and to further explore the systematics of Catenulifera, we analyzed nuclear rDNA and β-tubulin gene sequences of isolates identified as C. rhodogena, Hyphodiscus hymeniophilus, P. brachyconia, P. brevicollaris and P. hyalina. ITS-LSU and ITS-LSU-β-tubulin phylogenies positioned all isolates except P. hyalina in a single, well-supported clade that consisted of three subclades. Subclade 1 included fungicolous isolates of C. rhodogena and H. hymeniophilus that did not fluoresce when exposed to long-wave UV light. Subclade 2 contained fungicolous and lignicolous strains of C. rhodogena that produced fluorescent colonies and possessed a 366bp indel in the LSU rRNA gene. Neither lineage encompassed the ex-type strains of Cistella rubescens (=H. hymeniophilus) or S. rhodogena, but the former isolate was inferred as sister to Subclade 2. Subclade 3 included all isolates of P. brachyconia, a species recognized here as C. brachyconia comb. nov. A fourth isolate of P. brachyconia that was extralimital to Subclade 3 is described as C. luxurians sp. nov. The positions of C. brevicollaris comb. nov., a species based on P. brevicollaris, and C. luxurians were not resolved in the ITS-LSU phylogeny. P. hyalina is not closely related to Catenulifera.     

Colipila, a new genus in the Helotiales

Colipila, a new member of the Helotiales, is erected for two previously undescribed lignicolous species resembling Dasyscyphella and Lachnum by macroscopy. Species of Colipila are characterized by their long, entirely smooth, hyaline, thin-walled, multiseptate, subulate to basally fusoid hairs that tend to be curved on the stipe and lower flanks, and dimorphic, partly strongly protruding paraphyses which closely resemble the hairs. The type species, C. masduguana, is recorded repeatedly in southern France on rotten decorticated branches and trunks of Castanea sativa on the moist forest floor in sub-Mediterranean regions with siliceous soils, but also once on Quercus robur in a temperate forest with calcareous soil. The second species, C. pilatensis, was found on wood of an unidentified member of Rosaceae in a calcareous region of the Northern Alps and is known only from the holotype. The phylogenetic position of C. masduguana within the Helotiales was not resolved based on the analysis of nuclear LSU ribosomal DNA sequences. A key to the species of Colipila is provided.     

Xerombrophila crystallifera, a new genus and species in the Helotiales

Xerombrophila, a new member of the Helotiales, is erected for a previously undescribed species that macroscopically resembles genera such as Phaeohelotium or Pezicula. The new species, for which we propose the name X. crystallifera, is characterized by a strong gelatinization of the medullary excipulum as well as the covering layer of the ectal excipulum, by the presence of abundant octahedral crystals, asci with an euamyloid apical ring that resembles the Calycina-type, and paraphyses containing refractive vacuoles. It can also be distinguished from members of both Ombrophila and Phaeohelotium in that it is desiccation-tolerant by surviving several weeks in the dry state. The species appears to be confined to xeric bark of Salix and was exclusively found over waterlogged soil, irrespective of being acidic or calcareous. It is known from various planar and colline areas of temperate Europe, and can be found throughout the year. Phylogenetic analysis of partial LSU sequences positions X. crystallifera as a sister taxon of a clade within the Helotiaceae s.l. that includes Ascocoryne, Chloroscypha, Gelatinodiscus, Neobulgaria and "Sarcoleotia" turficola.