Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris

Understanding the origins of variation in agricultural pathogens is of fundamental interest and practical importance, especially for diseases that threaten food security. Fusarium oxysporum is among the most important of soil-borne pathogens, with a global distribution and an extensive host range. The pathogen is considered to be asexual, with horizontal transfer of chromosomes providing an analog of assortment by meiotic recombination. Here, we challenge those assumptions based on the results of population genomic analyses, describing the pathogen's diversity and inferring its origins and functional consequences in the context of a single, long-standing agricultural system. We identify simultaneously low nucleotide distance among strains, and unexpectedly high levels of genetic and genomic variability. We determine that these features arise from a combination of genome-scale recombination, best explained by widespread sexual reproduction, and presence-absence variation consistent with chromosomal rearrangement. Pangenome analyses document an accessory genome more than twice the size of the core genome, with contrasting evolutionary dynamics. The core genome is stable, with low diversity and high genetic differentiation across geographic space, while the accessory genome is paradoxically more diverse and unstable but with lower genetic differentiation and hallmarks of contemporary gene flow at local scales. We suggest a model in which episodic sexual reproduction generates haplotypes that are selected and then maintained through clone-like dynamics, followed by contemporary genomic rearrangements that reassort the accessory genome among sympatric strains. Taken together, these processes contribute unique genome content, including reassortment of virulence determinants that may explain observed variation in pathogenic potential.

Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

The identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the clonal and polyploid nature of the crop and the rapid evolution of the pathogen. A diversity panel of tetraploid potato germplasm bred for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and evaluated for late blight resistance in three countries where the International Potato Center (CIP) has established breeding work. Health-indexed, in vitro plants of 380 clones and varieties were distributed from CIP headquarters and tuber seed was produced centrally in Peru, China, and Ethiopia. Phenotypes were recorded following field exposure to local isolates of Phytophthora infestans. QTL explaining resistance in four experiments conducted across the three countries were identified in chromosome IX, and environment-specific QTL were found in chromosomes III, V, and X. Different genetic models were evaluated for prediction ability to identify best performing germplasm in each and all environments. The best prediction ability (0.868) was identified with the genomic best linear unbiased predictors (GBLUPs) when using the diploid marker data and QTL-linked markers as fixed effects. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT, and B3-LTVR populations. The results show that many of the advanced clones bred in Peru for high levels of late blight resistance maintain their resistance in Ethiopia and China, suggesting that the centralized selection strategy has been largely successful.

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy.

Malaria epidemics in the highlands of Ethiopia

OBJECTIVE

To confirm the occurrence and describe the patterns of the 2003 malaria epidemics reported in the highlands of Ethiopia.

DESIGN

A retrospective descriptive study.

SETTINGS

Fifty epidemic affected districts between altitude ranges of 1500 and 2500 m in three regions in Ethiopia.

RESULTS

Exaggerated seasonal transmission was observed in 25 districts, 16 in Oromia region and 9 in SNNPR. A sustained upward trend with 3-4 consecutive abnormal seasonal transmissions, which has started since 2002, has been identified in 22 districts. True explosive epidemic malaria was recorded at exceptionally high altitude (around 2500m) in at least one of the health facilities in seven districts. The incidence of malaria in 2003 epidemic has showed a six fold increase on average (range 2-20) from the threshold level.

CONCLUSION

Occurrence of a malaria epidemic was confirmed in all studied districts showing that the level of malaria endemicity and magnitude of the problem is increasing. The findings suggest the strategic importance of taking well-timed and appropriately targeted preventive and control interventions.

Further definition of the D1 dopamine receptor pharmacophore: synthesis of trans-6,6a,7,8,9,13b-hexahydro-5H-benzo[d]naphth[2,1-b]azepines as rigid analogues of beta-phenyldopamine

In an effort to define further the active geometry of the beta-phenyldopamine pharmacophore of certain dopamine D1 agonists, the title compounds have been synthesized as conformationally restricted homologues of the potent benzophenanthridine dopamine D1 agonist dihydrexidine 4a. The dihydroxy secondary amine 5b was evaluated as a potential agonist, whereas the N-methyl compounds 5a and 5c were hypothesized to be antagonists. Surprisingly, none of the three compounds had high affinity for dopamine D1 or D2 receptors. A comparison of the low-energy conformations of these molecules shows that the pendant phenyl ring of 5b is twisted about 28 degrees relative to that of the corresponding ring of 4a. Further, the additional methylene used to expand the C ring of 5b projects toward the alpha face of the molecule, perhaps suggesting that steric protrusion in this region of the molecule is not tolerated. Finally, the phenethylamine fragment incorporated into these molecules deviates about 30 degrees from the antiperiplanar conformation postulated to be necessary for agonist activity. On the other hand, the potential antagonist molecules 5a and 5c were compared with the dopamine D1 antagonist SCH 39166 2. The conformations of the former two structures differ quite dramatically from that of 2. The most notable differences lie in the relative orientations of the pendant phenyl rings in the two series, as well as the fact that the ethylamine fragment in 2 approximates a gauche conformation, while the comparable orientation in 5a and 5c more nearly approaches an antiperiplanar conformation. These findings will be used to refine further the model of the dopamine D1 agonist receptor that we have previously developed.