First report of Cassava Bacterial Blight caused by Xanthomonas axonopodis pv. manihotis in Burkina Faso

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Host candidate gene polymorphisms and clearance of drug-resistant Plasmodium falciparum parasites

Resistance to anti-malarial drugs is a widespread problem for control programmes for this devastating disease. Molecular tests are available for many anti-malarial drugs and are useful tools for the surveillance of drug resistance. However, the correlation of treatment outcome and molecular tests with particular parasite markers is not perfect, due in part to individuals who are able to clear genotypically drug-resistant parasites. This study aimed to identify molecular markers in the human genome that correlate with the clearance of malaria parasites after drug treatment, despite the drug resistance profile of the protozoan as predicted by molecular approaches

Characterization of new races of Xanthomonas oryzae pv. oryzae in Mali informs resistance gene deployment

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae represents a severe threat to rice cultivation in Mali. Characterizing the pathotypic diversity of bacterial populations is key to the management of pathogen-resistant varieties. Forty-one X. oryzae pv. oryzae isolates were collected between 2010 and 2013 in the major rice growing regions in Mali. All isolates were virulent on the susceptible rice variety Azucena; evaluation of the isolates on 12 near isogenic rice lines, each carrying a single resistance gene, identified six new races (A4 to A9) and confirmed race A3 that was previously reported in Mali. Races A5 and A6, isolated in Office du Niger and Selingue, were the most prevalent races in Mali. Race A9 was the most virulent, circumventing all of the resistance genes tested. Xa3 controlled six of seven races (i.e., 89% of the isolates tested). The expansion of race A9 represents a major risk to rice cultivation and highlights the urgent need to identify a local source of resistance. We selected 14 isolates of X. oryzae pv. oryzae representative of the most prevalent races to evaluate 29 rice varieties grown by farmers in Mali. Six isolates showed a high level of resistance to X. oryzae pv. oryzae and were then screened with a larger collection of isolates. Based on the interactions among the six varieties and the X. oryzae pv. oryzae isolates, we characterized eight different pathotypes (P1 to P8). Two rice varieties, SK20-28 and Gigante, effectively controlled all of the isolates tested. The low association observed among races and pathotypes of X. oryzae pv. oryzae suggests that the resistance observed in the local rice varieties does not simply rely on single known Xa genes. X. oryzae pv. oryzae is pathogenically and geographically diverse. Both the races of X. oryzae pv. oryzae characterized in this study and the identification of sources of resistance in local rice varieties provide useful information to inform the design of effective breeding programs for resistance to bacterial leaf blight in Mali

Broad-spectrum resistance and susceptibility to bacterial blight and bacterial leaf streak of rice

Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR) have been elusive targets of crop breeding programs. Bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzicola (Xoc) and Xanthomonas oryzae pv. oryzae (Xoo), respectively, are responsible for major losses in rice production in Asia and Africa. Controlling these two diseases is particularly important in Sub-Saharan Africa, where no sources of BSR are available in currently deployed varieties. Our goal is to identify novel, broad-spectrum resistance sources to control BLS and BB in rice, using a Multi-parent Advanced Generation Inter-Cross (MAGIC) population, derived from eight elite indica cultivars. MAGIC populations have an increased level of recombination and provide higher precision and resolution to detect QTL. The MAGIC parents and lines were genotyped and phenotyped in both greenhouse and field conditions by screening with diverse strains of Xoc and Xoo. Using genome-wide association and interval mapping analysis, we identified 37 strain-specific QTL, and 14 QTL effective against multiple X. oryzae strains. From these, three QTL are pathovar-specific and 11 confer resistance to both pathovars. By detecting phenotypic effects of causal alleles, we have identified resources that will facilitate a better understanding of how the involved genes contribute to resistance or susceptibility. Because the MAGIC founders are elite varieties, the BSR QTL identified can be rapidly incorporated into breeding programs to achieve more durable resistance to BLS and BB

Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population

Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub-Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar-specific QTL. The most promising BSR QTL (qXO-2-1, qXO-4-1 and qXO-11-2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes