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To satisfy growing demand for food, global agricultural production must in-crease by 70% by 2050. However, pests and crop diseases put global food supplies at risk. Worldwide, yield losses caused by pests and diseases are estimated to aver-age 21.5% in wheat, 30.0% in rice, 22.6% in maize, 17.2% in potato, and 21.4% in soybean [1]; these crops account for half of the global human calorie intake [2]. Climate change and global trade drive the distribution, host range, and impact of plant diseases [3], many of which can spread or re-emerge after having been under control [4] (see photo). Though many national and regional plant protec-tion organizations (NPPOs and RPPOs) work to monitor and contain crop disease outbreaks, many countries, particularly low-income countries (LIC) do not effi-ciently exchange information, delaying coordinated responses to prevent disease establishment and spread. To improve re-sponses to unexpected crop disease spread, we propose a Global Surveillance System (GSS) that will extend and adapt established biosecurity practices and networking facilities into LIC, enabling countries and regions to quickly respond to emerging disease outbreaks to stabilize food supplies, enhancing global food pro-tection.

This paper discusses the use of wild rice species to obtain an improved germplasm with a higher yield potential and a wider genetic base. Three wild species (O. rufipogon, O. glaberrima and O. barthii), and 12 improved varieties (recurrent parents) were selected to develop populations into which genes that control valuable agronomic cahracteristics are selectively transferred by the use of molecular markers. The 36 resulting populations from specific backcross schemes are now in different developmental phases, and underwent negative phenotypic selection against undesirable agronomic traits contributed by the wild parents. Between 220 and 300 BC2F2 families from specific crosses in replicated yield trials in severallocations in Colombia were evaluated. Transgressivesegregation for yield (kg/ha) was detected in the BG90-2*3/0 rufipogon population, and several families yielded between 5 and 15% more than the BG-90-2; transgressive segregation for resistance to the white leaf virus was detected in the O. llanos 5*3/0 rufipogon population. Preliminary data sugests that introgression of certain genes from O. rufipogon may contribute to yield increase in improved rice varieties. Este trabajo presenta el uso de especies silvestres de arroz en la obtención de germoplasma mejorado con mayor potencial de rendimiento y una base genética ampliada. Tres especies silvestres (O. rufipogon, O. glaberrima y O. barthii) y 12 variedades mejoradas (padres recurrentes) fueron selecciona-das para desarrollar poblaciones a las cuales transferir selec-tivamente genes que controlan características de gran valor agronómico mediante el empleo de marcadores moleculares; las 36 poblaciones resultantes de los retrocruzamientos se encuentran en estados diferentes de desarrollo y se les aplicó selección fenotípica negativa contra caracteres agronómicos indeseables aportados por los progenitores silvestres. Se evaluaron 220-300 familias BC2F2 de cruzamientos específicos en ensayos replicados de rendimiento en varios sitios en Colombia. Segregación transgresiva para rendimiento (kg/ha) se detectó en la población Bg90-2*3/0. rufipogon y varias familias rindieron entre 5 y 15% más que Bg90-2; segregación transgresiva para resistencia al virus de la hoja blanca se detectó en la población O. Llanos 5*3/0. rufipogon. Los datos preliminares sugieren que la introgresión de ciertos genes específicos presentes en O. rufipogon puede in-crementar el rendimiento en variedades mejoradas de arroz

To facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (Oryza sativa L.), we conceived of and developed a Universal Core Genetic Map (UCGM). With this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (SSR) markers arranged into non-recombining groups. Each anchor consists of at least three, closely linked SSRs, located within a distance below the genetic resolution provided by common, segregating populations (< 500 individuals). We chose anchors that were evenly distributed across the rice chromosomes, with spacing between 2 and 3.5 Mbp (except in the telomeric regions, where spacing was 1.5 Mbp). Anchor selection was performed using in silico tools and data: the O. sativa cv. Nipponbare rice genome sequence, the CHARM tool, information from the Gramene database and the OrygenesDB database. Sixteen AA-genome accessions of the Oryza genus were used to evaluate polymorphisms for the selected markers, including accessions from O. sativa, O. glaberrima, O. barthii, O. rufipogon, O. glumaepatula and O. meridionalis. High levels of polymorphism were found for the tested O. sativa x O. glaberrima or O. sativa x wild rice combinations. We developed Paddy Map, a simple database that is helpful in selecting optimal sets of polymorphic SSRs for any cross that involves the previously mentioned species. Validation of the UCGM was done by using it to develop three interspecific genetic maps and by comparing genetic SSR locations with their physical positions on the rice pseudomolecules. In this study, we demonstrate that the UCGM is a useful tool for the rice genetics and breeding community, especially in strategies based on interspecific hybridisation.

Xanthomonas oryzae pathovar oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) cause bacterial diseases in rice: leaf blight and leaf streak, respectively. Although both the Asian and the African strains of Xoo induce similar symptoms, they are genetically different, with the African Xoo strains being more closely related to the Asian Xoc. To identify the sequences responsible for differences between African and Asian Xoo strains and their relatedness to Xoc strains, a suppression-subtractive hybridization (SSH) procedure was performed, using the African Xoo MAI1 strain as a tester and the Philippine Xoo PXO86 strain and Xoc BLS256 strain as drivers. A nonredundant set of 134 sequences from MAI1 was generated. Several DNA fragments isolated by SSH were similar to genes of unknown function, hypothetical proteins, genes related to the type III secretion system, and other pathogenicity-related genes. The specificity of various fragments was validated by Southern blot analysis. SSH sequences were compared with several xanthomonad genomes. In silico analysis revealed SSH sequences as specific to strain MAI1, revealing their potential as specific markers for further epidemiological and diagnostic studies. SSH proved to be a useful method for rapidly identifying specific genes among closely related X. oryzae strains.

Background: Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs. Results: We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544) in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiapo). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11. Conclusions: Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor underlying resistance to this virus. This population is a powerful breeding tool. It also helps in overcoming hybrid sterility barriers between species of rice.

Cassava (Manihot esculenta Crantz) is a major root crop widely grown in the tropics. Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis (Xam), is an important disease in Latin America and Africa resulting in significant losses. The preferred control method is the use of resistant genotypes. Mapping expressed sequence tags (ESTs) and determining their co-localization with quantitative trait loci (QTLs) may give additional evidence of the role of the corresponding genes in resistance or defense. Twenty-one EST-derived simple sequence repeats (SSRs) were mapped in 16 linkage groups. ESTs showing similarities with candidate resistance genes or defense genes were also mapped using strategies such as restriction fragment length polymorphisms, cleaved amplified polymorphic sequences, and allele-specific primers. In total, 10 defense-related genes and 2 bacterial artificial chromosomes (BACs) containing resistance gene candidates (RGCs) were mapped in 11 linkage groups. Two new QTLs associated with resistance to Xam strains CIO121 and CIO151 were detected in linkage groups A and U, respectively. The QTL in linkage group U explained 61.6% of the phenotypic variance and was associated with an RGC-containing BAC. No correlation was found between the new EST-derived SSRs or other mapped ESTs and the new or previously reported QTLs.