Major QTLs control resistance to rice hoja blanca virus and its vector Tagosodes orizicolus.

Rice hoja blanca (white leaf) disease can cause severe yield losses in rice in the Americas. The disease is caused by the rice hoja blanca virus (RHBV), which is transmitted by the planthopper vector Tagosodes orizicolus. Because classical breeding schemes for this disease rely on expensive, time-consuming screenings, there is a need for alternatives such as marker-aided selection. The varieties Fedearroz 2000 and Fedearroz 50, which are resistant to RHBV and to the feeding damage caused by T. orizicolus, were crossed with the susceptible line WC366 to produce segregating F2:3 populations. The F3 families were scored for their resistance level to RHBV and T. orizicolus. The F2:3 lines of both crosses were genotyped using microsatellite markers. One major QTL on the short arm of chromosome 4 was identified for resistance to RHBV in the two populations. Two major QTL on chromosomes 5 and 7 were identified for resistance to T. orizicolus in the Fd2000 × WC366 and Fd50 × WC366 crosses, respectively. This comparative study using two distinct rice populations allowed for a better understanding of how the resistance to RHBV and its vector are controlled genetically. Simple marker-aided breeding schemes based on QTL information can be designed to improve rice germplasm to reduce losses caused by this important disease.

Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.).

Cultivated common bean germplasm is especially diverse due to the parallel domestication of two genepools in the Mesoamerican and Andean centers of diversity and introgression between these gene pools. Classification into morphological races has helped to provide a framework for utilization of this cultivated germplasm. Meanwhile, core collections along with molecular markers are useful tools for organizing and analyzing representative sets of these genotypes. In this study, we evaluated 604 accessions from the CIAT core germplasm collection representing wide genetic variability from both primary and secondary centers of diversity with a newly developed, fluorescent microsatellite marker set of 36 genomic and gene-based SSRs to determine molecular diversity and with seed protein analysis to determine phaseolin alleles. The entire collection could be divided into two genepools and five predominant races with the division between the Mesoamerica race and the Durango-Jalisco group showing strong support within the Mesoamerican genepool and the Nueva Granada and Peru races showing less diversity overall and some between-group admixture within the Andean genepool. The Chile race could not be distinguished within the Andean genepool but there was support for the Guatemala race within the Mesoamerican genepool and this race was unique in its high level of diversity and distance from other Mesoamerican races. Based on this population structure, significant associations were found between SSR loci and seed size characteristics, some on the same linkage group as the phaseolin locus, which previously had been associated with seed size, or in other regions of the genome. In conclusion, this study has shown that common bean has very significant population structure that can help guide the construction of genetic crosses that maximize diversity as well as serving as a basis for additional association studies.

Extent and structure of genetic diversity in a collection of the tropical multipurpose shrub legume Cratylia argentea (Desv.) O. Kuntze as revealed by RAPD markers

The tropical multipurpose shrub legume Cratylia argentea is well adapted to acid soils of low to medium fertility and has excellent drought-tolerance. Due to its high nutritive value it is particularly suited as forage for dry-season supplementation. A collection of 47 C. argentea accessions in a collection, derived from seed replicating of original accessions with differing geographic origin and morphological and agronomic characteristics was investigated using molecular markers (RAPD (random amplified polymorphic DNA)). Genetic diversity (H T = 0.145) in the collection was low, with 30% of differentiation among groups and high genetic similarity among accessions (GS = 0.805). Within-accession variability was high. One taxonomic mismatch and five possible duplicate accessions were identified. Our results suggest that the genetic diversity in the C. argentea accessions studied is relatively homogeneously distributed, indicating the likelihood of extensive outcrossing. The genetic diversity of original accessions should be assessed to determine if outcrossing has occurred during or before ex situ storage. This might also support any decision on whether accessions should be bulked rather than maintaining them individually.

Genetic structure and population dynamics of Xanthomonas axonopodis pv. manihotis in Colombia from 1995 to 1999.

Restriction fragment length polymorphisms (RFLPs) were used to study the population genetics and temporal dynamics of the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis. The population dynamics were addressed by comparing samples collected from 1995 to 1999 from six locations, spanning four different edaphoclimatic zones (ECZs). Forty-five different X. axonopodis pv. manihotis RFLP types or haplotypes were identified between 1995 and 1999. High genetic diversity of the X. axonopodis pv. manihotis strains was evident within most of the fields sampled. In all but one site, diversity decreased over time within fields. Haplotype frequencies significantly differed over the years in all but one location. Studies of the rate of change of X. axonopodis pv. manihotis populations during the cropping cycle in two sites showed significant changes in the haplotype frequencies but not composition. However, variations in pathotype composition were observed from one year to the next at a single site in ECZs 1 and 2 and new pathotypes were described after 1997 in these ECZs, thus revealing the dramatic change in the pathogen population structure of X. axonopodis pv. manihotis. Disease incidence was used to show the progress of cassava bacterial blight in Colombia during the 5-year period in different ecosystems. Low disease incidence values were correlated with low rainfall in 1997 in ECZ 1.