Daniel Z. Skinner

Restriction fragment length polymorphism and virulence analyses were used to evaluate the population structure of Xanthomonas oryzae pv. oryzae, the rice bacterial blight pathogen, from several rice-growing countries in Asia. Two DNA sequences from X. oryzae pv. oryzae, IS1112, an insertion sequence, and avrXa10, a member of a family of avirulence genes, were used as probes to analyze the genomes of 308 strains of X. oryzae pv. oryzae collected from China, India, Indonesia, Korea, Malaysia, Nepal, and the Philippines. On the basis of the consensus of three clustering statistics, the collection formed five clusters. Genetic distances within the five clusters ranged from 0.16 to 0.51, and distances between clusters ranged from 0.48 to 0.64. Three of the five clusters consisted of strains from a single country. Strains within two clusters, however, were found in more than one country, suggesting patterns of movement of the pathogen. The pathotype of X. oryzae pv. oryzae was determined for 226 strains by inoculating five rice differential cultivars. More than one pathotype was associated with each cluster; however, some pathotypes were associated with only one cluster. Most strains from South Asia (Nepal and India) were virulent to cultivars containing the bacterial blight resistance gene xa-5, while most strains from other countries were avirulent to xa-5. The regional differentiation of clusters of X. oryzae pv. oryzae in Asia and the association of some pathotypes of X. oryzae pv. oryzae with single clusters suggested that strategies that target regional resistance breeding and gene deployment are feasible.

Several inbred lines of acetolactate synthase (ALS)-inhibiting herbicide-resistant (ALS-R) Palmer amaranth and ALS-susceptible (ALS-S) common waterhemp were developed in the greenhouse. Interspecific hybrids were obtained by allowing several ALS-S common waterhemp females to be pollinated only by ALS-R Palmer amaranth in a growth chamber. Putative hybrid progeny were treated with an ALS-inhibiting herbicide, and the hybrid nature verified using a polymorphism found in the parental ALS gene. Polymerase chain reaction (PCR) was used to amplify a region of the ALS gene in both parental plants and putative hybrids. Restriction enzyme digestion of the ALS-R Palmer amaranth PCR fragment resulted in two smaller fragments, whereas the PCR fragment in the ALS-S common waterhemp was not cut. Restriction digestion of the putative hybrid PCR fragment showed a combination of ALS-R Palmer amaranth double fragments and an ALS-S common waterhemp single fragment. Approximately 4 million flowers were present on 11 common waterhemp females and produced about 44,000 seeds that appeared viable. From the approximately 3,500 putative hybrid seedlings that were screened, 35 were confirmed as hybrids using herbicide resistance as a phenotypic and molecular marker. The data collected here verify that interspecific hybridization does occur between these two species, and even at a low rate, it could contribute to the rapid spread of ALS resistance in these species.