Date of Graduation

8-2012

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Plant Science (PhD)

Degree Level

Graduate

Department

Plant Pathology

Advisor

James C. Correll

Committee Member

Richard D. Cartwright

Second Committee Member

James W. Gibbons

Third Committee Member

Yulin Jia

Fourth Committee Member

Brad Murphy

Fifth Committee Member

Craig S. Rothrock

Abstract

Rice sheath blight (ShB) is one of the most prevalent diseases in rice. The significance of this disease is increasing due to more intensive production practices globally. Rhizoctonia solani Kühn AG 1 - IA [teleomorph: Thanatephorus cucumeris (A.B. Frank) Donk] is considered the primary ShB pathogen of rice. However, Rhizoctonia oryzae-sativae, Rhizoctonia oryzae, and R. solani AG 2 and AG 11, have also been isolated from sheath blight-like lesions on rice.Up to now, there is little information on genetic diversity and patterns of molecular evolution of the fungus, and there is no study on the structure of the R. solani AG 1 - IA population associated with rice in Arkansas. The first objective of this research was to assess and compare the virulence/aggressiveness profiles, and the genetic and phenotypic diversity of a representative collection of isolates of R. solani AG 1 - IA and Rhizoctonia spp. Isolates were examined for their diversity as assessed by cultural morphological differences, genetic diversity at the species- and sub-species level by specific PCR markers, ITS-RFLP, UP-PCR, and by sequence analysis of the ITS, RPB2 and ß-tubulin genes. Differences in pathogenicity and aggressiveness/virulence among the isolates on rice, soybean and tomato were examined by greenhouse inoculation tests. Molecular markers showed a substantial degree of genetic variation. A considerable range in pathogenicity/virulence and a significant correlation among the disease severity among isolates in each crop, as well as differences in lesion type were detected in the inoculation experiments. The results indicated a high level of genetic and pathologic/virulence diversity among Rhizoctonia spp. associated with rice ShB in AR. Although the R. solani AG 1 - IA population the rice-growing areas of Texas and Louisiana have been described, there have been no systematic studies on the structure of the R. solani AG 1 - IA population associated with rice in AR. Thus, a second objective was to conduct an in-depth genetic and genotypic analysis of the rice ShB pathogen population using multilocus sequencing analysis of six nuclear loci and SSR diversity. The results indicated that that both nuclear and SSR loci identified a high number of multilocus genotypes. The analysis indicated that the population structure of R. solani AG 1 - IA in AR may have a mixed model of reproduction that includes some extent of clonal expansion and a significant sexual reproductive component (suggested by the high genotypic diversity, and the significant degree of inbreeding observed). These data are consistent with the population structure previously described for R. solani AG 1 - IA populations in Texas and Louisiana. Toxin production has been documented for more than 20 fungal plant pathogens, R. solani AG 1 - IA. The third objective of this study was to examine the production of specific toxins among isolates of R. solani and related species, and assess its correlation with pathogenicity/virulence. The ability to produce toxin was assessed by the presence of a signature peak in high pressure liquid chromatography (HPLC) assays. Among the R. solani isolates, the signature HPLC peak was detected not only in the R. solani AG 1 - IA isolates, but also in isolates from other genetically distinct anastomosis groups (AGs 1 - IC, 2, 3, 4, 7, and 8).Likewise, isolates of R. oryzae, R. o. sativae, R. zeae, R. cerealis and Sclerotium hydrophilum produce a HPLC peak which may indicate that they produce a similar toxin o the one produced by R. solani AG 1 - IA. In addition, the same toxin suspensions used for HPLC analysis, produced necrotic lesions in leaves of the rice cv. `Cypress' (ShB susceptible) in leaves infiltration bioassays. In general, results indicated that there is an association between the capacity of an isolate to produce the toxin, the ability of this toxin to cause necrosis in susceptible host tissue, and the capacity of the isolate to cause disease in greenhouse inoculation tests. However, exceptions of highly virulent isolates with undetectable levels of toxin production, and of isolates with low level of virulence but high levels of toxin production were observed. In rice, the resistance to ShB is a quantitative trait controlled by multiple genes and immunity to ShB has not been identified in any rice germplasm. However different levels of resistance to ShB have been observed among diverse cultivars. A fourth objective was to evaluate the segregation of ShB resistance in a population of 299 F2:5 lines derived from the cross of two elite Indica cultivars, `Fedearroz 2000' (susceptible) x `Palmar' (resistant), and map for potentially new quantitative trait loci associated with resistance to ShB (SB-QTLs). The analysis indicated that there were five significant SB-QTLs on chromosomes 5, 8, 9 and 11 that explained between 5.7 % and 12.6 % of the phenotypic variation associated with resistance to ShB. Among these, the QTL in chromosome 9 (qSB-9) was identified based on both field and greenhouse phenotyping analysis, and it was independent from other morphological traits (plant height and days to heading). Furthermore, the QTL on chromosome 5 (qSB-5) was disassociated from morphological traits, and according to previous reports, it might be a source of resistance to ShB only found in Indica germplasm. The research described in these studies have provided considerable information on the genotypic and phenotypic diversity of the ShB pathogen in Arkansas and the identification of possible new sources of resistance. These data will contribute to an increased the understanding of ShB-rice pathosystem and assist in efforts to improve disease management efforts and improve the effectiveness of ShB resistance breeding programs.

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