Analysis Of QTL And Ph-3 Gene Conferring The Resistance To Late Blight (Phytophthora Infestans) In Tomato

Late blight (LB), caused by the Oomycetes Phytophthora infestans (Mont.) de Bary, is a worldwide disease, mainly affecting the production of potato and tomato. In the past decades, a number of LB resistance genes have been cloned from potato. In contrast, much less work has been conducted on LB resistance in tomato. The purpose of this study was to analyze genetics and genomics of LB resistance in tomato species, based on quantitative and qualitative resistance resources. As the first report in this study, fine mapping of Ph-3 gene for LB resistance in tomato has been done, which would facilitate marker-assisted selection as well as the clone of this gene. The main contents and results in this study are as follows:(1) Solanum lycopersicoides LA2951 introgression line population were screened by detached-leaf assay with two different P. infestans race (T1,2 and T1,2,4) in order to identify the potential resistance loci in this wild relative. The results indicated that the resistance of this wild relative was controlled by quantitative trait loci (QTL). In total, five QTLs (Rpiq1b, Rpiq2b, Rpiq4b, Rpiq8a, Rpiq11) were identified after inoculation with race T1,2, which significantly reduced lesion size (LS), and three QTLs (Rpiq1a, Rpiq2a, Rpiq8b) were indentified, which clearly reduced disease incidence (DI). However, only two QTL (Rpiq4a and Rpiq5) reducing DI were indentified after inoculation with more virulent race T1,2,4. It proved that QTLs derived from LA2951 showed a clear race-specific resistance. Based on tomato high density genetic linkage map, all QTLs detected in this paper were co-localized with those previously identified in other tomato wild species. In addition, two susceptibility QTLs (Spiq4 and Spiq10) increasing DI were identified after inoculation with both race T1,2 and race T1,2,4.(2) Fine mapping of tomato LB resistance gene Ph-3 was conducted with F2 segregating population derived from a susceptible line LA3514 as male parent crossing with CLN2037B as a female parent. Based on tomato genome sequence, 146 pairs of PCR primers were developed, and 21 pairs of polymorphic markers between two parental lines which distributed evenly on the chromosome were used for the construction of a high-resolution genetic map. Meanwhile, the disease evaluation of F2 population was conducted, which indicated a monogenic segregating ration (χ23:1=1.95, P=0.16). Combination with the genotypes and phenotypes of F2 individuals, Ph-3 gene was mapped within 0.5 cM on chromosome 9, and the genetic distances between Ph-3 gene and flanking markers Indel₃ and P55 were 0.1 cM and 0.4 cM, respectively.(3) The SCAR marker RGA2M1 obtained presented a co-dominant character, which amplified a 800 bp band from susceptible parent, and a 500 bp band from resistant parent. To confirm the efficiency of this marker, 23 different tomato lines were used to confirm it, and most of them produced the consistent band patterns with resistance or susceptibility to P. infestans. Although it provides a convenient way for the marker-assisted selection of Ph-3 gene, the further manipulation still needs to be done as a functional marker. (4) Based on S. lycopersicum H1706 genome sequence as a reference, the flanking markers Indel₃ and P55 was localized within a 74 kb region, which contained 8 genes. Four of them showed a typical NB-ARC motif for plant resistance genes, and clustered on the chromosome. Reasonablely, these four RGAs were considered as the candidate alleles of Ph-3 gene. BLAST showed that four RGAs were homologous with Rpi-vnt1.1 conferring the resistance to late blight in potato.(5) A preliminary analysis of interactions of QTLs or/and R genes was conducted using resistance loci from wild tomato species S. pennellii, S. habrochaites, S. lycopersicoides and S. pimpinellifolium. It seemed that the majority of QTL showed recessive inheritance or smaller effect. Intraspecific interactions of QTLs usually showed the antagonism, while interapecific interactions of QTLs were complicated. Interactions of QTLs and single genes mainly depended on the genetic background of QTLs. However, the results still need to be further verified with more independent experiments.