Phenotypic and genotypic structure of Phytophthora infestans populations on tomato and potato in the North of Thailand in 2000–2002

A total of 80 single–lesion isolates of Phytophthora infestans were collected from tomatoes and potatoes in several locations in Chiang Mai and Tak provinces in 2000–2002. These isolates were analyzed for mating type, metalaxyl sensitivity, mitochondrial DNA (mtDNA) haplotype RFLP pattern as determined by probe RG57, and for microsatellite markers. All isolates were A1 mating type. Isolates from tomato were usually sensitive to metalaxyl, but isolates from potato were usually resistant to metalaxyl. With one exception, all tomato isolates were related to the US-1 clonal lineage. With two exceptions, all potato isolates were related to two European lineages. In these two provinces, the populations of P. infestans on tomatoes are clearly different from those on potatoes.     

SSR-based and grain yield-based diversity of hybrid maize in Thailand

Commercial hybrid maize varieties are often used to extract new inbred lines in hybrid breeding programs. Seven commercial hybrid maize varieties were crossed in a diallel design, and the resulting hybrids and selfed progeny were evaluated for yield and adaptability grown in six locations in Thailand. The parental varieties were analyzed with a set of 64 Simple Sequence Repeat (SSR) loci, spanning all 10 chromosomes. The average number of alleles per SSR locus was 4.98 with a range of 2–11. The polymorphic information content (PIC) varied from 0.24 to 0.89, with an average of 0.69. Using SSR-based genetic distance (GD), an UPGMA dendrogram showed seven field corn varieties classified into three distinct groups. Troyer's genetic distance (TGD) calculated from yield data, which is a function of inbreeding depression, varied from 0.493 to 1.015 between different parental combinations. A significant positive correlation was found between the GD and TGD across the six locations (0.66^**). The GD correlated positively with specific combining ability (SCA) as well across all locations (r = 0.76^**) heterosis was significant for grain yield and SCA, accounting for 47% of the sum of the square among entries. Therefore, we suggest that broad base populations derived from each of the distinct groups can be formed using combined criteria of SSR-based GD, TGD, grain yield, GCA and SCA.     

Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association

Association mapping relies on the variation and extent of linkage disequilibrium within a species to identify genes of interest; this is an alternative to linkage mapping in traditional biparental population, which exploits only the variation in the two parents of the mapping population. This study was designed to identify association between 48 SSR markers and downy mildew (DM) resistance using a set of 60 public and private maize inbred lines in Thailand. Genetic diversity and population structure in the set were calculated. A total of 489 alleles with an average gene diversity of 0.70 revealed two subpopulations among the 60 maize inbred lines. Analysis of variance resulted in significant effects of phenotypic values of tested entries, with significant effects of inbred lines, locations, and their interaction. In addition, the analysis of variance for broad sense heritability also indicated high heritability (0.97), and association analysis revealed three significant SSR-trait associations (P < 0.05). These three significant SSR loci have not been reported in previous linkage mapping studies. Our results suggest that new allelic variants associated with DM resistance in these germplasm collections should be useful to help identify new lines carrying alleles for DM resistance in breeding marker-assisted selection programs.     

Detection of candidate R genes and single nucleotide polymorphisms for downy mildew resistance in maize inbred lines by association analysis

Downy mildew (DM) is a plant disease that strongly limits maize production. The resistance (R) genes for this disease have been identified and characterized and serve as important tools for plant disease evaluation. In this study, partial genes for PIC15, PO145579, and zmcf5 were identified and analyzed in a panel of 60 public and private maize inbred lines using bioinformatics and statistics tools. These candidate R genes exhibited an average nucleotide diversity value of 0.015. The negative Tajima’s D values for these genes suggested that purifying selection has played a role in the evolution of maize DM resistance genes. In addition, linkage disequilibrium among these genes occurred across an extent of ~ 200 bp. Using association analysis methods, a general linear model, and a mixed linear model, five polymorphisms within the partial PIC15 and PO145579 genes were detected and associated with DM disease. These are new polymorphisms that have not previously been reported in association with DM disease traits. Therefore, correlations between these new polymorphisms and DM disease in these germplasm collections could advance the development of a functional marker for marker-assisted selection of DM disease resistance in maize breeding programs.     

Development and Characterization of Microsatellite Markers from an Enriched Genomic Library of Cucumber (Cucumis sativus)

The development, characterization and application of cucumber ( Cucumis sativus L.) microsatellite markers was accomplished using a library-enrichment procedure. Fifty-seven primer pairs flanking the microsatellite repeats were used for DNA amplification. Sixteen C. sativus accessions were assessed for polymorphisms using 45 primer pairs. The average number of alleles per locus was 3.6, and up to seven alleles were found at one locus. The maximum polymorphism information content value was 0.78 with an average of 0.47. The cucumber microsatellite makers could be useful for seed purity control in hybridity testing. Some of these cucumber markers were transferable to other cucurbit species (i.e. melon, watermelon, pumpkin and bitter gourd).     

Molecular Markers and Candidate Genes for Thermo-Sensitive Genic Male Sterile in Rice

The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations derived from crosses between IR68301 S, an indica TGMS rice line, and IR14632(tropical japonica), Supanburi 91062(indica) and IR67966-188-2-2-1(tropical japonica), respectively.Approximately 1:3 ratio between sterile and normal pollen of F_2 plants from the three populations revealed that TGMS is controlled by a single recessive gene. Bulked segregant analysis using simple sequence repeat(SSR) and insertion-deletion(InDel) markers were used to identify markers linked to the tms gene. The linkage analysis based on the three populations indicated that the tms locus was located on chromosome 2 covering the same area. Using IR68301S × IR14632 F_2 population, the results showed that the tms locus was located between SSR marker RM12676 and InDel marker 2gAP0050058. The genetic distance from the tms gene to these two flanking markers were 1.10 and 0.82 cM, respectively.InDel marker 2gAP004045 located between these two markers showed complete co-segregation with the TGMS phenotype. In addition, InDel marker vf0206114052 showed 2.94 cM linked to the tms gene using F_2 populations of IR68301S × Supanburi 91062. These markers are useful tool for developing new TGMS lines by marker-assisted selection. There were ten genes located between the two flanking markers RM12676 and 2gAP0050058. Using quantitative real-time PCR for expression analysis, 7 of the 10 genes showed expression in panicles, and response to temperatures. These genes could be the candidate gene controlling TGMS in IR68301S.