Segregation Analysis of SSR, SNP, and AFLP Markers in F2 Population of Solanum lycopersicum × S. arcanum (Analisis Segregasi Marka SSR, SNP, dan AFLP pada Populasi F2 Persilangan Solanum lycopersicum × S. arcanum)

Distorted marker segregation is a common phenomenon in interspecific cross of various crops. Previous mapping study of earlyblight fungus (Alternaria solani) resistance loci showed 52% marker distortion in the genetic linkage map of 176 F2 progeniesderived from Solanum lycopersicum cv. Solentos × S. arcanum LA2157. The objectives of this study were to analyze in detail themarker segregation in the map and to determine the cause of segregation distortion by calculating the allele and genotypefrequencies of each marker. Out of 371 mapped markers, 192 markers deviated from the expected Mendelian ratio of 1 : 2 : 1.Distorted markers occurred in all chromosomes, ranging from 1% to 92%. Surplus of S. arcanum homozygotes contributed mostto the skewness (40%), followed by heterozygotes (18%), and S. lycopersicum homozygotes (5%). The allele frequencies of 152markers deviated from the expected allele homogeneity frequency, indicating that their segregation might be affected bygamethophytic selection. Sixty-one markers deviated from the expected F2 genotype frequency distribution, indicating that theirsegregation might be influenced by zygotic selection. Thirty-seven of the distorted markers showed deviation from expectedfrequencies of allele homogeneity and F2 genotype frequency distribution. Distorted markers can be retained in linkage analysissince chromosomal regions containing distorted markers showed linkage with early blight fungus resistance loci. Furtheridentification of the mechanism contributing segregation distortion requires detailed and extensive mapping studies

Teori dan Aplikasi Optimisasi Dalam Masalah Strategi Vaksinasi

Paper ini membahas teori dan aplikasi bidang matematika riset operasi dan optimisasi pada masalah strategi vaksinasi dari kajian literatur hasil penelitian Hethcote dan Waltman (1973), Tanner dkk. (2008), Zaman dkk. (2008) dan beberapa hasil penelitian lainnya. Fokus utama pembahasan paper ini adalah memberikan argumentasi untuk menjamin pentingnya pemodelan optimisasi dalam masalah matematika epidemiologi, dengan topik kajian yang spesifik dalam masalah penentuan strategi vaksinasi yang optimal. Untuk memberikan pemahaman yang lebih baik tentang penentuan strategi vaksinasi, pada akhir pembahasan paper ini, disajikan aplikasi teori riset operasi dan optimisasi matematika epidemiologi pada penyakit tuberkulosis dari hasil penelitian Revelle dkk. (1969). Kata kunci: optimisasi, strategi vaksinasi, matematika epidemiologi

Variation In Aggressiveness And Aflp Among Alternaria Solani Isolates From Indonesia

Alternaria solani is a necrotroph fungus that causes three-phased diseases in tomato. Management of the pathogen by using resistant cultivars requires knowledge on the aggressiveness and genetic diversity of the fungus. The aims of this study were to isolate A. solani from major tomato and potato producing areas in Indonesia and to study their aggressiveness and genetic variability. Twenty two A. solani isolates were recovered from early blighted tomato and potato in Central and West Java. A. alternata was also isolated from tomato leaves in West Java and North Sumatra, indicating that early blight in Indonesia may be caused by more than one Alternaria species. Resistance tests of four tomato genotypes to selected A. solani isolates revealed that local isolates were more aggressive in inciting early blight and stem lesion than an imported isolate from USA. This implies that introduced breeding materials must be tested to local isolates to obtain effective resistance genes. Cluster analysis based on amplified fragment length polymorphism (AFLP) obtained from EcoRI+AG and MseI+C primer amplification separated 28 local and Taiwan isolates from the US isolate, which was coincided with aggressiveness separation between the local isolates and the US isolate. Three clusters of AFLP genotypes which did not associate with geographic origin were observed among tropical isolates. The low genetic diversity among the Indonesian isolates suggests clonal population structure with wide distribution. Successful local tomato breeding requires the availability of local A. solani collection with well-characterized aggressiveness level and molecular diversity to obtain effective resistance genes

QTL identification for early blight resistance (Alternaria solani) in a Solanum lycopersicum x S. arcanum cross.

Alternaria solani (Ellis and Martin) Sorauer, the causal agent of early blight (EB) disease, infects aerial parts of tomato at both seedling and adult plant stages. Resistant cultivars would facilitate a sustainable EB management. EB resistance is a quantitatively expressed character, a fact that has hampered effective breeding. In order to identify and estimate the effect of genes conditioning resistance to EB, a quantitative trait loci (QTL) mapping study was performed in F2 and F3 populations derived from the cross between the susceptible Solanum lycopersicum (syn. Lycopersicon esculentum) cv. `Solentos¿ and the resistant Solanum arcanum (syn. Lycopersicon peruvianum) LA2157 and genotyped with AFLP, microsatellite and SNP markers. Two evaluation criteria of resistance were used: measurements of EB lesion growth on the F2 plants in glasshouse tests and visual ratings of EB severity on foliage of the F3 lines in a field test. A total of six QTL regions were mapped on chromosomes 1, 2, 5¿7, and 9 with LOD scores ranging from 3.4 to 17.5. Three EB QTL also confer resistance to stem lesions in the field, which has not been reported before. All QTL displayed significant additive gene action; in some cases a dominance effect was found. Additive × additive epistatic interactions were detected between one pair of QTL. For two QTL, the susceptible parent contributed resistance alleles to both EB and stem lesion resistance. Three of the QTL showed an effect in all tests despite methodological and environmental differences

Early blight resistance in tomato: screening and genetic study

Tomato early blight (EB) caused by the fungus Alternaria solani is a field disease with a worldwide distribution, including Indonesia. The disease is currently controlled using frequent applications of fungicides. The use of resistant cultivar would be an attractive way to reduce fungicide application. The aims of the research are to support breeding of EB resistance cultivars for the Indonesian market, by identifying EB resistance genes effective in Indonesia and developing markers for MAS.In Chapter 1 the literature on A. solani, EB and resistance is reviewed. On the fungal side pathogenicity and genetic variation have been widely investigated. However, the existence of different physiological races has not been convincingly demonstrated or disproved. Reliable methods of screening are available for use in resistance breeding. Intensive screening of tomato accessions worldwide has shown that strong resistance is not available in the cultivated tomato but only in wild species. Resistance to A. solani is expressed quantitatively and is polygenically inherited. For that reason classical breeding has not been able to achieve high levels of resistance, and undesirable traits from the donors have been introgressed as well. Recently QTLs have been mapped in a few resistance sources, which could facilitate transferring such quantitative resistance genes and circumvent the problem of unfavourable linkage drag once markers tightly linked to the QTLs have been obtained.In Chapter 2 a resistance test method involving droplet inoculation is described, which is an adaptation of an existing but hardly-used technique. This method has advantages in comparison with the more widely used spray inoculation method, including a clear distinction between lesions caused by A. solani and necroses of 1eaf loss due to other causes, and an objective measurement of damage in contrast to subjective scoring. In the droplet inoculation method leaflets of intact plants are inoculated with droplets of an A. solani conidial suspension in water or an agar solution. Lesions are assessed quantitatively by measuring the length and the perpendicular width. In this way objective and accurate assessments, which are prerequisites for QTL analysis, can be achieved. This inoculation method was used to screen a collection of 54 tomato accessions for resistance to an Indonesian A. solani isolate,S. arcanum LA2157 is highly resistant to A. solani in the glasshouse screening tests. The genetics of the resistance in this wild relative of tomato was further studied using a QTL mapping approach (Chapter 3). The mapping population consisted of 176 F2 plants. A linkage map consisting of 12 linkage groups covering 1179 cM was based on 379 markers (33 SSR, 21 SNP and 316 AFLP markers). All linkage groups could be assigned to the 12 tomato chromosomes. About half of the markers showed deviation from the expected 1:2:1 segregation ratio. The F2 population was phenotyped in a glasshouse in Netherlands with an Indonesian isolate of A. solani. EB resistance was evaluated with respect to lesion size (LS) and related parameters (relative area under the lesion expansion curve [RAULEC] and percentage of small lesions [PSmL]). The derived F3 lines (156) were tested in a field in Indonesia. Percentage of EB index (PEBI) was assessed at six times and relative area under the disease progress curve (RAUDPC) was calculated. A total of six QTLs with a range of LOD scores 3.6 to 16.4 were mapped on chromosomes 1, 2, 5, 6, 7 and 9. Three of the QTLs showed effects in both tests despite differences in experimental method and observed traits. For the first time, three QTLs for resistance affecting the development of stem lesions, another disease symptom caused by the fungus on the main and secondary stems of the plant, were identified, which completely overlapped with QTL regions for early blight resistance. Two QTLs on chromosomes 2 and 9, which explained 7 to 16% of the phenotypic variation for EB resistance and 31% for stem lesion resistance, are recommended to be used in tomato breeding programs for resistance to A. solani