Potato breeding has been performed at the Vokė Branch of the Lithuanian Institute of Agriculture since 1958. The key objective of potato breeding is to produce early potato cultivars immune to wart disease Synchytrium endobioticum (Schilb.), resistant to Globodera rostochiensis (Woll.) pathotype of nematodes and major potato diseases. As a result of the breeding work seven potato cultivars of different maturity have been selected. Based on the high disease and pest resistance records, the cultivars and promising hybrids from this breeding program have been recommended for cultivation on ecological farms.

Potato (Solanum tuberosum L.) late blight, caused by Phytophthora infestans (Mont.) de Bary, is one of the most damaging diseases in any crop. Deployment of resistant varieties is the most effective way to control this disease. However, breeding for late blight resistance has been a challenge because the race-specific resistance genes introgressed from wild potato S. demissum Lindl. have been short lived and breeding for “horizontal” or durable resistance has achieved only moderate successes. We previously demonstrated that the high-level late blight resistance in a wild potato relative, S. bulbocastanum Dunal subsp. bulbocastanum, is mainly controlled by a single resistance gene RB Transgenic potato lines containing the RB gene have showed strong late blight resistance, comparable to the backcrossed progenies derived from the somatic hybrids between potato and S. bulbocastanum Here we report the development of a polymerase chain reaction-based DNA marker for tracking the RB gene in breeding populations derived from the potato × S. bulbocastanum somatic hybrids. Several marker-positive breeding lines showed the expected late blight resistance in greenhouse evaluations. Our results demonstrate that marker-based selection will allow us to effectively transfer the RB gene into potato using traditional breeding methods, an alternative to deploying the RB gene through genetic transformation.

Potato (Solanum tuberosum L.) late blight, caused by Phytophthora infestans (Mont.) de Bary, is one of the most damaging diseases in any crop. Deployment of resistant varieties is the most effective way to control this disease. However, breeding for late blight resistance has been a challenge because the race-specific resistance genes introgressed from wild potato S. demissum Lindl. have been short lived and breeding for "horizontal" or durable resistance has achieved only moderate successes. We previously demonstrated that the high-level late blight resistance in a wild potato relative, S. bulbocastanum Dunal subsp. bulbocastanum, is mainly controlled by a single resistance gene RB. Transgenic potato lines containing the RB gene have showed strong late blight resistance, comparable to the backcrossed progenies derived from the somatic hybrids between potato and S. bulbocastanum. Here we report the development of a polymerase chain reaction-based DNA marker for tracking the RB gene in breeding populations derived from the potato x S. bulbocastanum somatic hybrids. Several marker-positive breeding lines showed the expected late blight resistance in greenhouse evaluations. Our results demonstrate that marker-based selection will allow us to effectively transfer the RB gene into potato using traditional breeding methods, an alternative to deploying the RB gene through genetic transformation.

Amplified fragment length polymorphism (AFLP) was conducted on a set of 92 Nicotiana tabacum L. accessions from diverse types (flue-cured, dark air-cured, burley, oriental, and cigar wrapper) and breeding origins to identify markers associated with disease resistances. Eleven primer combinations were required to identify 33 polymorphic fragments. This allowed the identification of 92% of these accessions, and yielded sufficient information for building a neighbor joining tree. Clusters of accessions with common traits or breeding origins were observed. An important part of this polymorphism could be related to interspecific introgressions from other Nicotiana species, performed during the breeding history of N. tabacum to confer resistance to pathogens. Seven fragments were associated with three different resistances: two for the blue-mold (Peronospora tabacina Adam) resistance derived from Nicotiana debneyi Domin, two for the Va gene (Potato Virus Y susceptibility), and three for the black root rot (Chalara elegans) resistance of N. debneyi origin. Some of these markers were converted into sequence characterized amplified region markers, and validated on recombinant inbred lines or doubled-haploid lines.

Horizontal resistance to late blight with quantitative and durable characteristics is a major objective for potato breeding programs. With the aim of investigating the molecular aspects of horizontal resistance, a cDNA microarray was used to identify Phytophthora infestans-induced genes from 100 expressed sequence tags (ESTs) selected from a subtractive cDNA library. Of the 100 cDNA clones represented on the array, 76 were differentially expressed in infected plants as compared with mock-inoculated control plants. Four groups of genes could be identified according to their expression patterns at three time points, 24, 48 and 72 h postinoculation (hpi). Group A appeared to be strongly induced (>10-fold) at 72 hpi. Group B demonstrated up-regulated expression patterns at all the three time points. The transcripts of group C peaked at 48 hpi, while genes of group D were up-regulated at 24 hpi and decreased slightly thereafter. Blast algorithm searches revealed that the largest set of up-regulated genes (about 35%) was assigned to the primary/secondary metabolism. Other genes with known or putative functions included disease defense or cell rescue (about 18%), transcription, signal transduction, cellular transporter/transport facilitation, development, protein synthesis/destination, as well as those playing roles in cellular organization. Furthermore, 15 genes encoding unknown function proteins were also identified. The results indicated that multiple defense mechanisms are involved in horizontal potato resistance to late blight and alteration in metabolic pathways is one of the most important defense responses.

Thirty-five varieties/lines/clones were evaluated against natural and graft-inoculation of potato leaf roll virus and its vector Myzus persicae Suiz. under field conditions and in pots grown in greenhouse. Disease ratings taken according to a PLRV scale on field and graft-inoculated greenhouse grown plants, PLRV response on indicator plants, aphid population density and DAS-ELISA were the criteria to determine the level of resistance or susceptibility in the potato germplasm. None of the entries was immune or highly resistant to PLRV. The varieties/lines/clones viz., CIP 384046-3, CIP 391202-159, CIP 394033-82, TPS-9808, P. 332826, P. 332831 Bertina x Cardinal, Kiran, and Fd-4-2 were resistant. Dura and Sante were moderately resistant, CIP 391202-40, Desiree x Juse B, FSD-Red, Diamont and SH-20 were susceptible while the remaining 19 varieties/ lines/clones were moderately susceptible to PLRV. Aphid population per plant varied 2 to 11 under field conditions and 1-3 on the greenhouse grown plants with comparatively less aphid population (1-3) on the varieties/ lines/clones showing resistant response to PLRV. The scarcity of resistance in the majority of the varieties/lines/clones suggests the initiation of a strong breeding programme and aphid monitoring in relation to epidemiological factors to develop strategies to suppress PLRV inoculum level and M. persicae density below the economic threshold level.

Sweetpotato virus disease (SPVD), the most important virus disease of sweetpotato (Ipomoea batatas (L) Lam.), is caused by the synergistic interaction of whitefly-transmitted crinivirus Sweet Potato Chlorotic Stunt (SPCSV), and the aphid-transmitted potyvirus Sweet Potato Feathery Mottle Virus (SPFMV). The presence of SPFMV, SPCSV and Sweet Potato Chlorotic Fleck Virus (SPCFV) using CIP (International Potato Center)-developed NCM ELISA kit was detected in some sweetpotato commercial growing areas in the country. Double infection of SPFMV and SPCSV was found to be the most prevalent, causing the SPVD in these areas. The SPCSV was isolated from the complex virus using whitefly-transmission into propagation hosts (I. setosa and I. nil) and typical symptoms of vein clearing and sunken vein were observed on the diseased susceptible plants. Reverse-transcriptase polymerase chain reaction (RT-PCR) resulted to the positive amplification of the 460bp heat shock protein 70 homologue (HSP70h) fragment for the Ablang (Tarlac), Rang-ayan (Tarlac), Saysain (Bataan), Tranca (Laguna), Tanato (Bataan), ViSCA (Leyte) and Nagbunga (Zambales) isolates using primers specific to non-East African strains. Nucleic acid from the partial Hsp70h gene of Ablang (Tarlac), Rang-ayan (Tarlac), Saysain (Bataan), Tranca (Laguna) and Tanato (Bataan) isolates were sequenced with 99.3-100 percent and 97.2-100 percent homology based on nucleotide (nt) and derived amino acid sequences, respectively. All isolates obtained from Central Luzon were found to be 100 percent similar based on the deduced amino acid sequence. The Tranca isolate had variation of 99.1-99.5 percent on nt and 98.6 percent on deduced amino acid as compared to the other Philippine isolates. Phylogenetic analysis of the partial Hsp70h gene indicated that all the Philippine SPCSV isolates obtained belongs to the non-East African (NEA) strain group of SPCSV that confirmed the presence of SPCSV NEA strains in the Philippines. Comparison of the partial Hsp70h sequence of the four isolates to previously described sequences of Hsp70h of East Africa (EA) and NEA strains generated nt homology between 74.2-77.8 percent and derived amino acid similarity of 89.1-92.5 percent. The high sequence variation of EA and NEA SPCSV strains is not only relevant in the improvement of indexing methods of planting materials for quarantine measure but should also be considered in planning sustainable control strategies against SPVD, and for deploying various forms of resistance in sweetpotato breeding program.

The advent of DNA-marker technology has made the detection of quantitative trait loci (QTLs) a routine activity in plant breeding. While standard procedures are available for QTL mapping, more flexible strategies are required to analyse the complex data typically produced by plant breeding programs. This thesis presents a general and flexible mixed model QTL mapping approach. The philosophy is to include genotypic information derived from molecular markers as explanatory variables to model complex phenotypic responses, while exploiting the flexibility of mixed models to account for complex variance-covariance structures in the data. Attractive generalisations of our QTL models incorporate explicit information on genotypes and environments, for example, as obtained from crop growth models, thereby opening the way to eco-physiological QTL models.The application of the methodology to cases commonly found in plant breeding is illustrated throughout the various chapters of the thesis. In chapter 2, a QTL model is presented for probably the most typical experimental set up in plant breeding, the multi-environment trial. The QTL model describes the genetic basis of genotype by environment interaction for a single trait and tests for environment-specific QTL effects (QTL by environment interaction). After detection of QTLs underlying genotype by environment interaction, the model is extended to make QTL expression dependent on environmental variables. In a reanalysis of yield data stemming from the North American Barley Genome Mapping Project (NABGMP), a QTL for yield was detected on barley chromosome 2H whose effect was proportional to the temperature range at heading time. In chapter 3, the single trait multi-environment model is elaborated to the multi-trait multi-environment situation. We show with another reanalysis of data from the NABGMP how questions related to pleiotropy and genetic linkage as causing genetic correlations between traits can be addressed. Both pleiotropic and linked QTLs were found to explain genetic correlations between heading date and yield. In chapter 4, the linear mixed model is generalised to a non-linear mixed model to describe parameters of a growth curve as a function of QTL effects. The approach is illustrated by an example on potato leaf senescence. QTLs were identified that affect growth trajectories in different ways, thereby contributing to a better understanding of the genetic control of complex traits over time. In chapter 5, we show that not only designed bi-parental cross populations can be naturally handled by mixed model QTL formulations, but also non-designed populations within association mapping approaches. With another example in potato, we analyse historical disease resistance data produced over 25 years of potato variety trial testing in combination with targeted molecular marker techniques to detect interesting markers for breeders. Pedigree information was used to improve the modelling of genetic variances and correlations between genotypes. An association mapping approach using mixed models incorporating pedigree information performed better than commonly used association mapping strategies. Significant associations were detected that proved to be consistent when tested in a confirmatory data set. Finally, chapter 6 consists in a discussion of the mixed model approach as a general framework for QTL mapping in plant breeding.