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Key words: Potato (Solanum tuberosum L.), segregating population, canopy cover dynamics, tuber bulking dynamics, beta function, thermal time, components of variance, genotype-by-environment interaction (GE), heritability, QTL mapping, QTL-by-environment (QTLE) interaction, complex traits, ecophysiological crop model, GECROS, cultivar choice, maturity type, ideotype breeding, tuber yield. Due to increasing food demand and changing diets potato (Solanum tuberosum L.) is becoming a subsistence crop in many regions. However, the agronomy and whole crop physiology of tuber yield production is extremely complex, due to genotype and environment specific effects on crop physiological and morphological characteristics. Such intrinsic complexities complicate the manipulation of yield determining traits and make their prediction a challenging task. The genetic improvement of tuber yield can be understood more mechanistically by investigating and interpreting the relationships between the main attributes of crop growth. This thesis aims to develop an approach to quantify the yield of individual genotypes and to estimate parameters which may reveal the effects of genetic and environmental factors on the important plant processes controlling tuber yield variation among a large set of F1 (SH83-92-488  RH89-039-16) genotypes of potato and a set of standard cultivars covering a wide range of maturity types. It first presents a model approach to analyse the time course of canopy cover and tuber bulking during the entire crop cycle as a function of thermal time in terms of large number of physiological component traits and explain their inter-relationships and impact on crop maturity and tuber yield production across six contrasting field experiments. The results indicated that the length of the canopy build-up phase (DP1) was conservative with respect to genotype’s maturity type, but the duration of maximum canopy cover (DP2) and the decline phase (DP3) varied greatly, with later genotypes having longer DP2 and DP3 and thus a higher area under whole green canopy curve (Asum). Values of tuber bulking rate (cm) were highest for early maturing genotypes followed by mid-late and then late genotypes. Late maturing genotypes had longest effective duration of tuber bulking (ED) followed by mid-late and early genotypes. As a result tuber yield (wmax) was higher in late genotypes than in early genotypes. The radiation use efficiency (RUE) values were highest for early maturing genotypes followed by mid-late and late genotypes whereas nitrogen (N) use efficiency (NUE) was highest in late maturing genotypes followed by mid-early and early genotypes. High genetic variability and high heritability for most of these traits were found. Results indicated that increased tuber yield by indirect selection for optimal combination of important physiological traits can be achieved. While using these traits as a criterion for selection, the causal physiological relationships and trade-offs must be considered simultaneously. Our molecular dissection of traits determining the dynamics of canopy cover, tuber bulking, and resource (radiation, nitrogen) use efficiencies identified several QTLs, the mapping position of each identified QTL, the interaction of QTL with environment (QTLE) and the magnitude of the QTL effect in explaining genetic variance in both SH and RH parental genomes. The QTL results indicated that one particular chromosomal position at 18.2 cM on paternal (RH) linkage group V was tightly linked to the genotype’s earliness and controlling nearly all the traits and explaining the phenotypic variance by up to 79%. This suggested the pleiotropic nature of the QTL for most of the traits determining crop maturity and tuber yields. A number of QTLs for traits were not detected when tuber yield per se was subjected to QTL analysis. The phenotypic variance explained by the QTLs for tuber yield per se was also lower than for other traits. The physiological and quantitative knowledge gained was used to evaluate the conventional system of maturity type and to quantify and re-define the concept of maturity type on a physiological basis for a large set of genotypes. Four new physiological based maturity criteria were developed based on four canopy cover and tuber bulking traits. Physiological maturity type criteria tended to define maturity classes less ambiguously and were easily and clearly interpretable compared to the conventionally used method of defining maturity. The capability of an ecophysiological model ‘GECROS’ was tested to analyse differences in tuber yield of potato. The model yielded a reasonably good prediction of differences in tuber yield across environments and across genotypes. Model analysis identified the genotypic key-parameters affecting tuber yield production and Nmax (i.e. total crop N uptake) contributed most to the determination of tuber yield. The results concluded that genotypes with higher Nmax and lower tuber N content exhibited higher tuber dry matter yield. Further analysis of the genotypic parameters should be performed in conjunction with molecular markers in order to determine their genetic control and to proceed towards QTL-based crop modelling approach. This thesis identified the dominant component traits mostly involved in the formation of a tuber yield and gave insight into the possibilities of genetically and physiologically manipulating the size or number of such traits. The information obtained should help in marker-assisted selection as well as in designing ideotypes for specific and/or diverse environments. However, to make significant contributions for breeding, there is a need for further research efforts to evaluate the combined physiological and genetic approach.

Wageningen UR Plant Breeding has carried out studies on different developmental processes of potato making use of a segregating population evaluated in the field under different environmental conditions and day length regimens. The field trials have included the evaluation of below and above ground traits during different stages of the growing season. Extensive molecular data is available on this experimental potato population as well. Thus, this population provided an excellent opportunity for genetic studies based on information previously generated in research projects making use of statistical methods and models to integrate the different data sets and developmental stages. We have been able to get insights about the correlation between above and below ground traits over different environments, to identify stable QTLs under different multi-location and multi-year field trials, as well as QTLxE interactions. Valuable information have been generated regarding stability of developmental traits and common genetic factors influencing them. In this sense our study brings new insights related with potato development and adaptation to different environmental conditions.

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.

Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. Inthisstudyweexploredlinkagedisequilibrium(LD)mappingof traits in a set of modernbarleycultivars. LDbetweenmolecularmarkerswasfoundup to a distance of 10 centimorgan,whichislargecomparedtootherspecies.Thelarge distancemightbeinducedby LDincreasingfactorssuchasinbreedingandthefactthatthepopulationismostlikelybasedon arathersmallset offoundinggenotypes. Associationsbetweenmarkersandtraitswerefoundforyield,yieldstability,leafrustresistance(LR),barleyyellowdwarfvirusresistance(BYD), plantheight,anddaystoheading.Trait-associatedmarkersfromLDanalysiswerelocatedinregionswherealreadyQTLsforthetraitconsideredhadbeenreportedfromstudiesbasedonbi-parentalcrosses. In addition, newQTLswerefoundforyield,yieldstability, LRandBYD.WeexpectthatLDmappingwillbecomeavaluableextension toconventionalQTLanalysisin plantbreeding.Specialattentionwasgivento traitsdescribinggenotype×environmentinteractions.Statisticalmodelswereusedtodefinemeasuresforyieldadaptabilityandyieldstabilitywithoutincludingenvironmentalfactorsdirectlyinthemodels.Adaptabilitywasdefinedastheresponsivenessofthegenotypetotheenvironment,andstabilitywasdefinedastheunexplaineddeviationfromthestatisticalmodel. LDmappinginbarleycultivarsresultedinmarker-traitassociations foryieldstability. In addition, linkage analyses in fourdoubled-haploidpopulationsresultedindetectionofmanyQTLsforadaptability, butonlya single QTL forstability.Weconcludedthatadaptabilitymeasuresweregeneticallybetterdefinedthanstabilitymeasuresandthatselectionforadaptabilityshouldbepossible.

Keywords: Agro-biodiversity, farmer varieties, indigenous knowledge, farmer-participatory research, genetic diversity, genotype-by-environment interaction, germplasm collection, Ipomoea batatas , specific adaptation, yield stability, sweetpotato, variance component estimates.Between 1999 and 2001, the author conducted various studies, primarily in northeasternUganda, aimed at rapidly assessing the potential of farmer varieties of sweetpotato ( Ipomoea batatas ) from northeasternUgandain contributing to the varietal improvement programme inUganda. These studies included: (i) collection of germplasm (farmer varieties) and farmer knowledge about varieties from five districts in northeastern Uganda; (ii) assessment of morphological diversity and duplication in the collected germplasm; (iii) farmer participatory on-station selection of promising varieties from the collected germplasm for on-farm and multi-locational testing; (iv) farmer-managed on-farm testing in Soroti District (northeastern Uganda) of selected farmer varieties, cultivars from the Ugandan breeding programme and local farmer varieties; (v) multi-locational testing and stability analysis of selected farmer varieties and officially released cultivars from the Ugandan breeding programme in multiple test environments (20 tests over three seasons). Additionally, the author presents results from a multi-national, multi-locational test of elite sweetpotato germplasm in easternAfricaused to study selection efficiency.During germplasm collections, a total of 206 accessions were collected, along with farmer knowledge about them, and of these 188 were classified as distinct accessions, exhibiting considerable morphological variation. Many accessions were collected from remote locations where sweetpotato is not a commercial crop, while relatively few accessions were collected from areas where the crop is important commercially. During the on-station assessment of the collected germplasm, 11 accessions were selected for further testing from a total of 160 accessions evaluated at two sites. Nine of the 11 accessions selected by farmers werecommon to both sites. Farmer selection criteria were verified, with a high weighting given to fresh storage root yield, storage root number and harvest index, in addition to root dry matter content and appearance. During on-farm trials over two years, the 11 farmer varieties were generally preferred over local varieties, and cultivars from the Ugandan breeding programme. During multi-locational trials, the 11 farmer varieties on average performed better with respect to broad adaptation, specific adaptation and yield stability, than the cultivars from the breeding programme. In addition, some of the farmer varieties showed specific adaptation to local environments.Results of the multi-national trial were analyzed to generate recommendations for optimum selection efficiency, and indicated a two-step selection procedure with two locations and one replication at Selection Step 1 and five locations and two replications at Selection Step 2 (total test capacity of between 450 and 950 plots).During the farmer participatory phases of this research, farmers were highly competent in sweetpotato varietal selection and were aware of the genotype-by-environment interactions and biodiversity. Results illustrate the potential that farmer varieties can have in the improvement of sweetpotato inUgandaand other regions where high diversity of sweetpotato landraces exists, and allowed us to recommend an approach for the rapid and efficient selection of superior genotypes from local germplasm inEast Africa