Genetic analysis of the influence of the maternal environment on tomato seed and seedling performance

Nafiseh Geshnizjani

Research output: Thesisinternal PhD, WU


Quality of seeds is strongly affected by their genetic make-up, the environment during seed development and maturation and also the interaction between the genome and the environment. In this thesis, I tried to dissect the genetic basis of tomato seed quality by a combined study of physiology, genetics and genomics in relation to the maternal environment. Chapter 1 of the thesis (General introduction) describes the definition and different aspects of seed and seedling quality and the factors influencing them, with the emphasis on the maternal environment. Additionally background on the used genetic tools with emphasis on the generalized genetical genomics (GGG) approach is provided. Finally, integration of large ‘omics’ technology driven datasets is suggested as an approach to assist in the identification of the genes underlying QTLs.

Seed performance traits, such as seed dormancy and germinability, can be influenced by different maternal nutritional environmental conditions. In Chapter 2 I investigated the effect of different maternal nutritional environments on the quality of seeds from two tomato species (S. lycopersicum and S. pimpinellifolium). I showed that different phosphate and nitrate levels available for mother plants influences seed and seedling quality traits especially in stressful germination environments. Correlation analysis was done between physiological traits and metabolic changes caused by the different maternal environments in tomato and interesting positive and negative correlations were identified which shed light on the molecular regulation of seed quality in different maternal environments.

High quality seed is defined by high levels of seed germination and seedling establishment, especially under sub-optimal conditions. Seed quality however, is acquired during seed maturation and therefore in addition to the mother plant’s genetic background can be strongly influenced by the maternal environment in which the seeds develop. Chapter 3 of the thesis focuses on QTL analysis for seed quality with help of a tomato recombinant inbred line (RIL) population consisting of 100 lines to better understand the possible molecular mechanisms involved in acquisition of seed quality as there is little knowledge about the genetic and environmental factors, and their interaction, that influence seed quality and seedling establishment. For this analysis the RILs originating from a cross between Solanum lycopersicum (cv. Moneymaker) and Solanum pimpinellifolium together with these parental lines were grown in two maternal environments: at high phosphate and low nitrate contents. By analysing the interaction of QTLs with the maternal environment (QTL×E) I tried to enhance and extend detection of loci affected by the different maternal environments.

In Chapter 4 I describe the metabolic analysis of the seeds from the experiments described in Chapter 3. Correlation analysis of metabolite composition and seed phenotypic traits revealed several relations between metabolite contents and seed quality traits such as seed size, seed weight and seed germination percentage. A positive correlation was observed between seed size and -weight and several amino acids and some intermediates of the TCA cycle, such as succinate, citrate and malate. In this chapter I have also identified interesting mQTLs by performing metabolic correlation analysis and metabolic networks generation combined with QTL analysis.

I have investigated the physiological and the genetic variation of two tomato accessions (Solanum lycopersicum (cv. Moneymaker) and Solanum pimpinellifolium) in response to thermo-inhibition of tomato seeds to elevated temperatures in Chapter 5. I have also studied the putative molecular mechanisms that could explain the performance of the seeds at elevated temperature. This was done by analysing the expression levels of genes that have been reported to have a role in thermos-inhibition and dormancy in lettuce and Arabidopsis. Additionally, a QTL analysis on the previous described RIL population has been performed and this resulted in new QTLs and potential new regulators of seed germination and dormancy in tomato under high temperature conditions.

Chapter 6 of the thesis is where I discuss the main outcomes of the thesis. I have also made conclusions by combining and integrating the obtained data from the experimental chapters. Finally I draw a perspective for future research and explain the further required experiments/studies to obtain a comprehensive knowledge of seed and seed quality and their influencing factors. These suggestions will expectantly result in the further identification of the controlling mechanisms regulating seed and seedling quality.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
  • Hilhorst, Henk, Promotor
  • Ligterink, J.W., Co-promotor
Award date19 Jun 2019
Place of PublicationWageningen
Print ISBNs9789463439824
Publication statusPublished - 2019


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