Variability of Hybrid Seed Failure in Wild Tomatoes (Solanum sect. Lycopersicon): Phenotypic and Molecular Signatures in the Developing Endosperm

Seed development represents a critical stage for plant reproductive success. This dissertation focuses on phenotypic and molecular correlates of hybrid seed failure between closely-related species. Three main compartments comprise the angiosperm seed, each with different genomic make-up: the seed coat (maternal), the endosperm (2m:1p), and the embryo (1m:1p). The endosperm plays a central role in early seed development because it regulates embryo nutrient acquisition while synchronizing growth between seed compartments. Importantly, hybrid seed abortion is generally associated with an altered endosperm development. Moreover, genomic imprinting, i.e. parent-of-origin–dependent expression, is exceedingly rare in other plant tissues but widespread in the endosperm. Potential functional links between imprinting perturbation or -mismatch and seed abortion are predicted by evolutionary theory based on parental conflict, but have only begun to be elucidated at the molecular level. Wild tomatoes (Solanum sect. Lycopersicon) were chosen to compare seed development and gene expression in the endosperm of seeds from intraspecific and hybrid crosses, and to address the role of genomic imprinting in lineage divergence and hybrid seed failure. To this end, I used three tomato lineages with interesting hybrid seed phenotypes and patterns of genetic divergence: S. arcanum var marañón (A), S. chilense (C), and S. peruvianum (P). A large part of my study was based on laser-microdissected developing endosperm obtained from seeds of intra- and interspecific crosses and subsequent transcriptome sequencing. In Chapter 1, I hypothesized that seed abortion in wild tomatoes is triggered by endosperm failure and that viable hybrid progenies, after seed germination, may reveal additional symptoms of hybrid incompatibility. Jointly with my collaborators, I provided a comprehensive morphological description of seed development in intra- and interspecific crosses. I found that the incidence of hybrid seed failure was variable among species combinations, with marked phenotypic asymmetries between reciprocal crosses with near- complete seed inviability. For the latter, circumstantial evidence pointed to endosperm proliferation defects being responsible for embryo arrest at early globular stages. The reciprocal C×A and A×C hybrid crosses yielded intermediate levels of viable seeds, from which we grew an F1 hybrid cohort showing some developmental abnormalities, interpreted as reflecting post-germination genetic incompatibilities. Chapter 2 focuses on seeds from intraspecific crosses, i.e. those with normal seed development. My hypothesis was that genomic imprinting in the endosperm of normally developing seeds serves specific functions and is nonrandomly shared between recently diverged species. I found that the degree of overlap among imprinted genes across the three wild tomato lineages was significant, and higher for Paternally Expressed Genes (PEGs) than for Maternally Expressed Genes (MEGs). However, variation in imprinting status for many genes is suggestive of an evolutionarily fast turnover of imprinted expression. MEGs and PEGs appear to be associated with distinct functions, but I found evidence that they interact in functional and physical networks. In particular, I inferred that interactions between imprinted genes contribute to cell-cycle control. Candidate imprinted genes identified in this chapter should be representative of the typical imprinting landscape of wild tomato viable endosperm; they were used as a reference to compare parent-specific gene expression in within-lineage- and hybrid endosperms in Chapter 3. Chapter 3 aimed at testing the hypothesis that hybrid seed failure involves imprinting perturbation and/or large gene expression changes in wild tomato hybrid endosperms. When compared to intraspecific endosperms, those from strongly abortive crosses were characterized by extensive gene expression perturbation together with increased maternal expression proportions. Two homogeneous groups of hybrid endosperms were separated by the largest expression differences in the whole dataset, congruent with either maternal-excess-like (P×A and P×C) or paternal-excess-like (A×P and C×P) endosperms at the phenotypic level. I found strong evidence for perturbations of parental dosage mechanisms in these abortive endosperms, particularly the widespread loss of imprinting status of candidate PEGs. Crosses yielding only partial seed abortion (A×C and C×A) had far fewer expression changes than strongly abortive endosperms and also retained the imprinted status of most candidate PEGs. I discuss the potential roles of parental conflict and coadaptation in driving expression perturbation in abortive endosperm. Finally, I hypothesize that different ‘genetic strengths’ evolved since lineage divergence and identify candidate genes, such as AGAMOUS-LIKE transcriptions factors, that may underlie this dosage-related phenomenon. Such genes may significantly contribute to postzygotic reproductive isolation between wild tomato lineages. By revealing the widespread perturbation of imprinted expression in abortive hybrid endosperms, my project accrued molecular evidence for the fundamental role of parental dosage in successful seed development. As a collateral resource, it also provides a large number of candidate genes that are potentially useful for developmental and evolutionary biology and for plant breeding

Dare to be resilient: the key to future pesticide-free orchards?

International audienceIn a context of urgent need for a more sustainable fruit tree production, it's high time to find durable alternatives to the systematic use of phytosanitary products in orchards. To this aim, resilience can deliver a number of benefits. Relying on a combination of tolerance, resistance and recovery traits, disease resilience appears as a corner stone to cope with the multiple pest and disease challenge over the orchard’s lifetime. Here, we propose to describe resilience as the capacity of a tree to be minimally affected by external disturbances or to rapidly bounce back to normal functioning after being exposed to these disturbances. Based on a literature survey largely inspired from research on livestock, we highlight different approaches for dissecting resilience phenotypic and genotypic components. In particular, multisite experimental designs and longitudinal measures of so-called ‘resilience biomarkers’ are required. We identified a list of promising biomarkers relying on eco-physiological and digital measurements. Recent advances in high-throughput phenotyping and genomics tools will likely facilitate the fine and temporal monitoring of tree health, allowing to identify resilient genotypes with the calculation of specific resilience indicators. Although resilience can appear as ‘black box’ trait, we demonstrate how it could become a realistic breeding goal

Dare to be resilient: the key to future pesticide-free orchards?

In a context of urgent need for a more sustainable fruit tree production, it's high time to find durable alternatives to the systematic use of phytosanitary products in orchards. To this aim, resilience can deliver a number of benefits. Relying on a combination of tolerance, resistance and recovery traits, disease resilience appears as a corner stone to cope with the multiple pest and disease challenge over the orchard’s lifetime. Here, we propose to describe resilience as the capacity of a tree to be minimally affected by external disturbances or to rapidly bounce back to normal functioning after being exposed to these disturbances. Based on a literature survey largely inspired from research on livestock, we highlight different approaches for dissecting resilience phenotypic and genotypic components. In particular, multisite experimental designs and longitudinal measures of so-called ‘resilience biomarkers’ are required. We identified a list of promising biomarkers relying on eco-physiological and digital measurements. Recent advances in high-throughput phenotyping and genomics tools will likely facilitate the fine and temporal monitoring of tree health, allowing to identify resilient genotypes with the calculation of specific resilience indicators. Although resilience can appear as ‘black box’ trait, we demonstrate how it could become a realistic breeding goal

Deciphering plant resilience mechanisms to face the multiple disease challenge in fruit trees

International audienceAs perennial plants, fruit trees must cope, individually, with the fluctuating threat of multiple pathogens over the years. In this long-lasting battle for plant immunity, disease resilience is emerging as a key mechanism for tree survival and fitness. More fundamental research is required to improve our understanding of disease resilience mechanisms, which in turn could be particularly relevant for a more sustainable fruit production. As this approach is novel for that field, we propose i) a clear definition of resilience for fruit producing trees, ii) a methodology for studying its phenotypic components which requires repeated measures of “resilience biomarkers”, iii) to decipher the genetic architecture of resilience components, and iv) an innovative strategy based on high-throughput phenotyping and genomics for identifying resilient genotypes. All in all, disease resilience appears as a meaningful breeding perspective in a context of unprecedented plant protection restrictions

Deciphering plant resilience mechanisms to face the multiple disease challenge in fruit trees

International audienceAs perennial plants, fruit trees must cope, individually, with the fluctuating threat of multiple pathogens over the years. In this long-lasting battle for plant immunity, disease resilience is emerging as a key mechanism for tree survival and fitness. More fundamental research is required to improve our understanding of disease resilience mechanisms, which in turn could be particularly relevant for a more sustainable fruit production. As this approach is novel for that field, we propose i) a clear definition of resilience for fruit producing trees, ii) a methodology for studying its phenotypic components which requires repeated measures of “resilience biomarkers”, iii) to decipher the genetic architecture of resilience components, and iv) an innovative strategy based on high-throughput phenotyping and genomics for identifying resilient genotypes. All in all, disease resilience appears as a meaningful breeding perspective in a context of unprecedented plant protection restrictions

Using non-addive effects in genome-wide association studies and genomic predictions to improve biotic stress tolerance in peach

International audienceAccounting for genetic architecture is crucial to breed for sustainable disease resistances and tolerances in plants. Indeed, (i) harnessing together minor and major effects genes allows to design a more durable plant immunity with large spectrum (ii) access to non-additive variance allows for a better exploitation of the total genetic variance when it comes to breeding, which is particularly relevant for clonally propagated crops. Our study system, Prunus persica (peach tree), is a major temperate fruit crop characterized by an overall high susceptibility to several pests and diseases, illustrated by a frequency treatment index around five times higher than in cereals. In this work, we phenotyped symptoms of two pests (leafhopper and twig moth) and four diseases (rust, leaf curl, mildew and shot hole) under low pesticide cover over three years in a peach core-collection replicated at three sites. This population consists in 192 unique accessions representing peach worldwide diversity and has been genotyped with the IRSC 16K SNP array. We used linear mixed models and the natural orthogonal interactions approach (Vitezica et al. 2017) to explicitly decompose genetic variance into additive, dominant and epistatic effects, and genotype x environment interactions. Genome-wide associations studies (GWAS) were performed with single-locus mixed models including kinships accounting for different dominance inheritance patterns. Genomic predictions consisted in a comparison of five GBLUP models incorporating different combinations of non-additive and inbreeding effects. After describing significant non-additive genetic variance and inbreeding effects across traits, we show that in addition to additive quantitative trait loci (QTLs), three to eight additional QTLs have been detected when accounting for dominant architecture. We were also able to improve genomic predictions by up to +0.05 in predictive ability with models incorporating non-additive and inbreeding terms in comparison to the additive baseline GBLUP model. Our results indicate the presence of very contrasted genetic architectures within the six biotic stress responses studied, traits being more strongly influenced either by dominance, epistasis or inbreeding effects. We also present the exploitation of GxE variance to find robust QTLs and improve environment-specific predictions. Finally, we introduce a multitrait approach to exploit jointly the complementary between resistance and tolerance to several biotic stresses. Our results could translate into high genetic gain in peach given its long juvenile phase, and could contribute to a long-term reduction of pesticide reliance in fruit production

Investigating the multi-disease challenge in apricot through single and multienvironment genome wide association studies

International audienceOver their entire lifetime, apricot trees are exposed to a wide range of pests and diseases incurring for significant sanitary impacts and economic losses. Several sources of partial resistances have been identified but the underlying genetic architecture has yet to be elucidated for most diseases. In this study, the objective is to identify the genetic components underlying resistance – or low susceptibility – of two major diseases in apricot: blossom blight (Monilinia spp.) and leaf rust (Tranzschelia spp.). To do so, a core collection composed by 150 accessions replicated in 5 randomized blocs was grown under low phytosanitary conditions in two environmentally contrasted locations in South-East of France. These accessions have been densely sequenced with the Illumina HiSeq 2000 NGS technique. After monitoring rust and blossom blight damages from 2020 to 2023, we dissected the observed phenotypic variation into genotype, environment and their interactions effects via descriptive statistics and variance decompositions. To identify genetic markers linked to resistance components, we firstly performed genome wide association studies (GWAS) for each environment separately. We found stable genetic effects across the environment, reflected by robust quantitative trait loci (QTLs). In contrasts, some QTLs were only detected in a specific set of trial. To jointly analyse site-specific GWAS results and improve statistical power, we used a meta-analysis GWAS approach. By using a random effect procedure, we were able to consider the heterogeneity of the QTL effects across environments and the correlation between the single-environment GWAS. In the last approach we performed multi-environment GWAS with the MTMM package to dissociate QTLs from QTL by environment interactions effects. The present results provide insights into the genetic basis of blossom blight and rust susceptibility in apricot and therefore contribute to the development of genomics-assisted breeding to improve biotic resilience in apricot varieties