Abstract: Seeds are important to agriculture and conservation of plant biodiversity. In agriculture, seed germination performance is an important determinant of crop yield, in particular under adverse climatic conditions. Deterioration in seed quality is associated with the accumulation of cellular damage to macromolecules including lipids, protein, and DNA. Mechanisms that mitigate the deleterious cellular damage incurred in the quiescent state and in cycles of desiccation-hydration are crucial for the maintenance of seed viability and germination vigour. In early-imbibing seeds, damage to the embryo genome must be repaired prior to initiation of cell division to minimize growth inhibition and mutation of genetic information. Here we review recent advances that have established molecular links between genome integrity and seed quality. These studies identified that maintenance of genome integrity is particularly important to the seed stage of the plant lifecycle, revealing new insight into the physiological roles of plant DNA repair and recombination mechanisms. The high conservation of DNA repair and recombination factors across plant species underlines their potential as promising targets for the improvement of crop performance and development of molecular markers for prediction of seed vigour.

Abstract: Genetic improvement of grain yield (GY) and grain protein concentration (GPC) is impeded by large genotype×environment×management interactions and by compensatory effects between traits. Here global uncertainty and sensitivity analyses of the process-based wheat model SiriusQuality2 were conducted with the aim of identifying candidate traits to increase GY and GPC. Three contrasted European sites were selected and simulations were performed using long-term weather data and two nitrogen (N) treatments in order to quantify the effect of parameter uncertainty on GY and GPC under variable environments. The overall influence of all 75 plant parameters of SiriusQuality2 was first analysed using the Morris method. Forty-one influential parameters were identified and their individual (first-order) and total effects on the model outputs were investigated using the extended Fourier amplitude sensitivity test. The overall effect of the parameters was dominated by their interactions with other parameters. Under high N supply, a few influential parameters with respect to GY were identified (e.g. radiation use efficiency, potential duration of grain filling, and phyllochron). However, under low N, >10 parameters showed similar effects on GY and GPC. All parameters had opposite effects on GY and GPC, but leaf and stem N storage capacity appeared as good candidate traits to change the intercept of the negative relationship between GY and GPC. This study provides a system analysis of traits determining GY and GPC under variable environments and delivers valuable information to prioritize model development and experimental work.

Abstract: Environmental conditions can change the activity of plant genes via epigenetic effects that alter the competence of genetic information to be expressed. This may provide a powerful strategy for plants to adapt to environmental change. However, as epigenetic changes do not modify DNA sequences and are therefore reversible, only those epi-mutations that are transmitted through the germline can be expected to contribute to a long-term adaptive response. The major challenge for the investigation of epigenetic adaptation theories is therefore to identify genomic loci that undergo epigenetic changes in response to environmental conditions, which alter their expression in a heritable way and which improve the plant’s ability to adapt to the inducing conditions. This review focuses on the role of DNA methylation as a prominent epigenetic mark that controls chromatin conformation, and on its potential in mediating expression changes in response to environmental signals.