Plasticity of maternal environment-dependent expression-QTLs of tomato seeds

Abstract

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

Systems genomics of salinity stress response in rice

“…We observed that 49.64% (29,623 of a total 59,669) of cis -eQTLs were common in both environments, as compared to 18.62% (25,528 of a total 137,100) of trans -eQTLs; this result was robust to FDR cutoff (FDR of 0.01 and 0.05). Moreover, this is consistent with previous observations from studies on other species that have found 48%−77% overlapping cis -eQTLs and 9%−60% common trans -eQTLs across environments ( Smith and Kruglyak, 2008 ; Snoek et al, 2012 ; Sterken et al, 2023 ). It further indicates that trans -eQTLs might be more environment-specific than cis -eQTLs.…”

“…Moreover, this is consistent with previous observations from studies on other species that have found 48%-77% overlapping cis-eQTLs and 9%-60% common trans-eQTLs across environments (Smith and Kruglyak, 2008;Snoek et al, 2012;Sterken et al, 2023). It further indicates that trans-eQTLs might be more environment-specific than cis-eQTLs.…”

“…We examined the genetic architecture of gene expression variation as well, and found that trans-eQTLs rather than cis-eQTLs are primarily associated with rice gene expression under salinity stress, potentially via a few master-regulators. Trans-eQTLs may be important in environment-dependent gene expression changes, while cis-eQTLs may be more robust to environmental changes as has been observed in other species (Smith and Kruglyak, 2008;Snoek et al, 2012;Sterken et al, 2023). This can be attributed to trans-eQTLs' larger mutational target along with a larger effect of drift than of positive selection in fixing them.…”

An Evaluation of Recycled Papers as Storage and Germination Medium of Vegetable Seeds

“…Seed germination and storage methods are crucial for optimal plant growth and sustainable agriculture [9]. While soil and peat have traditionally been used, there is a growing need for ecological alternatives.…”