12The oncogenic Ras/MAPK pathway is evolutionary conserved across metazoans and is 13 essential for many cellular functions. Mutant screens in the model nematode Caenorhabditis 14 elegans have been invaluable for elucidating Ras/MAPK pathway characteristics and 15 identification of the genes involved. Almost all of these screens have been conducted in a 16 single genetic background. However, phenotypic traits of induced mutations can vary widely 17 depending on the genetic background. At the moment, we lack insight into how different 18 genetic backgrounds modulate Ras/MAPK-signaling and which genetic modifiers are 19 involved. 20 We previously introduced a gain-of-function mutation in the Ras/MAPK pathway 21 gene let-60 in over 200 recombinant inbred lines (mutant introgressed RILs: miRILs) and 22 detected genetic modifiers affecting this pathway by studying variation in vulval 23 development. In the present study, we investigate how gene expression regulation is affected 24 by the let-60 gain-of-function mutation and the genetic background by mapping eQTL using 25 33 miRILs. We found that the majority (~73%) of the 1516 detected cis-eQTL are not specific 26 for the let-60 mutation, whereas most (~76%) of the 898 detected trans-eQTL are associated 27 with the let-60 mutation. We detected 6 eQTL trans-bands that were specific for the 28 interaction between the genetic background and the mutation. One of these eQTL hotspots co-29 localizes with the previously identified polymorphic Ras/MAPK modifier amx-2. Comparing 30 gene expression profiles between transgenic lines expressing either the N2 or the CB4856 31 alleles of amx-2 showed the involvement of amx-2 in 79% of the trans-eQTLs for genes 32 mapping to this trans-band. 33 Together, our results have revealed hidden loci affecting Ras/MAPK signaling using 34 sensitized backgrounds in C. elegans. These loci harbor putative polymorphic modifier genes 35 that would not have been detected using mutant screens in single genetic backgrounds. 37The Ras/MAPK pathway is highly conserved across metazoans and regulates a wide range of 38 physiological responses, such as cell proliferation, apoptosis, cell differentiation, and tissue 39 morphogenesis (GOKHALE AND SHINGLETON 2015). In humans, activating ("gain-of-40 function") mutations in HRas and KRas are strong tumor initiating mutations (PRIOR AND 41 HANCOCK 2012). Activation of MAP kinase components in model organisms has been shown 42 to cause cell transformation and is implicated in tumorigenesis (COWLEY et al. 1994; 43 MANSOUR et al. 1994). As a key pathway in vertebrates and invertebrates, Ras/MAPK-44 signaling has been thoroughly studied in model organisms. Genetic studies in the model 45 nematode Caenorhabditis elegans have provided insight into let-60 Ras/MAPK signaling. 46 Activated LET-60, a member of the GTP-binding RAS family (BEITEL et al. 1990; HAN AND 47 STERNBERG 1990), induces the phosphorylation of LIN-45 (a Raf ortholog), MEK-2 (a 48 MAPK kinase), and MPK-1 (an ERK ortholog) (WU AND HAN 1994). Af...

Rice feeds more than half of the world's human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plant's ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.

20The detrimental effects of a short bout of stress can persist, and potentially turn lethal, long after the return 21 to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme 22 temperatures, is influenced by the response during stress exposure, as well as the recovery process 23 afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal 24 tolerance remains a challenge. Here, we use the nematode Caenorhabditis elegans to measure 25 transcriptional resilience to heat stress and predict thermotolerance. Using high dimensionality reduction 26 techniques in combination with genome-wide gene expression profiles collected in three high resolution 27 time-series during control, heat stress and recovery conditions, we infer a quantitative scale capturing the 28 extent of stress-induced transcriptome dynamics in a single value This scale provides a basis for evaluating 29 transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during 30 recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional 31 resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival 32 after heat stress. Our findings imply that thermotolerance is an intrinsic property that pre-determines long 33 term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the 34 transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies 35 after stresses such as disease and trauma. 36

Most ectotherms obey the temperature-size rule, meaning they grow larger in a colder environment. This raises the question of how the interplay between genes and temperature affect the body size of ectotherms. Despite the growing body of literature on the physiological life-history and molecular genetic mechanism underlying the temperature-size rule, the overall genetic architecture orchestrating this complex phenotype is not yet fully understood. One approach to identify genetic regulators of complex phenotypes is Quantitative Trait Locus (QTL) mapping. Here, we explore the genetic architecture of body size phenotypes, in different temperatures using Caenorhabditis elegans as a model ectotherm. We used 40 recombinant inbred lines (RILs) derived from N2 and CB4856, which were reared at four different temperatures (16°C, 20°C, 24°C, and 26°C) and measured at two developmental stages (L4 and adult). The animals were measured for body length, width at vulva, body volume, length/width ratio, and seven other body-size traits. The genetically diverse RILs varied in their body-size phenotypes with heritabilities ranging from 0.20 to 0.99. We detected 18 QTL underlying the body-size phenotypes across all treatment combinations, with the majority clustering on Chromosome X. We hypothesize that the Chromosome X QTL could result from a known pleiotropic regulator – npr-1 – known to affect the body size of C. elegans through behavioral changes. In conclusion, our findings shed more light on multiple loci affecting body size plasticity and allow for a more refined analysis of the temperature-size rule.