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Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.

Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.

Local adaptation is key for ecotypic differentiation and species evolution. Understanding underlying genomic patterns can allow the prediction of future maladaptation and ecosystem stability. Here, we report the whole-genome resequencing of 874 individuals from 100 range-wide populations of European beech ( Fagus sylvatica L.), an important forest tree species in Europe. We show that genetic variation closely mirrors geography with a clear pattern of isolation-by-distance. Genome-wide analyses for genotype-environment associations (GEAs) identify relatively few potentially adaptive variants after correcting for an overwhelming signal of statistically significant but non-causal GEAs. We characterize the single high confidence genomic region and pinpoint a candidate gene possibly involved in winter temperature adaptation via modulation of spring phenology. Surprisingly, allelic variation at this locus does not result in any apparent fitness differences in a common garden. More generally, reciprocal transplant experiments across large climate distances suggest extensive phenotypic plasticity. Nevertheless, we find indications of polygenic adaptation which may be essential in natural ecosystems. This polygenic signal exhibits broad- and fine-scale variation across the landscape, highlighting the relevance of spatial resolution. In summary, our results emphasize the importance, but also exemplify the complexity, of employing natural genetic variation for forest conservation under climate change.

We investigated the utility of nuclear and cytoplasmic single nucleotide polymorphism (SNP) markers for timber tracking of the intensively logged and commercialized Amazonian tree Jacaranda copaia. Eight hundred and thirty-two trees were sampled (cambium or leaves) from 38 sampling sites in Bolivia, Brazil, French Guiana, and Peru. A total of 128 SNP markers (113 nuclear, 11 chloroplastic, and 4 mitochondrial) were used for genotyping the samples. Bayesian cluster analyses were carried out to group individuals into homogeneous genetic groups for tests to self-assign groups of individuals or individuals to their population of origin. Cluster analysis based on all the SNP markers detected seven main genetic groups. Genetic differentiation was high among populations (0.484) and among genetic groups (0.415), and populations showed a strong isolation-by-distance pattern. Self-assignment testing of the groups of individuals for all loci was able to determine the population origin of all the samples (accuracy = 100%). Self-assignment tests of individuals were able to assign the origin of 94.5%–100% of individuals (accuracy: 91.7%–100%). Our results show that the use of the 128 SNP markers is suitable to correctly determine the origin of J. copaia timber, and they should be considered a useful tool for customs and local and international police.

We used double digest restriction site associated DNA sequencing (ddRAD) to develop new geographically informative nuclear SNP loci inQuercus roburandQuercus petraea. Genotypes derived from sequence data of 95 individuals covering the distribution range of the species were analysed to select geographically informative and polymorphic loci within Russia and Germany. We successfully screened a selected set of 119 loci on a MassARRAY (R) iPLEX (TM) platform on 190 individuals from 19 locations in Russia. The newly developed loci will be useful for genetic studies over the whole distribution range of both species.

The timber of the speciesLophira alata(azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes.

The vulnerable African timber species Nauclea diderrichii is threatened because of its overexploitation and illegal trade. We sampled individuals across Ghana, Nigeria, Cameroon, Congo Brazzaville, Gabon and Democratic Republic of Congo and performed restriction associated DNA sequencing and low coverage MiSeq genome sequencing to discover SNP and INDEL loci. After MassARRAY genotyping of 95 individuals covering the sampled distribution range at 205 loci, a set of 88 loci were selected according to their differentiation among geographical regions. It is the first time that molecular markers are described for N. diderrichii and it should encourage genetic studies in this valuable species.

We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed.

We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.

Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin.