Identifying adaptive variation in the wild progenitors of two cereal crops, maize and pearl millet – AdaptInWild

The first task will combine Next Generation Sequencing (NGS) of individuals sampled in two most ‘extreme’ populations of each environmental gradient. It will identify candidate adaptive polymorphism. The second task will assess transcriptome variation in each species between parents sampled in the most ‘extreme’ populations and their progenies. It will focus on gene expression. The third task will investigate the immediate epigenetic response of adapted genotypes to environmental changes, in environmental swapping experiments. The fourth task will establish a link between candidate variation and phenotypic variation at multiple agronomic or adaptive traits measured in the field.

AdaptInWild is an innovative project that will make use of the most recent NGS technologies, develop some new experimental and statistical tools to investigate the adaptive variation of the wild gene pools of two cereal crops.

By exploring diverse sources of genomic variation, from mutations to epimutations, and linking genotype to phenotype, it will contribute to greatly enhance our knowledge of plant adaptation to environmental changes and also bring more applied insights on the use and conservation of wild genetic resources.

Characterization of teosinte populations (location, ecology) used in this project has been published in Muñoz Diez C. et al. (2013) New Phytologist. A poster on the field experimental assays has been presented at the PhD students INRA meeting by Margaux-Alison Fustier (Clermont-Ferrand, mai 2013).

Climate changes are rapidly modifying the biotic and abiotic environment of cultivated crops. Fast adaptation of crops is therefore necessary to sustain human demand particularly in developing countries. Cereal crops are the major source of food calories worldwide. While maize is the first cereal crop in terms of production, pearl millet produced in the driest environment on earth is a staple crop in Africa and India. Both crops, like most cereals, have undergone genetic bottlenecks as a consequence of domestication and subsequent improvement. Hence, part of the adaptive cryptic variability in their wild progenitors, Zea mays ssp. parviglumis and P. glaucum spp. monodii respectively, has been lost.
AdaptInWild proposes to explore the wild reservoir of both crops and evaluate its potential as a contributor to future breeding efforts. The proposed project thus aims at gaining a better understanding of the genetic and epigenetic bases of plant adaptation. We have collected original material along two altitudinal and two humidity gradients in wild maize and pearl millet, respectively. Those gradients mimic slight and continuous climate variation. We will use wild populations sampled along those gradients to undertake an integrative approach revealing the various facets of plant adaptation: natural selection of nucleotide and structural variants, transcriptomic variations (both coding and non-coding), and epigenetic responses to environmental changes.
The proposed project is articulated around 4 interconnected main scientific tasks, that will collectively provide an holistic view of adaptive forces. The first task will combine Next Generation Sequencing (NGS) of pooled individuals sampled in two most ‘extreme’ populations of each environmental gradient (2 gradients per species) and Illumina VeraCode genotyping of intermediate populations, i.e. populations located in between the two most ‘extremes’. It will identify candidate adaptive sequence polymorphism (SNPs), and candidate adaptive insertion of Transposable Elements (TE indels). The second task will assess transcriptome and non-coding small RNA variation in each species between 4 parents sampled in the most ‘extreme’ populations and their F1 hybrid progenies. It will address the question of cis versus trans regulation of gene expression, i.e. percentage of cis-regulated genes among selected genes versus genome-wide expectation, as well as paternal and maternal effects. The third task will investigate the immediate epigenetic response of adapted genotypes to environmental changes, and the relationship between the genomic and epigenomic levels in short-term adaptation. For this, we will apply an environmental swap between individuals sampled in the most ‘extreme’ populations and follow their response in term of genome-wide epigenetic remodelling of histones and DNA methylation. The fourth task will establish, using an association mapping framework, a link between sequence variation (SNPs and TE indels) and phenotypic variation at multiple agronomic or adaptive traits measured in the field.
AdaptInWild is an innovative project that will make use of the most recent NGS technologies, develop some new experimental and statistical tools to investigate the adaptive variation of the wild gene pools of two cereal crops. By exploring diverse sources of genomic variation, from mutations to epimutations, and linking genotype to phenotype, it will contribute to greatly enhance our knowledge of plant adaptation to environmental changes and also bring more applied insights on the use and conservation of wild genetic resources. In addition, the project will create a long-lasting collaboration opportunity between two partners, the UMR GV at Gif-sur-Yvette (P1) and the UMR DIADE at the Institut de la Recherche pour le Développement in Montpellier (P2) and sustain the training of several students.