WP1: Analyses and development of methods for detecting allelic variation associated with geographic/ temporal climatic variation

Test of available methodologies to look for footprints of selection:This study comparing 6 methods allowed to formulate general guidelines for selecting a method to detect footprint of selection.

Development of a specific tool to estimate selection coefficient from temporal sample of outbreeding population: We develop a simple approximate Bayesian approach to this endeavor and assessed the effectiveness of the method for varying effective size, sample size and strength of selection. The method was applied to pearl millet varieties sampled across two years.

Development of a specific tool to analyse the haplotypic structure of selfing populations : A specific tool  was built, that identifies the different multilocus genotypes present in the studied sample, estimates the relative frequency of each multilocus genotype in the population as well as the genetic distance between each pair of multilocus genotypes The software also allows identifying specific multilocus genotypes resembling recombinant inbred lines as expected if some rare outcrossing events are occurring in the populations.   It can be used to analyse large molecular datasets (> 10000 SNPs).

WP 2: Spatial contrasts

In Medicago truncatula, 61 SNPs were found, located in 40 candidate genes for flowering time variation significantly associated with (one or several) environmental variable(s). Genotype/phenotype association analyses allowed to validate the implication of eight of the climate-associated genes in flowering time variation.

In pearl millet spanning West-Africa climatic variation, no variants were significant for flowering time, whereas 87 variants remained associated with the number of tiller, 169 with plant height and 234 with spike lenght.

In rice accessions collected along altitudinal gradient in Madagascar, a first studies shows  that none of the candidate locus was declared outlier by all the genome-scan tests we implemented. Analysis of genes and gene families co-localising with outlier SNPs detected with at least three different methods, colocalised with a MADS-box transcription factors (involved in floral organ specification and other aspects of plant growth and development), Na+ and K+ transporters, and some defence genes, not with any of the 167 flowering time related genes known in rice. These results confirmed the need for the development of dedicated resources, and that’s why a new collecting campaign was undertaken in 2012. Some 600 accessions were collected, phenotyped and genotyped and are analysed for detection of selection footprint.

All these results suggest that genome scan analyses along climatic gradients enable to detect footprints of selection in genes involved in the adaptation to climate variation. Altogether, this research should bring light to the molecular process leading to adaptation to spatial climate variation. Such study could help favor the temporal adaptation of crop to future climate changes.

WP 3: Temporal contrasts

Pearl millet landraces evolution under climate change in Niger:

We analyzed samples of pearl millet landraces collected in the same villages in 1976 and 2003 throughout the entire cultivated area of Niger. We found no major changes in the main cultivated varieties or in their genetic diversity, but we observed a significant shift in adaptive traits: shorter life cycle, reduction in plant and spike sizes, and increased locus frequency of an early flowering allele. We conclude that recurrent drought can lead to selection for earlier flowering in a major Sahelian crop.

Temporal evolution of rice varieties in Guinea:

A large number of rice accessions were collected in 1979 and 1982, and in 2011 (T2). Seeds collected were genotyped and phenotyped, and climate data were acquired for the 1961-2010 period. In brief, the genotyping analysis revealed a significant increase in frequency of rainfed lowland accession to the detriment of rainfed upland accessions, as well as a significant decrease of the frequency of O. glaberrima at the benefit of O. sativa varieties. Analysis of phenotypic data revealed significant differences between the two panels for the number of days to flowering, especially for O. glaberrima accessions and accessions collected in upland ecosystem. Global population differentiation over the period of 1979-2011 was very low for the three compartments of diversity considered. Analyses are still ingoing

Medicago truncatula and climate change in the Mediterranean basin:

At the beginning of the Arcad project, M. truncatula accessions collected between 1985 and 1990 in 110 sites located in Corsica, the south of France and Spain were already available in our laboratory. To determine if phenological changes have occurred in these three regions during the 30 last years, we organized new campaigns of collection in these regions, giving access to a set of 72 localities for the 2005-2009 period. We detected no clear pattern of phenological change between plants collected in 1985 and 2005-2009. To go further into our understanding of the evolution of these populations, 8 geographical locations in which plants were collected both in 1985 and in 2005-2009 were chosen for further molecular and phenotypic analyse. This experiment showed that the modern genotypes flower significantly earlier than old plants as expected if adaptation for warmer temperatures had occurred.