Mining allelic diversity of maize landraces for tolerance to abiotic and biotic stresses – MineLandDiv

Climate change, soil degradation and fertilizer costs threaten food security and agriculture sustainability in Europe. Traditional varieties of
crops or landraces are a valuable source of genetic diversity for addressing these challenges. Landraces have been selected for adaptation
to local agro-climatic conditions and human uses and could therefore carry favorable alleles for tolerance to abiotic or biotic stresses.
However, landraces remain underutilized in modern breeding programs and agriculture because they are poorly characterized, genetically
heterogeneous and exhibit limited agronomic performance compared to elite material. Great effort has been recently made to characterize
the genotypic variation of thousands of maize landraces but few resources have been mobilized for analyzing their phenotypic variation and
genetic diversity for complex traits as tolerance to abiotic and biotic stresses. The project MineLandDiv (Mining Allelic Diversity in Landraces
for Tolerance to Abiotic and Biotic stress) proposes to fill this gap by combining different up-to-date genomic approaches, genetic and
statistical methods with high throughput phenotyping tools including sensors / metagenomics for fine environmental characterization.
MineLandDiv aims at (i) identifying maize landraces and favorable alleles for tolerance to abiotic (heat/drought - cold - nitrogen) and biotic
stresses (Corn borer) that could be used to broaden genetic diversity of modern breeding germplasms and (ii) better understanding their
resilience to variable environmental conditions. To achieve these objectives, MineLandDiv proposes to:
1. Optimize a collection of 300 maize landraces representative of American and European genetic diversity and adapted to various agroclimatic
conditions based on previous knowledge and mid density genotyping data available for more than 1200 landraces.
2. Evaluate, across a large European network, these 300 landraces for different agronomic and physiologic traits with contrasted treatments
(well-watered vs water deficit, low vs high nitrogen, early sowing for cold, heat, and corn borer infestation) for studying the effect of these
stresses on agronomic performances. We will use high-throughput phenotyping tools (Drones, NIRs), phenotyping platforms and
environmental sensors to assess the environmental conditions felt by plants. Because roots and symbiosis with soil microorganisms are
essential for nutrient and water uptake, we will phenotype root architecture in an aeroponics platform and characterize soil microorganism
content of different trials by metagenomics.
3. Identify genomic regions involved in agronomic performance and tolerance to abiotic stresses by (i) conducting association studies for
agronomical, physiological and roots traits as well as environmental variables associated with the landrace collecting sites, by (ii) detecting
selective footprints between landraces from contrasting environments. We will genotype DNA pool of 15 plants from each landrace using
high density genotyping array (600K).
4. Develop an original DNA pooling targeting sequencing approach to explore allelic diversity in these genomic regions but also candidate
genes putatively involved in abiotic tolerance or plant-microorganism interactions for all landraces as well as for a set of inbred lines for
comparison.
5. Predict, for a larger number of landraces, agronomic performance and tolerance to abiotic/biotic stresses by calibrating a model based on
phenotypic evaluation and deep genomic characterization of these 300 landraces.
This project will increase our knowledge about adaptation mechanisms of maize landraces to different agro-climatic conditions. We will
identify promising alleles / landraces that could be used to broaden the genetic basis of breeding germplasm for tolerance to abiotic / biotic
stresses by releasing new inbred lines or using other bridging/technology approaches.