QTL analyses of seed germination and seedling pre-emergence growth under abiotic stresses in Medicago truncatula

Increasing knowledge on the genetic basis of seed germination and seedling heterotrophic growth under abiotic stresses is of major importance for improving crop establishment in the context of climate changes. Among stresses, sub‐ and supra‐optimal temperatures and water deficit, highly compromise these early stages of development and limit crop distribution. The present chapter synthesizes genetic analyses carried out in Medicago truncatula on seed germination and seedling heterotrophic growth under stress conditions, with a focus on low temperatures. A specific attention was paid to hypocotyl growth, as varieties with high potential for upward shoot elongation were required in stressful environments. Traits were characterized at seed, organ, or cellular levels on nested core collections and recombinant inbred line populations (RIL4 and RIL5) considered for the contrasted behaviors of the parental accessions based on an ecophysiological model framework for crop emergence predictions. A first Quantitative Trait Loci (QTL) analysis was carried out at sub‐ (5 °C, 10 °C) and supra‐optimal (20 °C) temperatures. At 20 °C, imbibition and germination rates as well as early embryonic axis growth were measured in RIL4 using an automated image capture and analysis device. At low temperatures, seed germination and hypocotyl heterotrophic growth were characterized on RIL5. The phenotypic framework defined for measuring traits allowed distinguishing stages and thus identifying distinct QTLs for seed mass, imbibition, germination, and heterotrophic growth. A common QTL was found for hypocotyl elongation under both low temperature and water deficit. Finally, those QTLs controlling hypocotyl elongation at low temperature due to epidermal cell number pre‐established in the seeds and those due to elongation of these cells, two key determinants of hypocotyl elongation under stress at cellular level, were identified in RIL5. Together with working on a model plant, the QTL approach developed will facilitate the identification of genes specific to each stage. With this aim in view, an initial set of putative candidate genes was highlighted within the support intervals of some QTLs based on the role of hormone balance regulating germination at high temperature, the molecular cascade in response to cold‐stress and hypotheses on changes in cell elongation with changes in temperature based on studies at the whole plant scale.