Using genome conservation between Lotus japonicus and agronomically important Lotus species for discovering drought tolerance QTLs

Lotus tenuis is a perennial forage legume species closely related to the model legume L. japonicus. Genetic relatedness between cultivated and model Lotus species has not been exploited so far. Furthermore, L. tenuis drought tolerance cultivars for marginal environments are in high demand. Marker-assisted selection is a modern breeding tool that allows to dissect genetically complex traits such as drought tolerance and to select for favorable alleles. However, L. tenuis is considered an orphan crop because no genome sequencing effort has been made. The objective of this work was to perform association mapping analyses on a L. tenuis population (LtAM) comprised of 100 genotypes for identifying genomic regions (QTLs) controlling drought tolerance. The LtAM population was established on a two-water regime (rainfed and irrigated) under a Mediterranean climate condition. Phenotyping was carried out during two growing seasons and included the measurement of important physiological and agronomical traits. Genetic characterization was performed with 88 transferable simple sequence repeats (SSR) molecular markers from L. japonicus genome. Association mapping analyses allowed to identify 40 marker-trait associations, almost 50% of them were found on chromosomes two and six of L. japonicus genome. For seven SSR-markers, 11 putative candidate genes were found. Based on annotations from the Medicago truncatula and Arabidopsis thaliana genomes, these genes could plausibly be candidates of causative polymorphism altering biochemical and physiological functions involved in the abiotic stress responses.