Exploiting Genome Conservation Between Model and Forage Lotus Species: Association Mapping Analyses to Discover Drought Tolerance QTL in Lotus Tenuis.

Lotus tenuis is a diploid (2n=12), self-incompatible perennial forage species. Whereas, Lotus. japonicus is a model species because of its diploid small genome, self-crossing, and short ontogenetic cycle. Due to its simpler genetics, L. japonicus has been the focus of legume genome and functional genomic programs allowing rapid generation of useful products for legume breeding (i.e. molecular makers, high-density linkage maps, genome database). Furthermore, comparative genetic studies showed genome-structure conservation among both species. An association mapping (LtAM) population including 100 L. tenuis genotypes were developed for identifying phenotypic traits and genomic region (QTL) controlling drought tolerance in L. tenuis. The LtAM population was phenotypically characterized during two growing season in a spaced plants experiment stablished under irrigation and rainfed conditions.  The population was genetically characterized with 88 simple sequence repeats (SSR) molecular markers, previously developed in L. japonicus (http://www.kazusa.or.jp/lotus/markerdb_index.html). Population structure analysis was performed using the STRUCTURE software, whereas, the phenotypic data were analyzed using a mixed linear model using lme4 package in R. The association mapping analyses were performed using a General Linear Model implemented in TASSEL v3.0. Structure analysis identified three cluster within the LtAM population. The clusters were related to the origin of each individual. All phenotypic traits showed significant genotypic effect and most of them showed a significant genotype × environment interaction (P<0.05). The association mapping analysis revealed 25 chromosomal regions that were highly associated to the expression of 10 drought tolerance related phenotypic traits. The marker effect varied between 5 (NDVI canopy reflectance index) and 30% (canopy temperature). The SSR-markers TM0181 and TM0133, located in the chromosome two of L. japonicus, were associated to four QTLs controlling specific leaf area, canopy temperature and drought tolerance index based on dry matter yield. This is the first study where the genome information available in L. japonicus is transferred to an agronomically important Lotus spp., which are considered orphan crops.