Association analysis of salt tolerance in sunflower (Helianthus annuus L.) using retrotransposon markers

Salinity is a serious impediment to agricultural production in the world. Development of salt tolerant hybrid varieties using marker aided selection (MAS) is a pioneering strategy to combat salinity stress. Here we used retrotransposon based molecular markers and salinity tolerance related characters in a panel of eighty-four sunflower inbred lines for marker-trait association (MTA) analysis. Characters such as grain yield per plant, leaf relative water content (RWC), K+, Na+ and Cl- concentration in leaf lamina and petiole were measured separately under normal and 8 ds/m salt stress conditions. The impact of salinity was significant on grain yield, RWC, Na+ concentrations in lamina and petiole as well as on K+ to Na+ ratio. To study genomic variability and survey of LTR retrotransposons activity, the lines were fingerprinted with retrotransposon-based DNA markers; IRAP and REMAP. In hierarchical cluster analysis using IRAP+REMAP markers data, the 84 inbred lines were categorized in four main groups, whereas in Bayesian model-based cluster analysis, the lines were assigned into 2 subpopulations (K=2). A mixed linear model was implemented to detect marker–trait associations incorporating membership coefficient of individuals in the subpopulation (Q matrix) and relationship coefficient (kinship matrix) as covariates in the model. In association analysis by using IRAP+REMAP markers; 8 and 12 loci were identified to be significantly linked with the studied characters in normal and salt stress states, respectively. After developing specific primers for identified markers, they could be potentially applied in marker aided selection (MAS) programs to achieve suitable parental lines and also the improvement of traits of interest.