Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers

•Rice is a staple food for more than three billion people, and rice cultivars have evolved over thousands of years of adaptation to different environmental stresses in different regions. Domestication of rice cultivation led to the diversity of cultivars though phenotypic selection for desirable characters. India is blessed with great diversity of rice germplasm, and these are still conserved for many reasons. The aim of the study was to show the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu, India. Using a hydroponic system, we studied the different agronomic characters from seedling to plant growth hight 14 days after exposure to six different concentrations of saline solution. Rice genotypes showed significant interaction and differential response towards salinity were assessed at the molecular level using simple sequence repeat (SSR) markers linked with salt-tolerance QTL. We found wide genetic distance among the genotypes studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes. This is, to the best of our knowledge, the first study on the indigenous rice landraces of coastal Tamil Nadu, India. We evaluated the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu. Using a hydroponic system, we studied the different agronomic characters 14 days after exposure to six different concentrations of saline solution. Shoot and root length as well as plant biomass at seedling stage decreased with increasing salinity. Genotypes showing significant interaction and differential response towards salinity were assessed at the molecular level using 20 simple sequence repeat (SSR) markers linked with salt-tolerance QTL. These genotypes were grouped into eleven clusters based on molecular diversity analysis and eight clusters based on D2 statistical analysis. We found wide genetic distance among the genotypes studied. Simple correlation analysis revealed highly significant associations among the traits studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes viz. Kuzhi adichan, Poonkar, Kallundai, and Sornamugi.