Population Structure and Marker-Trait Association in Indigenous Aromatic Rice

Joha rice of Assam is a class of rice with aroma, good cooking qualities and excellent palatability, which are grown in different places of Assam with their adaptability to local situations. A total of 143 simple sequence repeat markers were used in this study to reveal sufficient genetic variations among the 40 Joha and 14 non-Joha rice genotypes. Polymorphism information content of these markers were from 0.17 to 0.88, where the average of 3.7 alleles were observed. The model-based population assignment and dendrogram analysis identified three distinct groups in the 54 rice accessions, which established a clear identity of Joha accessions from the Basmati accessions, indicating high diversity and strong population structure in Joha rice. Furthermore, a total of 29 significant marker-trait associations (P < 0.05) for 10 characters were detected. The QTLs related with yield and grain quality can be used effectively in crop improvement programs and for further fine mapping and validation of specific genes to develop gene-based perfect markers in rice breeding and for mining of better alleles of these genes in Joha rice collections.