Population structure and association studies for reproductive stage salinity tolerance in rice (Oryza sativa L.)

Warraich, A S; Krishnamurthy, S L; Sooch, B S; Lokeshkumar, B M; Vinaykumar, N M; Dushyanthkumar, B M; Rai, V ; Singh, N K; Sharma, P C


Salinity is a major abiotic stress responsible for yield loss in rice as it severely affects various yield contributing traits. Rice is categorised as salt sensitive crop and it is important to identify genomic regions associated to salinity tolerance. In the present study, association mapping was performed to investigate the functional relationship between microsatellite markers and salinity related traits in a set of 180 diverse rice accessions. Association analysis was carried out by employing mixed linear model (MLM) approach. Population structure analysis revealed four subgroups in entire study panel while the admixture level ranged from 0.7-57.2%. A total of 22 marker-trait associations were discovered and four marker-trait associations explained phenotypic variation (R2) greater than 10%. Furthermore, 7 markers were found close to the candidate genes loci. Several markers were significantly associated with more than one trait, suggesting pleiotropic effects. The phenotypic variation explained by associated markers ranged from 2.92 to 18.50%. Comparative genomic search revealed that associated markers were close to candidate genes which play significant role in signal transduction, metabolic pathways and transcription factor activity. The significant associations identified in the present study could be used to improve salt tolerance in rice with introgression of favourable alleles through marker assisted breeding.


Abiotic stress, Association mapping, GWAS, Quantitative trait loci

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