Doctor of Philosophy (PhD)


School of Plant, Environmental and Soil Sciences

Document Type



Alkaline stress is a major threat to rice production globally. The resources for genetic improvement of alkalinity tolerance in rice are limited. We performed genome-wide association study (GWAS) and QTL mapping integrated with whole genome sequencing and expression analysis to identify and confirm QTLs and candidate genes. We developed a near-isogenic line (NIL) population to fine map the two important QTLs. In GWAS experiment, we genotyped and phenotyped a panel of indica and japonica genotypes for alkalinity tolerance and identified genomic regions and candidate genes conferring alkalinity tolerance. Principal component analysis revealed that alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variation in tolerance, while shoot Na+ concentration, shoot Na+:K+ ratio, and root to shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five groups. Several salt susceptible genotypes like IR29, Cocodrie, and Cheniere were placed in a highly tolerant group suggesting different tolerance mechanism underlying salinity and alkalinity tolerance. Significant negative correlation between SNC and SKC showed the capacity of tolerant genotypes to exclude Na+ from root and shoots and maintain low Na:K ratio. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. Four important QTLs, qSNK4, qSNC9, qSKC10, and qSNC7 were identified based on linkage disequilibrium analysis. Six selected candidate genes showed clear differences in expression pattern between tolerant and susceptible genotypes. Using high density single nucleotide polymorphism (SNP) map generated by genotyping-by-sequencing (GBS), 42 and 50 QTLs were identified at the seedling stage in two RIL populations developed from the crosses Cocodrie × N22 and Cocodrie × Dular, respectively. Six important QTLs, qSKC10.18, qAKT9.19, qAKT8.002, qSNC3.32, qSKC9.22, and qSNK8.01 were targeted for whole genome sequencing to narrow down the candidate genes present within the QTL interval. Eighteen genes were selected for qRT-PCR to evaluate their expression pattern in response to alkalinity stress and sixteen genes were differentially expressed under alkaline stress. The QTLs, qSKC10.18 and qSNC3.32 were introgressed in the IL population and a near-isogenic line population was developed from the selected IL for fine mapping in future. The tolerant lines, QTLs, and candidate genes will be used as genetic resource for improving alkalinity and high pH tolerance in rice and understanding the molecular and physiological mechanisms of alkalinity tolerance.



Committee Chair

Subudhi, Prasanta K.