Evaluation for Parental Polymorphism and Identification of Microsatellites Linked to Drought Tolerance in Rice (Oryza sativa L.)

Aims: To identify the ready-to-use polymorphic microsatellite markers associated with drought tolerance for marker-assisted backcross breeding through a polymorphism survey between Jyothi and Chuvannamodan rice varieties.

Place and Duration of Study: Centre for plant biotechnology and molecular biology, Thrissur, Kerala, India, during January to May 2023.

Methodology: The genomic DNA of Jyothi and Chuvannamodan was isolated by following CTAB (Cetyltrimethyl Ammonium Bromide) method with modification. Isolated DNA from both varieties was subjected to PCR amplification using 208 Simple Sequence Repeats (SSRs) primer pairs distributed in 12 chromosomes. The amplified PCR products were electrophoresed in 3% agarose gel and separated fragments were visualized and documented in the Gel Documentation System. Different allele sizes produced by the same SSRs primers between two varieties are identified as polymorphic markers. Polymorphism per-cent was calculated, and frequency distribution and chromosome distribution of polymorphic markers were analyzed.

Results: A total of 208 SSR primers were surveyed for the parental polymorphism. Out of which, 85 SSR primers exhibited clear polymorphism between Jyothi and Chuvannamodan and the remaining 123 were monomorphic primers. The amplicon size ranged from 83bp (RM430) to 495bp (RM18919) among the different primers. The survey revealed maximum parental polymorphism on chromosome 4 (69.23%), followed by chromosome 5 (64.28%), and minimum polymorphism on chromosome 8 (21.73%). The average per cent of polymorphism between the parents was 40.86%. Among the 85 polymorphic markers, 66 had dinucleotide repeats, 17 had trinucleotide repeats, and 1 had tetranucleotide repeats.

Markers with dinucleotide repeats showed higher level of polymorphism. A group of 28 polymorphic markers were identified to be linked with traits including root-related traits, grain yield, leaf rolling and leaf drying under drought conditions.

Conclusion: The polymorphic markers identified in the present study form the basis for tagging drought-tolerant QTLs/genes, fine mapping of those genes, and subsequently in marker-assisted breeding programs. The polymorphic markers linked with the QTLs for grain yield under drought can be pyramided in Jyothi through marker-assisted backcross breeding.