Parental Polymorphism Survey for Evaluation and Selection of Contrasting Parents for Drought Tolerance in Rice (Oryza sativa L.) by Using SSR Markers

Aim: This study aims to find the informative polymorphic Microsatellite (SSR) markers for drought tolerance between the recipient parent (Pratishya) and donor parent (CR Dhan 801) of rice. The drought tolerant QTLs (qDTY1.1, qDTY2.1, and qDTY3.1) from the donor parent were subsequently introgressed into the popular variety Pratikshya via marker-assisted backcross breeding.

Place and Duration of Study: The parental polymorphism study was conducted at Molecular Drought Breeding Laboratory, Department of Genetics and Plant Breeding and Central Laboratory, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi; and at Crop Improvement Division, ICAR-NRRI, Cuttack during Rabi 2018-19.

Methodology: The parents used for the study were Pratikshya (recurrent parent) and CR Dhan 801 (donor parent). The leaf samples were collected from 20-25 days old seedlings which were used for parental polymorphism survey after DNA extraction. The genomic DNA isolation was done by using CTAB method. A set of 510 SSR markers covering all the 12 chromosomes of rice were used for parental polymorphism survey in the present study. The standard protocol of polymerase chain reaction (PCR) and agarose gel electrophoresis was used. The DNA fragments were documented using gel documentation system. The graphical representation of marker data was obtained with GGT 2.0 software.

Results: Out of 510, total 108 SSR primer pairs exhibited polymorphism between recipient parent (Pratikshya) and donor parent (CR Dhan 801) and remaining 392 SSR primers were monomorphic. The highest percentage of parental polymorphism was observed on chromosome 2 (26.53%) and 3 (26.46%) followed by chromosome 1 (23.08%); and least on chromosome number 10 (14.71%). The average per cent of polymorphism on all the 12 chromosomes were 21.28%. Out of 108 polymorphic markers obtained from screening of 510 SSRs, 69 contained dinucleotide repeats, 32 showed trinucleotide repeats and 5 were having tetranucleotide repeats.

Conclusion: The screening of markers by parental polymorphism in rice cultivars gives the basis for tagging of the target gene, fine mapping of the gene on the rice chromosome, and subsequent application in Marker Assisted Selection (MAS) programmes. The polymorphic markers identified in this study were be used for genotyping the entire mapping population and for the introgression of the QTLs/genes linked with grain yield during the reproductive stage of drought.