Identification and Characterization of Candidate Genes Underlying Genomic Regions Governing Drought Tolerance in Rice (Oryza Sativa L.)

Abstract

The present investigation with thirty eight rice varieties/genotypes including IR 64, a high yielding variety and N 22, drought tolerant land race was laid out in Randomly Complete Block Design, with replicating thrice during kharif session 2020 and 2021 at the CRC of S. V. P. U. Ag & Tech. Analysis of variance revealed substantial amount of variability in the material. Rice (Oryza sativa L.) yield and its component traits have complex inheritance and involved several genes with small effect. Although several genome regions or quantitative trait loci (QTLs) are identified for galaxy of traits in rice, only few candidate genes underlying these QTLs have been functionally characterized as it involved the laborious and time consuming fine mapping and map based cloning strategies. The candidate genes for drought tolerant QTLs has been endorsed by the literature mining, QTG finder, GO analysis, sequence variation and gene expression analysis and 15 primers designed by insilico analysis. Later, these primers were used for identifying differentially expressed genes in IR 64 and N 22 by providing drought stress treatment. Only four primers belongs to two QTLs, primer vg0712623096 from rn7a (LOC_Os07g22450) located on chromosome 7 encoding NAC domain containing protein and the primers vg0431750843 (LOC_Os04g53310) encoding soluble starch synthase 3-chloroplast precursor, vg0432626757 (LOC_Os04g54850) encoding pectinacetylesterase domain containing protein and vg0433031562 (LOC_Os04g55520) encoding AP2 domain containing protein, located on chromosome 4 found to have higher differential expression in N 22 in comparision with IR 64 during drought stress as per qRT PCR 2–ΔΔCt values. Considering the overall study, these four primers/genes were identified as candidate genes underlying genomic regions governing drought tolerance and thus used for screening of 38 basmati rice genotypes and the genotypes Taravadi, Pusa Sugandh-5, Hariyana Basmati-1, Hariyana basmati-2, Palim basmati, Sanwal basmati, Ranbir basmati, Vallabh basmati-21, Vallabh basmati- 22, Vallabh basmati-24, Vallabh Nagina-1, Kasturi, Malviya and Type-3 were considered as drought tolerant as they have characteristic drought tolerant genomic regions in comparision with other genotypes, which can be used for betterment of marker assisted selection (MAS) also very useful in developing the drought resistant\ tolerant variety or RILs and NILs which can be used in future as drought tolerant lines/genotypes. Through molecular marker analysis 712 bands are obtained with 15 primers with an average of 47.47 bands per primer which shows 100% polymorphism. A total of 712 bands were obtained using 15 InDel primers which had amplified out of 15 designed primers with an average 47.47 bands per primer. PIC value and resolving power indicated that primer vg0432626757 used in the study was found to be most polymorphic and could be utilized for screening of drought tolerance trait among genotypes and for future drought breeding programs. Based on the studies on genetic variability and correlation analysis, it may be concluded that, harvest index, relative water content, number of spikelets per panicle and number of panicles per plant characters seems to be primary yield contributing characters and could be relied upon for selection of genotypes to improve genetic yield potential of rice. Thus, these traits should be given top priority during rice plant selection for single plant yield enhancement and the establishment of new plant types.