ESTIMATION OF GENETIC EFFECTS FOR LOW TEMPERATURE TOLERANCE IN boro RICE OF ASSAM THROUGH QTL ANALYSIS

Abstract

In recent years, boro rice cultivation in Assam has gained popularity among farmers due to its higher productivity than sali and ahu rice, and has become an alternative to flood affected areas. However, the advantages of boro rice cultivation are limited by low-temperature stress during seedling stage, leading to seedling mortality. Therefore, understanding genetic basis has become a prerequisite and hence the present study was aimed to detect the genetic effects for low temperature stress through QTL (Quantitative trait loci) analysis. The donor parent had been selected based on phenotypic evaluation and marker based genotypic variations for low temperature tolerance in 219 boro rice cultivars collected from Regional Agricultural Research Station (RARS), Karimganj, AAU. Among these cultivars, the donor parent was selected based on its ability to survive the lowest temperature of 5°C. On the other hand, the recipient parent was chosen from high yielding varieties (HYVs), showing susceptibility to low temperatures at 12oC, 8oC and 5oC. Two cultivars were selected as parents, namely PSBRC2 (donor) and Jyotiprasad (recipient), and were crossed to obtain true F1 seed. Subsequently, single F1 seed was selfed, F2 seeds were advanced to F7 generations using the SSD (single seed descent) method to develop a mapping population consisting of 188 RILs (Recombinant Inbred Lines). Parental polymorphism study was conducted using 600 microsatellite markers; among which 90 markers were found to be polymorphic (15% marker polymorphism). The RILs along with parents were then genotyped using 90 microsatellite markers. A linkage map was constructed covering 4391 cM based on 90 microsatellite markers spanning 12 linkage groups using the software Join Map 4.0. The phenotypic scores under field and controlled environment were compared with genotypic data using software, Map QTL6 and R/QTL for identification of the QTLs. The analysis detected six QTLs associated with seedling stage traits in controlled environment under cold stress, located on chromosomes 2 (qCTGRS2, LOD score 2.7; qCTSUR2, LOD score 2.3), 5(qREC5, LOD score 2.9; qSUR5, newlineLOD score 2.7), 8(qREC8, LOD score 2.16), and 12 (qSUR12, LOD score 2.06). Additionally, one QTL was found to influence colouration at seedling stage in field condition on chromosome 1 (qCTS1, LOD score 3.24), and six QTLs were detected for yield attributing traits on chromosomes 2 (qNOT2, LOD score 2.47), 4 (qGY4, LOD score 1.93) and 9 (qNOG9, LOD score 2.27; qDFF9,LOD score 2.47; qSF9, LOD score 2.01).The detected QTL regions were scanned to identify candidate genes associated with cold tolerance in rice. A 10Mb region for each QTL was scanned and a total of 6995 genes newlinewere detected; out of which 3171 were annotated. From the annotated genes 32 genes were found to be stress related genes and from these, eleven(11) candidate genes associated with cold stress were detected (OsICE-1, ICE-1, ATG6A, OsATG6a, OsOFP4, OsOFP06, OsOFP6, OFP6, OsPUB3, OsPUB03, PUB3, P5CS2, OsP5CS2, OsALDH18B2, PYL/RCAR3, OsCTZFP8, BIP120, OsUGT90A1, OsFKBP65, OsFKBP62b). These findings hold significant promise for enhancing low temperature tolerance in boro rice, if candidates are identified and introgressed through fine mapping and further map based cloning.