Genetic tolerance to ferrous and aluminium toxicities for seed germination in oryza sativa L.

Abstract

Direct seeded culture is famous for rice cultivation due to its low inputs and less labour demand. However seeds are exposed to various abiotic stresses in direct seeding culture. Ferrous (Fe2+) and aluminium (Al3+) are toxic metals that severely affect seed germination and growth traits. Genetic tolerance to metal toxicity would be one of the possible solutions to combat with these challenges. The genetic study on Fe2+ and Al3+ for seed germination can hardly be found in literature. The present study was conducted to identify the potential loci linked with genes controlling tolerance to Fe2+ and Al3+ for seed germination. A segregating mapping population of F2:3 was developed from the cross between selected Fe2+ and Al3+ tolerant parent Pokkali and sensitive parent, Pak Basmati. Parental DNA was used for polymorphic survey and F2 DNA was used for genotyping. A molecular linkage map was constructed using 84 markers data. The molecular linkage map covered 3435.5cM with an average distance of 7.63cM except 4 larger gaps on chromosome 1, 2, and 4. F3 progenies (129) were evaluated against the optimized toxic level of Fe2+ and Al3+ under controlled environment. Germination traits such as final germination percentage (FG%), germination energy (GE), germination rate (GR), germination speed (GS), germination index (GI), mean time of germination (MGT), germination value (GV), germination velocity (GVe), peak value of germination (PV), germination capacity (GC) and growth traits such as root length (RL), shoot length (SL), total dry biomass (TDB), and germination vigour index (GVI) were measured. In the present study, screening of six rice varieties showed significant differences for seed germination, however Pokkali exhibited the minimum and Pak Basmati showed the maximum influence in seed germination. A 20mM (at pH4.0) of both Fe2+ and Al3+ was found to be the optimized toxic level, as most germination and growth parameters were found to significantly affected at this concentration. Phenotypic data showed significant variations in germination and growth parameters. Total of 39 QTLs (Quantitative Trait Loci) for germination traits and 8 QTLs for growth parameters linked with Fe2+ toxicity tolerance were determined by Simple Interval Mapping (SIM) at 0.06% to 39.9% of phenotypic variations, respectively. Thirty four QTLs for germination parameters and 8 QTLs for growth traits with phenotypic variations 0 to 47% traits linked with Fe2+ toxicity tolerance were mapped by Composite Interval Mapping (CIM). Forty nine QTLs for germination and 23 putative QTLs for growth parameters with phenotypic variations 0.01% to 69% were determined using Multiple Interval Mapping (MIM). Epistasis analysis revealed that the QTLs are mostly dependent on the alleles at other loci. For Al3+ toxicity tolerance 40 markers linked with germination and growth parameters with phenotypic variation 0 to 62.64% were identified by Simple Interval Mapping. Forty-six putative QTLs with phenotypic variation 0 to 28.1% were detected for germination and growth parameters for Al3+ toxicity tolerance using Composite Interval Mapping. Sixty five markers linked with germination and growth traits, at 0 to 72.7% phenotypic variations were mapped by Multiple Interval Mapping. Epistasis analysis showed that Al3+ toxicity tolerance is polygenic and controlled by additive effect. The results suggested that the QTL regions (18cM) and (72cM) were tightly linked to Al3+ tolerance genes could be used for marker assisted selection programme using fine mapping. Moreover, this study also provides an understanding to exclusion tolerance mechanism of Al3+ toxicity as known in the Triticeae within sub-family Pooideae. The identified major QTLs of this research would be useful for rice hybridization programs to induce tolerance against these toxic metals.