BREEDING FOR COLD TOLERANCE IN RICE (Oryza Sativa L.) FOR THE HIGH ALTITUDE AREAS OF MADAGASCAR

Abstract

Low temperature or cold stress is one of the major abiotic stresses limiting rice (Oryza sativa L.) production and productivity in the high altitude of Madagascar; it is affecting an estimated 12.3% of the total rice cultivation. It causes poor seedling establishment and at the reproductive stage causes high sterility and decreases production. This study aimed to (i) introgress cold tolerance gene by crossing an Indica with a japonica rice, (ii) identify a BC1F2 population for cold tolerance at seedling and reproductive stage under control screening conditions and (iii) identify quantitative trait loci (QTLs) related to cold tolerance at seedling and reproductive stage using single nucleotide polymorphism (SNP) markers. Introgression was done by advance until BC1F2 from a cross between Indica rice (Vary botry, Soameva) used as the recurrent parent with Japonica rice (Chomrongdhan) used as a donor parent. Identification of BC1F2 plants as cold tolerance was done by phenotyping study of BC1F2 plants and their parents using a cold room at seedling and reproductive stages, cold room at temperature 12oC and 15oC for 10 days at seedling and reproductive stage respectively for cold treatment. At seedling stage after cold treatment, Chomrongdhan (Chom) showed higher percentage of survival plant (100%) than Vary botry (Var Bot) and Soameva (Soa) (50 and 15%) and BC1F2 plants 59 and 40% to Var bot//Chom and Soa//Chom respectively. The BC1F2 from the Var bot//Chom cross showed significant differences in seedling growth, seedling vigor while those from Soa// Chom showed significant differences for seedling growth, seedling vigor and seedling leaf growth at seedling stage. At the reproductive stage, BC1F2 from Var bot//Chom cross showed significant differences in plant height, panicle exsertion, number of full seeds, panicle weight, phenotypic acceptability, thousand seed weight and heading date while those from the Soa//Chom cross showed significant differences for tiller number, panicle weight, thousand seed weight, plant height, spikelet fertility and number of full seeds. Linkage map was constructed in 1566 (Var bot//Chom) and 1250 (Soa//Chom) polymorphic SNP markers and QTL declared at Logarithm of odds (LOD) greater than 2.5. Crosses between Indica and Japonica for this study produced fertile BC1F2 plants confirm that there are Introgress of cold tolerance gene from the japonica rice to the indica. A number of BC1F2 plants showed a good performance compared to the susceptible parent, and different QTLs for different traits related to cold tolerance at seedling and reproductive stage were identified in this study. The cold-tolerant breeding lines selected in this study had a QTL associated with cold tolerance. Four putative QTLs located on chromosome 2 and 10 conferred tolerances to cold at seedling stage and twelve putative QTLs located on chromosomes 2, 4, 5, 7, 8, 10 and 12 conferred tolerances to cold at reproductive stage from BC1F2 progeny of Var bot//Chom, while seven putative QTLs located on chromosome 1, 2, 4 and 9 were identified at seedling stage and six putative QTLs located on chromosome 2, 5,7, and 10 were identified tolerances to cold at reproductive stage from BC1F2 progeny of Soa//Chom. QTL associated with spikelet fertility of Var bot//Chom, and QTL associated with the panicle weight of Soa//Chom showed similar map position. Validation of the promising QTLs observed in this study could be useful to enhance the level of cold tolerance in Madagascar. BC1F2 populations should be tested under cold conditions in the field to validate the current results.