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Drought stress is the major constraint in rainfed rice production. Deep and thick roots are thought to contribute in drought resilience. Selection for root traits is hampered by difficulty in phenotypic measurements. Mapping quantitative trait loci (QTLs) for root traits and their use in marker assisted breeding (MAB) will hasten the development of genotypes with improved root system. Consistent QTLs for root traits have been mapped in rice. Developing and testing near iso-genic lines (NILs) with QTLs for root traits in target populations of environment (TPE) will help to verify the agronomic value of the QTLs. NILs were developed by introgression of three root QTLs from CT9993, an upland japonica into IR20, a lowland indica cultivar through MAB. Considerable variation in drought response and grain yield under rainfed condition in TPE was observed among the NILs. Five out of 41 NILs gave higher yields under rain-fed and irrigated conditions as compared to IR20. Two NILs viz. , 212 and 297, with three and two root QTLs, respectively had thicker and longer nodal roots and higher total and deep nodal root weights than IR20. In addition, NIL 297 had more nodal root volume and surface area, while NIL 212 had more number of nodal roots compared to IR20. Further evaluation of the NILs with farmers for yield and grain quality may help in identification of high-yielding, resilient rice suitable for drought-prone rainfed ecosystems. The NILs may also be useful to study the genes underlying the QTLs and their functions for drought resilience improvement in rice.

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212-RM302-RM8085-RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.

Drought is a major abiotic stress limiting rice production and yield stability in rainfed ecosystems. Identifying quantitative trait loci (QTL) for rice yield and yield components under water limited environments will help to develop drought resilient cultivars using marker assisted breeding (MAB) strategy. A total of 232 recombinant inbred lines of IR62266/Norungan were used to map QTLs for plant phenology and production traits under rainfed condition in target population of environments. A total of 79 QTLs for plant phenology and production traits with phenotypic variation ranging from 4.4 to 72.8% were detected under non-stress and drought stress conditions across two locations. Consistent QTLs for phenology and production traits were detected across experiments and water regimes. The QTL region, RM204-RM197-RM217 on chromosome 6 was linked to days to 50% flowering and grain yield per plant under both rainfed and irrigated conditions. The same genomic region, RM585-RM204-RM197 was also linked to harvest index under rainfed condition with positive alleles from Norungan, a local landrace. QTLs for plant production and drought resistance traits co-located near RM585-RM204-RM197-RM217 region on chromosome 6 in several rice genotypes. Thus with further fine mapping, this region may be useful as a candidate QTL for MAB, map-based cloning of genes and functional genomics studies for rainfed rice improvement.