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Drought is the most predominant constraint to rainfed rice production. Identifying molecular markers associated with drought resistance traits and deploying them in marker-assisted breeding will hasten the development of drought-resilient cultivars. A total of 49 diverse rice accessions, including traditional landraces, were evaluated for plant production and root traits under natural drought stress in rainfed target populations of environment (TPE) in six successive field trials from 2010 to 2015. Significant variation for phenology, plant production and root traits under drought was noticed among the accessions. Genotyping of the rice accessions using 599 polymorphic simple sequence repeat (SSR) markers showed considerable variation among them. STRUCTURE analysis grouped the 49 accessions into three subpopulations. Similarly, three clusters were observed in Neighbor joining tree created using Nei's genetic distance. The subpopulation POP1 consisted mostly of landraces, while subpopulation POP3 consisted of advanced breeding lines and POP2 accessions from all groups. Genome-wide association mapping detected 61 markers consistently associated in two or more trials with phenology, plant production and root traits under drought in TPE. The markers PSM52 (Chr 3), RM6909 (Chr 4), RM242 (Chr9) and RM444 (Chr 9) were consistently associated with grain yield and root traits under drought. The markers PSM127 (Chr 3) and PSM133 (Chr 4) were consistently associated with yield, plant height and spikelet fertility. These markers with pleiotropic and consistent associations with yield and secondary traits under drought in TPE may be robust candidates for marker-assisted breeding for drought resistance in rice.

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In order to identify the more toxic novel cry gene, the cry1 gene was screened in six indigenous isolates of Bt by PCR with degenerate primers showed amplification in all the Bt isolates. Subsequent screening of cry1 subfamily gene(s) by gene specific primer showed amplification of cry1A gene in the five Bt isolates, three out of the six cry1 positive isolates showed the presence of cry1Aa gene. One of the six Bt isolates showed the presence of cry1Ab gene. Five Bt isolates showed amplification for cry1Ac gene and a variation in size of amplification was observed in one of the Bt isolates Bt, T27. Further, SDS-PAGE analysis of a spore crystal mixture isolated from new isolates of Bt, T27 showed a single band of ~135 kDa indicating presence of cry1Ac gene. The toxicity analysis of Bt strain T27 against Dichocrocis punctiferalis showed 100 per cent mortality on the fifth day after treatment. The varied ~925 bp amplicon of cry1Ac gene of Bt, T27 was amplified and cloned in a T/A vector. Comparison of nucleotide sequence data generated from the cry1Ac (~925 bp) gene showed 99 percent homology and two amino acid variation when comparison with its holotype sequence of Cry1Ac1.

Drought stress is a major constraint for rice production in rainfed ecosystems. Landraces are reservoir of genes that can help in breeding drought tolerant cultivars. Utilizing the genetic potential of these locally adapted resilient germplasm using quantitative trait loci (QTL) mapping and marker-assisted breeding (MAB) will hasten development of high yielding drought resilient cultivars. A total of 60 genomic regions linked to phenology and plant production traits under drought predominant in rainfed target populations of environment (TPE) were mapped using rice lines derived from a locally adapted landrace, Nootripathu and drought susceptible elite cultivar, IR20 evaluated in three drought stress and one non-stress experiments in the field. QTLs important in rice adaptation to drought have been saturated and refined with additional markers. For example, consistent QTL, RM8085-RM3825 on chromosome 1 for grain yield under drought in TPE, with additive effect from the landrace has been narrowed down to 42.8 Kb (from 1.6 Mb) between RM11873-RM3825. Another QTL for yield under drought was also identified at RM11943 on chromosome 1 with additive effect from IR20 and is also linked to sd1 locus governing plant height. Similarly, the consistent QTL detected for days to 50% flowering (DFF), between RM314-RM6836 on chromosome 6 was also narrowed down to 279.8 Kb (from 4.9 Mb) between RM19715-RM19727. This QTL also harbours Hd1 locus regulating heading date. A QTL for yield under drought was also mapped on chromosome 6 near RM314. Both these QTLs for DFF and yield are located within the meta-QTL for yield under drought (MQTL6.1). These consistent QTLs for yield and DFF under drought in TPE with linkage or pleiotropy to sd1 and Hd1 loci mapped using rice lines derived from locally adapted landrace may be useful in MAB of rice cultivars suitable for water-limited environments.

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