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Background and Aims Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined. Methods Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis. Key Results The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], −σ−1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22–1.86. Conclusions This is the first study to describe the extent of variation in σ within a species’ variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.

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Rice production in most areas of coastal deltas is affected adversely by numerous abiotic stresses, including salinity and other soil-related problems, submergence, stagnant flooding and drought. These stresses affect poor farmers disproportionately. We identify sources of tolerance of these abiotic stresses, understand the causal mechanisms and transfer tolerance into popular varieties and elite breeding lines using marker-assisted backcrossing (MABC). This approach also helps in pyramiding multiple QTLs and genes for tolerance. Previously, several salt-tolerance QTLs were identified, including Saltol, a major QTL on chromosome 1. Currently, Saltol is being introgressed into popular varieties such as IR64, BRRI dhan 28 and BR11. The long-term goal is to identify and combine multiple genes and QTLs controlling different tolerance traits for higher salt tolerance in high yielding rice varieties. Substantial progress in developing submergence-tolerant cultivars was made after cloning SUB1, a major QTL for submergence tolerance, and MABC was used successfully to introgress it into six popular varieties within 3 years, shortening the breeding cycle significantly. The SUB1 locus provided a two- to threefold increase in yield over intolerant varieties under submergence in field trials. Developing varieties combining tolerance for both salinity and submergence is in progress through the introgression of Saltol and SUB1 into popular varieties using MABC. Direct seeding is becoming more important during the dry season in coastal deltas because of its relatively lower cost. However, this approach is hindered by the risk of early fl ooding. We identified several genotypes with tolerance of fl ooding during germination, identified major QTLs and transferred tolerance into elite breeding lines. In most coastal areas, water stagnation for 20-50 cm for several months is a serious problem and modern rice varieties are sensitive to such conditions. Reasonable genetic variation in tolerance of stagnant fl ooding was observed and is being explored. Combining tolerance of abiotic stresses predominant in coastal areas, together with proper management strategies, could contribute substantially to increasing and sustaining rice production in these fragile coastal deltas.