Abstract
BackgroundIncreasing numbers of rice farmers are adopting direct-seeding methods to save on costs associated with labor and transplanting. Successful seedling establishment in flooded conditions requires rapid coleoptile growth to ensure access to oxygen near the water surface. It is important that the natural variations in coleoptile growth of submerged rice plants are identified.ResultsColeoptile responses of submerged plants at the germination stage were analyzed in diverse rice accessions and recombinant inbred lines. Several genomic regions identified from a genome-wide association analysis were significantly associated with anaerobic germination, with many that corresponded to published quantitative trait locus (QTL) intervals. In the recombinant inbred line population derived from a cross between japonica and indica varieties, only one unique and strong signal explaining about 27 % of the phenotypic variation was detected. Distinct haplotypes associated with variations in coleoptile length were identified in diverse germplasm.ConclusionsWe demonstrated the value of combining genome-wide association analysis and biparental QTL mapping approaches to identify chromosomal regions regulating coleoptile elongation in submerged rice plants. The significant genomic regions detected in this study are potential candidates for incorporation into elite cultivars to improve seedling survival during anaerobic germination. Future studies that map the QTLs and investigate the effects and functions of candidate genes may lead to new rice varieties that can be used in direct-seeding systems.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0072-3) contains supplementary material, which is available to authorized users.
Highlights
Increasing numbers of rice farmers are adopting direct-seeding methods to save on costs associated with labor and transplanting
Variability of Anaerobic Germination in Two Mapping Populations The coleoptile lengths of plants from two mapping populations grown under normal conditions or submerged in 5 cm of water are provided in Additional file 1: Table S1
The analysis of variance (ANOVA) of coleoptile growth for all genotypes indicated that the effects of treatment, genotype, and genotype × treatment were all significant (Additional file 2: Table S2)
Summary
Increasing numbers of rice farmers are adopting direct-seeding methods to save on costs associated with labor and transplanting. Successful seedling establishment in flooded conditions requires rapid coleoptile growth to ensure access to oxygen near the water surface. It is important that the natural variations in coleoptile growth of submerged rice plants are identified. Direct seeding is becoming a popular method in some rice-growing areas, especially in Southeast Asian countries, because of its low cost and convenience. Breeding rice varieties capable of surviving under flooded conditions during germination and early growth. When germinating while submerged in water, rice seeds are exposed to oxygen deficiency and limited sources of energy. The faster the coleoptile elongates, the sooner the seedling is able to avoid flooding stress, which improves the chances the plant will survive. Unique anaerobic germination processes may be more efficient in some rice genotypes (Miro & Ismail 2013)
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