Dataset Information

Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice.

ABSTRACT: BACKGROUND: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. RESULTS:Coleoptile 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. CONCLUSIONS:We 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.

SUBMITTER: Hsu SK

PROVIDER: S-EPMC4689725 | biostudies-other | 2015 Dec

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice.

Hsu Sheng-Kai SK Tung Chih-Wei CW

Rice (New York, N.Y.) 20151223 1

<h4>Background</h4>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.<h4>Results</h4>Coleoptile responses of submerged plants at the germination stage were analyzed in diverse ...[more]

PMID: 26699727

Similar Datasets

Project description:BackgroundRice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding.ResultsIn this study, an indica landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BC1F2 population derived from the crossing WJZ/Nip (japonica, Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under H2O and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under H2O conditions and nine QTLs under salt conditions. Six QTLs, qGR6.1, qGR8.1, qGR8.2, qGR10.1, qGR10.2 and qGI10.1 were simultaneously identified under two conditions. Under salt conditions, three QTLs, qGR6.2, qGR10.1 and qGR10.2 for GR were identified at different time points during seed germination, which shared the same chromosomal region with qGI6.2, qGI10.1 and qGI10.2 for GI respectively. The qGR6.2 accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore, qGR6.2 was verified via the BC2F2 population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which LOC_Os06g10650 and LOC_Os06g10710 were differentially expressed after seed imbibition. RT-qPCR results showed the expression of LOC_Os06g10650 was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that LOC_Os06g10650, encoding tyrosine phosphatase family protein, might be the causal candidate gene for qGR6.2.ConclusionsIn this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under H2O and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS).

Dataset Information

Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice.

Publications

Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets