Euphytica

, 214:38 | Cite as

Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

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Abstract

Drought is a major abiotic constraint for rice production worldwide. The quantitative trait loci (QTLs) for drought tolerance traits identified in earlier studies have large confidence intervals due to low density linkage maps. Further, these studies largely focused on the above ground traits. Therefore, this study aims to identify QTLs for root and shoot traits at the vegetative growth stage using a genotyping by sequencing (GBS) based saturated SNP linkage map. A recombinant inbred line (RIL) population from a cross between Cocodrie and N-22 was evaluated for eight morphological traits under drought stress. Drought was imposed to plants grown in 75 cm long plastic pots at the vegetative growth stage. Using a saturated SNP linkage map, 14 additive QTLs were identified for root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. Majority of the drought responsive QTLs were located on chromosome 1. The expression of QTLs varied under stress and irrigated condition. Shoot length QTLs qSL1.38 and qSL1.11 were congruent to dry shoot mass QTL qDSM1.38 and dry root mass QTL qDRM1.11, respectively. Analysis of genes present within QTL confidence intervals revealed many potential candidate genes such as laccase, Calvin cycle protein, serine threonine protein kinase, heat shock protein, and WRKY protein. Another important gene, Brevis radix, present in the root length QTL region, was known to modulate root growth through cell proliferation and elongation. The candidate genes and the QTL information will be helpful for marker-assisted pyramiding to improve drought tolerance in rice.

Keywords

Candidate genes Drought tolerance Genotyping by sequencing Quantitative trait loci Recombinant inbred lines 

Notes

Acknowledgements

This research was supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture (Grant No. 2013-67013-21238). This manuscript is approved for publication by the Director of Louisiana Agricultural Experiment Station, USA as manuscript number 2018-306-31630.

Compliance with ethical standards

Conflict of interest

The authors have no conflicts of interest in this study.

Supplementary material

10681_2018_2117_MOESM1_ESM.tif (6.8 mb)
Fig. S1 (A) Experimental setup for drought experiment to evaluate root traits in rice, (B) drought stressed (left) and irrigated plants (right). Supplementary material 1 (TIFF 6983 kb)
10681_2018_2117_MOESM2_ESM.tif (2.3 mb)
Fig. S2 Frequency distributions for various root and shoot traits under drought stress condition in Cocodrie x N-22 F8 RIL population. The traits are root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. The arrowheads indicate the trait means of Cocodrie, N-22, and the RIL population. Supplementary material 2 (TIFF 2399 kb)
10681_2018_2117_MOESM3_ESM.tif (1.9 mb)
Fig. S3 Difference in root length between N-22 and Cocodrie under drought stress and non-stress condition. Supplementary material 3 (TIFF 1989 kb)
10681_2018_2117_MOESM4_ESM.docx (23 kb)
Table S1 Additive QTLs for various root and shoot related traits identified by Interval Mapping (IM) in Cocodrie x N-22 RIL population under drought stress condition. Supplementary material 4 (DOCX 23 kb)
10681_2018_2117_MOESM5_ESM.docx (24 kb)
Table S2 Additive QTLs for various root and shoot related traits identified by Interval Mapping (IM) in the Cocodrie x N-22 RIL population under irrigated condition. Supplementary material 5 (DOCX 23 kb)
10681_2018_2117_MOESM6_ESM.docx (37 kb)
Table S3 Epistatic QTLs for various root and shoot related traits identified by Interval Mapping (IM) in the Cocodrie x N-22 RIL population under drought stress condition. Supplementary material 6 (DOCX 36 kb)
10681_2018_2117_MOESM7_ESM.docx (16 kb)
Table S4 Mapping of segregation distortion loci in the Cocodrie x N-22 mapping population. Supplementary material 7 (DOCX 16 kb)
10681_2018_2117_MOESM8_ESM.xlsx (68 kb)
Table S5 List of candidate genes contained in the QTL regions identified under drought stress condition. Supplementary material 8 (XLSX 68 kb)
10681_2018_2117_MOESM9_ESM.xlsx (44 kb)
Table S6 List of gene ontology terms identified for each trait using agriGO and their classification into various sub-classes. Supplementary material 9 (XLSX 43 kb)

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Authors and Affiliations

  1. 1.School of Plant, Environmental, and Soil SciencesLouisiana State University Agricultural CenterBaton RougeUSA

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