Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map
- 226 Downloads
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.
KeywordsCandidate genes Drought tolerance Genotyping by sequencing Quantitative trait loci Recombinant inbred lines
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.
- Blum A (2002) Drought tolerance-is it a complex trait? In: Saxena NP, OToole JC (ed) Field screening for drought tolerance in crop plants with emphasis on rice. Proceedings of an International workshop on field screening for drought tolerance in rice, December 2000, International Crop Research Institute for Semi-arid Tropics, Patancheru, India, pp 17–24Google Scholar
- Holland JB, Nyquist WE, Martinez CT (2003) Estimating and interpreting heritability for plant breeding: an update. Plant Breed Rev 22:9–112Google Scholar
- SAS Institute Inc. (2011) Base SAS® 9.3 procedures guide. SAS Institute Inc, CaryGoogle Scholar
- Sinha P, Pazhamala T, Singh VK, Saxena RK, Krishnamurthy L, Azam S, Khan AW, Varshney RK (2016) Identification and validation of selected universal stress protein domain containing drought-responsive genes in pigeonpea (Cajanus cajan L.). Front Plant Sci 6:1065CrossRefPubMedPubMedCentralGoogle Scholar
- Yoshida S, Hasegawa S (1985) The rice root system: its development and function. Drought resistance in crops with emphasis on rice. International Rice Research Institute, Philippines, pp 97–114Google Scholar
- Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S, Blum A, Nguyen HT (2001a) Locating genomic regions associated with components of drought resistance in rice: comparative mapping within and across species. Theor Appl Genet 103:19–29CrossRefGoogle Scholar