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Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.)

School of Plant, Environment, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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Present address: Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
Plants 2019, 8(2), 33; https://doi.org/10.3390/plants8020033
Received: 19 December 2018 / Revised: 15 January 2019 / Accepted: 27 January 2019 / Published: 29 January 2019
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice. View Full-Text
Keywords: consensus map; meta-QTL; Oryza sativa; salinity; shoot sodium content; sodium–potassium ratio consensus map; meta-QTL; Oryza sativa; salinity; shoot sodium content; sodium–potassium ratio
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Islam, M.S.; Ontoy, J.; Subudhi, P.K. Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.). Plants 2019, 8, 33.

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