New allelic variants found in key rice salt‐tolerance genes: an association study

Summary Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt‐sensitive. High‐throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve...

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Bibliographic Details
Published in:Plant biotechnology journal 2013-01, Vol.11 (1), p.87-100
Main Authors: Negrão, Sónia, Cecília Almadanim, M., Pires, Inês S., Abreu, Isabel A., Maroco, João, Courtois, Brigitte, Gregorio, Glenn B., McNally, Kenneth L., Margarida Oliveira, M.
Format: Article
Language:English
Subjects:
Alleles
association analysis
Breeding
Destabilization
Genes
Genes, Plant
Genetic diversity
Genetic engineering
Genetic Variation
Genomes
Genomics
Genotype
High-throughput screening
Kinases
Mutation
Oryza - genetics
Oryza - metabolism
Oryza sativa
OsCPK17
OsHKT1
5 (SKC1) (HKT8)
OsNHX1
OsRMC
Phosphorylation
Potassium - metabolism
Proteins
Rice
Salinity
Salinity effects
Salinity tolerance
Salt
Salt-Tolerance - genetics
Salts
salt‐stress
Single-nucleotide polymorphism
Sodium - metabolism
Transmembrane domains
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Summary:Summary Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt‐sensitive. High‐throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve salinity tolerance in breeding programmes. To search for genotypic differences related to salt stress, we genotyped 392 rice accessions by EcoTILLING. We targeted five key salt‐related genes involved in mechanisms such as Na+/K+ ratio equilibrium, signalling cascade and stress protection, and we found 40 new allelic variants in coding sequences. By performing association analyses using both general and mixed linear models, we identified 11 significant SNPs related to salinity. We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt‐stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. The K24E mutation can putatively affect SalT interaction with other proteins thus impacting its function. Our results have uncovered allelic variants affecting salinity tolerance that may be important in breeding.
ISSN:1467-7644
1467-7652
DOI:10.1111/pbi.12010