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Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Pantalião, Gabriel Feresin, Narciso, Marcelo, Guimarães, Cléber, Castro, Adriano, Colombari, José Manoel, Breseghello, Flavio, Rodrigues, Luana, Vianello, Rosana Pereira, Borba, Tereza Oliveira, Brondani, Claudio
Genetica 2016 v.144 no.6 pp. 651-664
Oryza sativa, abiotic stress, breeding programs, cultivars, drought, drought tolerance, genes, genome-wide association study, genotype, grain yield, highlands, marker-assisted selection, polymerase chain reaction, protein kinases, regression analysis, rice, single nucleotide polymorphism, stress tolerance, transcription factors
The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.