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

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Abstract

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.

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Acknowledgments

National Council for Scientific and Technological Development (CNPq) for the grants to CB and RPV; the Coordination for the Improvement of Higher Education Personnel/Ministry of Education (CAPES/MEC) for the grants to GFP; and the Brazilian Agricultural Research Corporation (EMBRAPA) for financial support for this research.

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Authors and Affiliations

  1. Escola de Agronomia, Universidade Federal de Goiás, Goiânia, GO, CEP 74.690-900, Brazil

    Gabriel Feresin Pantalião

  2. Embrapa Arroz e Feijão, CP 179, Goiânia, GO, CEP 74001-970, Brazil

    Marcelo Narciso, Cléber Guimarães, Adriano Castro, José Manoel Colombari, Flavio Breseghello, Luana Rodrigues, Rosana Pereira Vianello, Tereza Oliveira Borba & Claudio Brondani

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  1. Gabriel Feresin Pantalião
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  2. Marcelo Narciso
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  3. Cléber Guimarães
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  4. Adriano Castro
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  5. José Manoel Colombari
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  6. Flavio Breseghello
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  9. Tereza Oliveira Borba
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  10. Claudio Brondani
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Correspondence to Claudio Brondani.

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Electronic supplementary material

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10709_2016_9932_MOESM1_ESM.docx

List of rice accessions drought-evaluated in field (Porangatu, F) and greenhouse (Sitis platform, S) experiments (DOCX 31 kb)

10709_2016_9932_MOESM2_ESM.docx

Putative annotation of rice transcripts identified by SNP markers related to yield in drought and control experiments (DOCX 22 kb)

10709_2016_9932_MOESM3_ESM.docx

Arabidopsis, Brachypodium, maize and sorghum transcripts homologous of rice transcripts identified by SNP markers related to yield in drought and control experiments (DOCX 21 kb)

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Pantalião, G.F., Narciso, M., Guimarães, C. et al. Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit. Genetica 144, 651–664 (2016). https://doi.org/10.1007/s10709-016-9932-z

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  • DOI: https://doi.org/10.1007/s10709-016-9932-z

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