Genetica

, Volume 144, Issue 6, pp 651–664

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

  • Gabriel Feresin Pantalião
  • Marcelo Narciso
  • Cléber Guimarães
  • Adriano Castro
  • José Manoel Colombari
  • Flavio Breseghello
  • Luana Rodrigues
  • Rosana Pereira Vianello
  • Tereza Oliveira Borba
  • Claudio Brondani
Article

DOI: 10.1007/s10709-016-9932-z

Cite this article as:
Pantalião, G.F., Narciso, M., Guimarães, C. et al. Genetica (2016) 144: 651. doi:10.1007/s10709-016-9932-z

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.

Keywords

Oryza sativa L. SNPs Rice core collection Genotyping by sequencing 

Supplementary material

10709_2016_9932_MOESM1_ESM.docx (32 kb)
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 (22 kb)
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 (21 kb)
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)

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Gabriel Feresin Pantalião
    • 1
  • Marcelo Narciso
    • 2
  • Cléber Guimarães
    • 2
  • Adriano Castro
    • 2
  • José Manoel Colombari
    • 2
  • Flavio Breseghello
    • 2
  • Luana Rodrigues
    • 2
  • Rosana Pereira Vianello
    • 2
  • Tereza Oliveira Borba
    • 2
  • Claudio Brondani
    • 2
  1. 1.Escola de AgronomiaUniversidade Federal de GoiásGoiâniaBrazil
  2. 2.Embrapa Arroz e FeijãoGoiâniaBrazil

Personalised recommendations