Genetic mapping of quantitative trait loci for grain yield under drought in rice under controlled greenhouse conditions

Julio Solis, Andres Gutierrez, Venkata Mangu, Eduardo Sánchez Timm, Renesh Bedre, Steve Linscombe, Niranjan Baisakh

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32 Scopus citations


Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associated with DR traits is a prerequisite for marker-assisted breeding. Grain yield is the most important trait and to this end drought yield QTLs have been identified under field conditions. The present study reports identification of drought yield QTLs under controlled conditions without confounding effects of other factors prevalent under natural conditions. A linkage map covering 1,781.5 cM with an average resolution of 9.76 cM was constructed using an F2 population from a cross between two Japonica cultivars, Cocodrie (drought sensitive) and Vandana (drought tolerant) with 213 markers distributed over 12 rice chromosomes. A subset of 59 markers (22 genic SSRs and 37 SNPs) derived from the transcriptome of the parents were also placed in the map. Single marker analysis using 187 F2:3 progeny identified 6 markers distributed on chromosomes 1, 5, and 8 to be associated with grain yield under drought (GYD). Composite interval mapping identified six genomic regions/quantitative trait loci (QTL) on chromosome 1, 5, 8, and 9 to be associated with GYD. QTLs located on chromosome 1 (qGYD1.2, qGYD1.3), chromosome 5 (qGYD5.1) and chromosome 8 (qGYD8.1) were contributed by Vandana alleles, whereas the QTLs, qGYD1.1 and qQYD9.1 were contributed by Cocodrie alelles. The additive positive phenotypic variance explained by the QTLs ranged from 30.0 to 34.0%. Candidate genes annotation within QTLs suggested the role of transcription factors and genes involved in osmotic potential regulation through catalytic/metabolic pathways in drought tolerance mechanism contributing to yield.

Original languageEnglish
Article number129
JournalFrontiers in Chemistry
StatePublished - 1 Jan 2018

Bibliographical note

Funding Information:
United States Department of Agriculture-National Institute of Food and Agriculture, Louisiana Rice Research Board.The research was supported by grants to NB from the USDANIFA (Hatch) and the Louisiana Rice Research Board. The manuscript has been approved for publication by the Louisiana Agricultural Experiment Station as manuscript # 2017-306-31471.

Publisher Copyright:
© 2018 Solis, Gutierrez, Mangu, Sanchez, Bedre, Linscombe and Baisakh.


  • Controlled condition
  • Drought stress
  • QTL
  • Rice
  • Yield


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