Plant Cell Reports

, Volume 39, Issue 1, pp 149–162 | Cite as

QTL-seq reveals genomic regions associated with spikelet fertility in response to a high temperature in rice (Oryza sativa L.)

  • Phakchana Nubankoh
  • Samart Wanchana
  • Chatree Saensuk
  • Vinitchan Ruanjaichon
  • Sulaiman Cheabu
  • Apichart Vanavichit
  • Theerayut Toojinda
  • Chanate Malumpong
  • Siwaret ArikitEmail author
Original Article


Key message

The QTL-seq approach was used to identify QTLs for spikelet fertility under heat stress in rice. QTLs were detected on chromosomes 1, 2 and 3.


Rice is a staple food of more than half of the global population. Rice production is increasingly affected by extreme environmental fluctuations caused by climate change. Increasing temperatures that exceed the optimum temperature adversely affect rice growth and development, especially during reproductive stages. Heat stress during the reproductive stages has a large effect on spikelet fertility; hence, the yield decreases. To sustain rice yields under increasing temperatures, the development of rice varieties for heat tolerance is necessary. In this study, we applied the QTL-seq approach to rapidly identify QTLs for spikelet fertility under heat stress (air temperature of 40–45 °C) based on two DNA pools, each consisting of 25 individual plants that exhibited a heat-tolerant or heat-sensitive phenotype from an F2 population of a cross between M9962 (heat tolerant) and Sinlek (heat sensitive). Three QTLs, qSF1, qSF2 and qSF3, were detected on chromosomes 1, 2 and 3, respectively, according to the highest contrasting SNP index between the two bulks. The QTLs identified in this study were found to overlap or were linked to QTLs previously identified in other crosses using conventional QTL mapping. A few highly abundant and anther-specific genes that contain nonsynonymous variants were identified within the QTLs and were proposed to be potential candidate genes. These genes could be targets in rice breeding programs for heat tolerance.


Rice Heat tolerance QTL-seq Bulk-segregant analysis 



Quantitative trait loci


Single-nucleotide polymorphism




Heat tolerant


Heat sensitive


QTL of spikelet fertility


Kilobase pair


Mega base pair


Bulk-segregant analysis


DNA sequencing


RNA sequencing



This work was supported by the Agricultural Research Development Agency (ARDA) (Grant No. PRP5905021150).

Author contribution statement

SW, CM, TT, AV and SA conceived and designed the experiment. PN, SC and VR conducted the experiments. SW and CS analyzed the data. SW, SA and PN wrote the manuscript. SW and SA revised the final version of the paper. All authors approved the final version of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

299_2019_2477_MOESM1_ESM.xlsx (19 kb)
Supplementary material 1: Table S1. List of genes annotated within the detected QTLs on chromosomes 1, 2 and 3 and the expression of these genes in the anthers of M9962 and Sinlek. (XLSX 19 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Phakchana Nubankoh
    • 1
  • Samart Wanchana
    • 2
  • Chatree Saensuk
    • 3
  • Vinitchan Ruanjaichon
    • 2
  • Sulaiman Cheabu
    • 4
  • Apichart Vanavichit
    • 3
    • 5
  • Theerayut Toojinda
    • 2
  • Chanate Malumpong
    • 5
  • Siwaret Arikit
    • 3
    • 5
    Email author
  1. 1.Faculty of Agriculture at Kamphaeng SaenKasetsart University Kamphaeng Saen CampusNakhon PathomThailand
  2. 2.National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Khlong LuangThailand
  3. 3.Rice Science CenterKasetsart University Kamphaeng Saen CampusNakhon PathomThailand
  4. 4.Faculty of AgriculturePrincess of Naradhiwas UniversityNaradhiwasThailand
  5. 5.Department of Agronomy, Faculty of Agriculture at Kamphaeng SaenKasetsart University Kamphaeng Saen CampusNakhon PathomThailand

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