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Fine-mapping and validating qHTSF4.1 to increase spikelet fertility under heat stress at flowering in rice

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Abstract

Key message

This study fine mapped and validated a QTL on rice chromosome 4 that increases spikelet fertility under high temperature (over 37 °C) at the flowering stage.

Abstract

Climate change has a negative effect on crop production and food security. Understanding the genetic mechanism of heat tolerance and developing heat-tolerant varieties is essential to cope with future global warming. Previously, we reported on a QTL (qHTSF4.1) from an IR64/N22 population responsible for rice spikelet fertility under high-temperature stress at the flowering stage. To further fine map and validate the effect of qHTSF4.1, PCR-based SNP markers were developed and used to genotype BC2F2, BC3F2, BC3F3, and BC5F2 populations from the same cross. The interval of the QTL was narrowed down to about 1.2 Mb; however, further recombination was not identified even with a large BC5F2 population that was subsequently developed and screened. The sequence in the QTL region is highly conserved and a large number of genes in the same gene family were observed to be clustered in the region. The QTL qHTSF4.1 consistently increased spikelet fertility in all of the backcross populations. This was confirmed using 24 rice varieties. Most of the rice varieties with the QTL showed a certain degree of heat tolerance under high-temperature conditions. In a BC5F2 population with clean background of IR64, QTL qHTSF4.1 increased spikelet fertility by about 15 %. It could be an important source for enhancing heat tolerance in rice at the flowering stage. PCR-based SNP markers developed in this study can be used for QTL introgression and for pyramiding with other agronomically important QTLs/genes through marker-assisted selection.

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Abbreviations

MAGIC:

Multiparent advanced generation intercross

PCR:

Polymerase chain reaction

QTL:

Quantitative trait locus

SNP:

Single nucleotide polymorphism

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Acknowledgments

This study was supported by the Bill & Melinda Gates Foundation project, Cereal Systems Initiative for South Asia (CSISA), and the German Federal Ministry for Economic Cooperation and Development (BMZ) project, Safeguarding Asian Rice Production from a Rapidly Warming Climate. The authors thank Dr. Abdelbagi Ismail, Dr Kshirod Jena, Ms Priscilla Grace Cañas and the assigned reviewers of TAG journal for the critical review of the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

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Author notes

  1. Edilberto D. Redoña

    Present address: Mississippi State University, P.O. Box 197, Stoneville, MS, 38776, USA

Authors and Affiliations

  1. International Rice Research Institute, DAPO Box 7777, 1301, Metro Manila, Philippines

    Changrong Ye, Fatima A. Tenorio, Edilberto D. Redoña, Krishna S. V. Jagadish & Glenn B. Gregorio

  2. Laguna State Polytechnic University, 4009, Santa Cruz, Laguna, Philippines

    Portia S. Morales–Cortezano & Gleizl A. Cabrega

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  1. Changrong Ye
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  2. Fatima A. Tenorio
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  6. Krishna S. V. Jagadish
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Corresponding author

Correspondence to Changrong Ye.

Additional information

Communicated by M. Wissuwa.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2015_2526_MOESM1_ESM.pdf

Supplementary material 1 (PDF 59 kb): Supplemental Figure 1. Population development and marker assisted selection scheme

122_2015_2526_MOESM2_ESM.pdf

Supplementary material 2 (PDF 175 kb): Supplemental Figure 2. Background of a BC2F2 plant and a BC5F2 plants. Chromosomal regions colored red carry the IR64 genotype (A), blue the N22 genotype (B), and gray the heterozygote (H)

122_2015_2526_MOESM3_ESM.pdf

Supplementary material 3 (PDF 24 kb): Supplemental Table 1. Environmental settings for high-temperature treatment in indoor growth chamber

Supplementary material 4 (PDF 68 kb): Supplemental Table 2. Predicted genes in the QTL region

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Ye, C., Tenorio, F.A., Redoña, E.D. et al. Fine-mapping and validating qHTSF4.1 to increase spikelet fertility under heat stress at flowering in rice. Theor Appl Genet 128, 1507–1517 (2015). https://doi.org/10.1007/s00122-015-2526-9

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  • DOI: https://doi.org/10.1007/s00122-015-2526-9

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