Plant Molecular Biology

, Volume 73, Issue 1–2, pp 97–104 | Cite as

The qSD12 underlying gene promotes abscisic acid accumulation in early developing seeds to induce primary dormancy in rice

  • Xing-You Gu
  • Tianlei Liu
  • Jiuhuan Feng
  • Jeffrey C. Suttle
  • James Gibbons


Seeds acquire primary dormancy during their development and the phytohormone abscisic acid (ABA) is known to play a role in inducing the dormancy. qSD12 is a major seed dormancy quantitative trait locus (QTL) identified from weedy rice. This research was conducted to identify qSD12 candidate genes, isolate the candidates from weedy rice, and determine the relation of the dormancy gene to ABA. A fine mapping experiment, followed by marker-assisted progeny testing for selected recombinants, narrowed down qSD12 to a genomic region of <75 kb, where there are nine predicted genes including a cluster of six transposon/retrotransposon protein genes and three putative (a PIL5, a hypothetic protein, and a bHLH transcription factor) genes based on the annotated Nipponbare genome sequence. The PIL5 and bHLH genes are more likely to be the QTL candidate genes. A bacterial artificial chromosome (BAC) library equivalent to 8–9 times of the haploid genome size was constructed for the weedy rice. One of the two BAC contigs developed from the library covers the PIL5 to bHLH interval. A pair of lines different only in the QTL-containing region of <200 kb was developed as isogenic lines for the qSD12 dormancy and non-dormancy alleles. The dormant line accumulated much higher ABA in 10-day developing seeds than the non-dormant line. In the QTL-containing region there is no predicted gene that has been assigned to ABA biosynthetic or metabolic pathways. Thus, it is concluded that the qSD12 underlying gene promotes ABA accumulation in early developing seeds to induce primary seed dormancy.


Seed dormancy Quantitative trait locus Fine mapping Abscisic acid Rice 



We thank B. Carsrud, Y. Wang and E. Castaneda for technical support and Dr. Carter for help with BAC library screening. Funding for this research was supported by grants from National Science Foundation (0641376) and in part from South Dakota Agriculture Extension Station (SD00H171-06IHG) and United States Department of Agriculture Cooperative State Research, Education, and Extension Service (SD00074-G).


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Xing-You Gu
    • 1
  • Tianlei Liu
    • 1
  • Jiuhuan Feng
    • 1
  • Jeffrey C. Suttle
    • 2
  • James Gibbons
    • 3
  1. 1.Plant Science DepartmentSouth Dakota State UniversityBrookingsUSA
  2. 2.Northern Crop Science LaboratoryUSDA-ARSFargoUSA
  3. 3.Rice Research and Extension CenterUniversity of ArkansasStuttgartUSA

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