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Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice

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Abstract

A days to heading QTL (dth1.1) located on the short arm of rice chromosome 1 was sub-divided into eight sub-introgression lines (SILs) to analyze the genetic basis of transgressive variation for flowering time. Each SIL contained one or more introgression(s) from O. rufipogon in the genetic background of the elite Oryza sativa cultivar, Jefferson. Each introgression was defined at high resolution using molecular markers and those in the dth1.1 region were associated with the presence of one or more flowering time genes (GI, SOC1, FT-L8, EMF1, and PNZIP). SILs and controls were evaluated for flowering time under both short- and long-day growing conditions. Under short-day lengths, lines with introgressions carrying combinations of linked flowering time genes (GI/SOC1, SOC1/FT-L8, GI/SOC1/FT-L8 and EMF1/PNZIP) from the late parent, O. rufipogon, flowered earlier than the recurrent parent, Jefferson, while recombinant lines carrying smaller introgressions marked by the presence of GI, SOC1, EMF1 or PNZIP alone no longer flowered early. Under long-day length, lines carrying SOC1/FT-L8, SOC1 or PNZIP flowered early, while those carrying GI or EMF1 delayed flowering. Across all experiments and in the field, only SIL_SOC1/FT-L8 was consistently early. A preliminary yield evaluation indicated that the transgressive early flowering observed in several of the SILs was also associated with a measurable and positive effect on yield. These SILs represent a new source of variation that can be used in breeding programs to manipulate flowering time in rice cultivars without the reduction in yield that is often associated with early maturing phenotypes.

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Acknowledgments

We would like to thank Mrs. Marie Lavallard and the Department of Plant Breeding and Genetics for financial support for the PhD program of LFM (via a Frank T. Rhodes Fellowship), the National Science Foundation (Grant DBI #0606461 to SMc) for research funding, Lisa Polewczak for assistance with the field work in the Dale Bumpers National Rice Research Center in Stuttgart, AR and the USDA-ARS Rice Research Unit in Beaumont, TX. We express our gratitude to Michael Thomson and Jeremy Edwards for seeds from the parental pre-SILs provided for this study, and to Michael Gore and Walter de Jong for constructive comments and suggestions during manuscript preparation. We gratefully acknowledge Lois Swales for her assistance in preparing the figures and for formatting the manuscript.

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Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA

    Luis F. Maas & Susan McCouch

  2. USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA

    Anna McClung

Authors
  1. Luis F. Maas
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  2. Anna McClung
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  3. Susan McCouch
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Corresponding author

Correspondence to Susan McCouch.

Additional information

Communicated by M. Wissuwa.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

. Genomic distribution of homologous flowering time genes in Arabidopsis and O. sativa. (PDF 383 kb)

Supplementary Table 1

. List of indel and SSR markers, chromosomal locations, primer sequences and expected size (bp) in cv Nipponbare. (XLS 40 kb)

Supplementary Table 2

. Summary of agronomic trait means in SILs and parental lines. (XLS 18 kb)

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Maas, L.F., McClung, A. & McCouch, S. Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Theor Appl Genet 120, 895–908 (2010). https://doi.org/10.1007/s00122-009-1219-7

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  • DOI: https://doi.org/10.1007/s00122-009-1219-7

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