Academic journal article Genetics

Substitution Mapping of Dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated with Transgressive Variation in Rice, Reveals Multiple Sub-QTL

Academic journal article Genetics

Substitution Mapping of Dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated with Transgressive Variation in Rice, Reveals Multiple Sub-QTL

Article excerpt

ABSTRACT

A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.

A wide range of natural variation for flowering time exists in wild and cultivated rice (Oryza saiiva) varieties around the world. In contrast to Arabidopsis, which is a long-day plant, short days promote flowering in rice. Tropical rice varieties tend to be most sensitive to variations in photoperiod, with especially prolonged flowering under long days. As rice has been adapted to more temperate climates, it has been selected for photoperiod insensitivity to ensure normal flowering times under long days. Recent quantitative trait loci (QTL) studies have confirmed that multiple genes control the time to flowering, with multiple flowering-time loci, or heading-date QTL, segregating in any one population. Hundreds of heading-date QTL reported in >20 different studies in rice are documented at http://vwm. gramene.org. Strategies involving near-isogenic lines (NIL) development, high-resolution mapping, and QTL cloning have further characterized several headingdate QTL in rice (YAMAMOTO et al. 1998; LIN et al. 2000, 2003; YANO et al. 2000; TAKAHASHI et al. 2001; KOJIMA et al. 2002; MONNA et al. 2002).

The regulation of flowering time in plants has been most thoroughly studied in the model plant Arabidopsis where at least four distinct genetic pathways are involved in the transition from the vegetative to the reproductive stage. They are the photoperiod promotion pathway, the constitutive or autonomous pathway, the vernalization pathway, and the gibberellic acid promotion pathway (MOURADOV et al. 2002; SIMPSON and DEAN 2002; YANOVSKY and KAY 2003; PUTTERILL et al. 2004). Recent studies have identified putatively orthologous floweringtime genes in rice and Arabidopsis (IzAWA et al. 2003). These studies confirm the presence of a conserved photoperiod pathway between Arabidopsis and rice, while at the same time providing clues to the reversal of gene function leading to the difference between shortday and long-day plants (HAYAMA and COUPLAND 2004; PUTTERILL et al 2004).

One of the unresolved questions in the study of quantitative traits concerns the molecular basis for transgressive variation. The occurrence of progeny displaying phenotypes more extreme than either parent has been observed for decades, and selection of offspring that are "better than the better parent" has long been practiced in the field of plant breeding. QTL analysis provides a way of identifying specific regions of chromosomes that contain genes associated with transgressive variation (DEVICENTE and TANKSLEY 1993; TANKSLEY and McCoucH 1997; RIESEBERG et al 2003). Transgressive variation for flowering time in rice has been detected in studies employing the wild relative Oryza rufipogon in crosses with four different cultivated varieties (XiAO et al. …

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