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Comparative Study
. 2007 Jul 3;104(27):11376-81.
doi: 10.1073/pnas.0704145104. Epub 2007 Jun 26.

Conserved Noncoding Genomic Sequences Associated With a Flowering-Time Quantitative Trait Locus in Maize

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Free PMC article
Comparative Study

Conserved Noncoding Genomic Sequences Associated With a Flowering-Time Quantitative Trait Locus in Maize

Silvio Salvi et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

Flowering time is a fundamental trait of maize adaptation to different agricultural environments. Although a large body of information is available on the map position of quantitative trait loci for flowering time, little is known about the molecular basis of quantitative trait loci. Through positional cloning and association mapping, we resolved the major flowering-time quantitative trait locus, Vegetative to generative transition 1 (Vgt1), to an approximately 2-kb noncoding region positioned 70 kb upstream of an Ap2-like transcription factor that we have shown to be involved in flowering-time control. Vgt1 functions as a cis-acting regulatory element as indicated by the correlation of the Vgt1 alleles with the transcript expression levels of the downstream gene. Additionally, within Vgt1, we identified evolutionarily conserved noncoding sequences across the maize-sorghum-rice lineages. Our results support the notion that changes in distant cis-acting regulatory regions are a key component of plant genetic adaptation throughout breeding and evolution.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Positional cloning of Vgt1. (A) QTL logarithm of odds (LOD) profile for node number (ND) and relative position for Vgt1 and relevant markers (redrawn and integrated from ref. 12). (B) Identification of Mo17 BAC covering the Vgt1 locus and sequence annotation. Gray arrows indicate coding sequences. Details on the nature and position of all 30 sequence polymorphisms between N28 and C22–4 (carrying the Gaspé Flint allele) at Vgt1 are provided in SI Fig. 5. (C) Graphic genotypes of the parental lines N28 and C22–4 and 17 segmental QTL nearly isogenic lines (NILs) carrying crossovers around Vgt1. Column codes indicate marker names, details of which are given in SI Table 2. Orange and green colors indicate homozygosity for Gaspé Flint and N28 alleles, respectively. (D) Phenotypic values recorded for the parental lines N28 and C22–4 and the 17 QTL NILs. Blue columns indicate the total number of plant nodes (ND). Bars indicate SD.
Fig. 2.
Fig. 2.
Association of DNA polymorphisms with flowering time across the Vgt1 chromosome region. Level of statistical association for each SNP is expressed as −Log(P). Blue diamonds and white squares indicate association with male flowering date [expressed as days to pollen shed (DPS)] and total number of nodes of the plant (ND). Red points indicate r2 LD scores for all marker pairs involving Mite (value at Mite and at Mite totally linked markers is therefore r2 = 1). The nine numbers (1, 3, 6, …, 18) under the horizontal axes indicate codes for amplicons that were sequenced for SNP identification (SI Table 3). To simplify the view, the positions of other markers used in association analysis are not shown (for full details see SI Table 3).
Fig. 3.
Fig. 3.
Effect of overexpressing ZmRap2.7 on maize flowering time. Plants shown belong to a T1 family derived by selfing a transgenic T0 plant. Molecular genotypes of all plants were checked by PCR (data not shown). Segregating transgenic plants (two on left, homozygous or heterozygous for the transgenic event) are taller (have a higher number of nodes) and late flowering. Segregating nontransgenic plants (three on right) are smaller and early flowering, as typical of this genetic background.
Fig. 4.
Fig. 4.
CNSs between the maize Vgt1 region and orthologous sorghum and rice sequences. (Upper) mVISTA plot of sequence identity of the maize BAC sequence spanning Vgt1 and the two most proximal genes (length of maize sequence considered was 81 kb) with the corresponding sorghum and rice orthologous sequences (50 and 35 kb, respectively). Peaks indicate region of similarity (percent of identity) for a window length set to 100 bp. Position of coding sequences and Vgt1 are indicated by the arrows and box. The lack of synteny observed within ZmRad51 is likely due to a transposon insertion in the maize gene (data not shown). Numbers refer to base pair position on maize BAC b0288K09. (Lower) Alignment of maize (C22–4/Gaspé Flint and N28), sorghum, and rice sequences corresponding to CNS1 (shown by an asterisk) and identified by using BLAST 2 Sequences. Nonconserved nucleotides within CNS1 are shown in bold. The sequence corresponding to the Mite element disrupting the C22–4/Gaspé Flint allele and the 3-bp duplicated target site are shown in blue and red, respectively. The numbers report the base pair position on BAC clones or genomic sequences (SI Materials and Methods).

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