Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome

Chardon, Fabien; Virlon, Bérangère; Moreau, Laurence; Falque, Matthieu; Joets, Johann; Décousset, Laurent; Murigneux, Alain; Charcosset, Alain

doi:10.1534/genetics.104.032375

Cited by 363 publications

(366 citation statements)

References 78 publications

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“…While the effect is relatively weak, this may be explained by the fact that many genes appear to affect flowering time in maize (Chardon et al 2004). A role in flowering time has also been demonstrated for LFY in Arabidopsis with a dosage series experiment that clearly demonstrated that increasing functional LFY copies results in a quantitative dosage-dependent acceleration of flowering time analogous to what we observed in maize (Blázquez et al 1997).…”

Section: Discussionsupporting

confidence: 64%

Pleiotropic Effects of the Duplicate Maize FLORICAULA/LEAFY Genes zfl1 and zfl2 on Traits Under Selection During Maize Domestication

Bomblies¹,

Doebley

2006

Genetics

121

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Phenotypic variation on which selection can act during evolution may be caused by variation in activity level of developmental regulatory genes. In many cases, however, such genes affect multiple traits. This situation can lead to co-evolution of traits, or evolutionary constraint if some pleiotropic effects are detrimental. Here, we present an analysis of quantitative traits associated with gene copy number of two important maize regulatory genes, the duplicate FLORICAULA/LEAFY orthologs zfl1 and zfl2. We found statistically significant associations between several quantitative traits and copy number of both zfl genes in several maize genetic backgrounds. Despite overlap in traits associated with these duplicate genes, zfl1 showed stronger associations with flowering time, while zfl2 associated more strongly with branching and inflorescence structure traits, suggesting some divergence of function. Since zfl2 associates with quantitative variation for ear rank and also maps near a quantitative trait locus (QTL) on chromosome 2 controlling ear rank differences between maize and teosinte, we tested whether zfl2 might have been involved in the evolution of this trait using a QTL complementation test. The results suggest that zfl2 activity is important for the QTL effect, supporting zfl2 as a candidate gene for a role in morphological evolution of maize.T HE identification of genes involved in morphological evolution in both plants and animals has benefited greatly from quantitative trait locus (QTL) studies. Genes underlying QTL causing trait differences in various plant and animal species have been identified, providing an opportunity to study the mechanisms of morphological change under selection. Two important questions for better understanding the mechanisms of the evolution of development are (1) What role do developmental regulatory genes play in the control of quantitative traits?, and (2) Do these genes underlie QTL?Several genes responsible for QTL play important roles in normal development (Mackay 2001). Interestingly, some of the genes identified as QTL have complex or pleiotropic effects on development. For example, the teosinte branched1 (tb1) gene, underlying a QTL involved in maize domestication, affects inflorescence sex, ear size, branch length and tiller number , while in tomato, the fw2.2 locus, which controls changes in fruit shape and size during domestication (Cong et al. 2002;Liu et al. 2003), also plays a quantitative role in fruit number and photosynthate distribution (Nesbitt and Tanksley 2001). Identifying pleiotropic quantitative effects of regulatory genes putatively involved in evolution will help us understand the possibilities and limitations for morphological evolution in populations by shedding light on how trait correlations may arise.In this study, we examine phenotypic variation of several traits associated with maize domestication for association with varying wild-type copy number of the paralogous maize regulatory genes zfl1 and zfl2 (Bomblies et al. 2003). These genes...

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Section: Discussionsupporting

confidence: 64%

Pleiotropic Effects of the Duplicate Maize FLORICAULA/LEAFY Genes zfl1 and zfl2 on Traits Under Selection During Maize Domestication

Bomblies¹,

Doebley

2006

Genetics

121

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“…Early and recent reviews on the genetics of maize flowering time recognized the chromosome region bin 8.05, bearing Vgt1, as a ''hot spot'' for flowering-time QTLs and genes (3,20). Although the genetic resolution reported in those studies was never at the gene level, it is likely that at least some of the reviewed QTLs were due to allele segregation at Vgt1.…”

Section: Discussionmentioning

confidence: 99%

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

Salvi

Sponza

Morgante

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

527

459

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Central America (1), natural genetic variations in flowering time enabled early Native Americans to select maize adapted to a range of latitudes and lengths of growing seasons, including the very short summer season typical of the eastern Canadian region of Quebec. Under such conditions, early flowering allows seed to mature before the onset of frost. Flowering time is also a key trait of improved drought tolerance. Indeed, it has been shown that a single day of drought during flowering can decrease yield by as much as 8% (2). One way to address such losses is to develop and grow cultivars characterized by a short cycle and able to flower before predictable drought episodes.The genetic variability available for maize breeding is essentially quantitative; i.e., it involves allelic variation at different quantitative trait loci (QTLs), which are influenced by environmental effects. Although a large body of mapping information on QTLs is available for flowering time (3), relatively little is known about the molecular basis of QTLs, with only one gene, Dwarf8, correlated thus far with quantitative effects (4, 5). Furthermore, a few mutants for flowering time have been described (6, 7), two of which, id1 (8) and dlf1 (9), have been cloned. Our results (i) show that the allelic variation responsible for the major flowering-time QTL, Vegetative to generative transition 1 (Vgt1) (10, 11) on chromosome 8, is confined to an Ϸ2-kb intergenic region upstream of an Ap2-like flowering-time gene, (ii) identify maize-sorghum-rice evolutionarily conserved noncoding sequences (CNSs) within Vgt1, and (iii) support a cisacting transcription-regulatory role for Vgt1. ResultsPositional Cloning of Vgt1. Previous work (12) mapped Vgt1 to a 1.3-cM region (Fig. 1A) on bin 8.05, based on a mapping population derived from the cross N28 ϫ C22-4. The strain C22-4 is nearly isogenic to N28 and carries the early Vgt1 allele in an Ϸ7-cM introgression originating from the early maize variety Gaspé Flint. By using standard positional cloning, Vgt1 was confined to an Ϸ2-kb region (Fig. 1 B-D). Sequence annotation of the original BAC clone and the corresponding sequences derived from N28 and Gaspé Flint genetic backgrounds showed that Vgt1 is apparently noncoding and is located Ϸ70 kb (61-76 kb, depending on the genetic background) upstream of an Ap2-like gene identified here as ZmRap2.7. This gene is orthologous to Rap2.7 (also known as TOE1), a transcription factor that regulates flowering time in Arabidopsis (13,14). No other genes were annotated between Vgt1 and ZmRap2.7. Pseudogenes due to transduplication events mediated by nonautonomous helitron elements (15) were observed in N28 and other genetic backgrounds but not in Gaspé Flint (data not shown). Within the Vgt1 region, the contrasting QTL alleles showed 29 SNPs and insertion/deletion-type polymorphisms (Indels) and one 143-bp insertion into the Gaspé Flint allele of a Mite transposon belonging to the Tourist (16) family [ Fig. 4 Lower and supporting information (SI) Fig. 5].Association M...

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“…In systems where more QTL studies have been conducted, more formal meta-analyses and computation of a composite map combining several densely genotyped panels may further improve the confidence of QTL/candidate gene colocalization and thus also improve the efficiency of this approach (Arcade et al 2004;Chardon et al 2004). Several observations suggest that genetic hitchhiking is a concern that impacts how effectively improvement loci can be identified, however.…”

Section: Discussionmentioning

confidence: 99%

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

et al. 2011

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Determining the identity and distribution of molecular changes leading to the evolution of modern crop species provides major insights into the timing and nature of historical forces involved in rapid phenotypic evolution. In this study, we employed an integrated candidate gene strategy to identify loci involved in the evolution of flowering time during early domestication and modern improvement of the sunflower (Helianthus annuus). Sunflower homologs of many genes with known functions in flowering time were isolated and cataloged. Then, colocalization with previously mapped quantitative trait loci (QTLs), expression, or protein sequence differences between wild and domesticated sunflower, and molecular evolutionary signatures of selective sweeps were applied as step-wise criteria for narrowing down an original pool of 30 candidates. This process led to the discovery that five paralogs in the FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family experienced selective sweeps during the evolution of cultivated sunflower and may be the causal loci underlying flowering time QTLs. Our findings suggest that gene duplication fosters evolutionary innovation and that natural variation in both coding and regulatory sequences of these paralogs responded to a complex history of artificial selection on flowering time during the evolution of cultivated sunflower.

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Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome

Cited by 363 publications

References 78 publications

Pleiotropic Effects of the Duplicate Maize FLORICAULA/LEAFY Genes zfl1 and zfl2 on Traits Under Selection During Maize Domestication

Pleiotropic Effects of the Duplicate Maize FLORICAULA/LEAFY Genes zfl1 and zfl2 on Traits Under Selection During Maize Domestication

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

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