Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

Blackman, Benjamin K.; Rasmussen, David A.; Strasburg, Jared L.; Raduski, Andrew R.; Burke, John M.; Knapp, Steven J.; Michaels, Scott D.; Rieseberg, Loren H.

doi:10.1534/genetics.110.121327

Cited by 82 publications

(76 citation statements)

References 151 publications

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“…Because c4973 had been sequenced previously only on a small sample of American landraces, we obtained additional sequences from our diversity panel to sample c4973 sequence diversity more thoroughly in North American landraces (Tables S1 and S5). Sequence data for seven putative neutral loci were obtained for a previously published study of this diversity panel (Table S5) (31). HaFT1 PCR products were digested with BstEII to genotype individuals for the frameshift mutation nearly fixed in domesticated haplotypes.…”

Section: Methodsmentioning

confidence: 99%

“…An 885-bp portion of the gibberellin 2-oxidase homolog HaGA2ox was examined as part of an ongoing study of a genetic diversity panel from the United States and Canada (31). This panel included 18 individuals from improved modern crop lines, 19 individuals from Native American landraces, and 23 individuals from a geographically diverse sample of wild sunflower populations (Table S1).…”

Section: Selection On Gibberellin 2-oxidase Homolog Haga2ox During Earlymentioning

confidence: 99%

“…All coding substitutions along the branch distinguishing the domesticated and wild haplotypes were synonymous changes. A maximumlikelihood Hudson-Kreitman-Aguadé (HKA) test, which compares the likelihood of a neutral evolutionary model of polymorphism and divergence with the likelihood of a model in which a candidate gene is under selection, was conducted for HaGA2ox and seven previously sequenced putative neutral loci (31,32). Although HaGA2ox was found to be evolving neutrally in wild populations (P = 0.9748), there were significant signatures of a selective sweep in the landrace (P = 0.0032) and improved pools (P = 0.0002).…”

Section: Selection On Gibberellin 2-oxidase Homolog Haga2ox During Earlymentioning

confidence: 99%

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Sunflower domestication alleles support single domestication center in eastern North America

Blackman

Scascitelli

Kane

et al. 2011

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

105

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Phylogenetic analyses of genes with demonstrated involvement in evolutionary transitions can be an important means of resolving conflicting hypotheses about evolutionary history or process. In sunflower, two genes have previously been shown to have experienced selective sweeps during its early domestication. In the present study, we identified a third candidate early domestication gene and conducted haplotype analyses of all three genes to address a recent, controversial hypothesis about the origin of cultivated sunflower. Although the scientific consensus had long been that sunflower was domesticated once in eastern North America, the discovery of preColumbian sunflower remains at archaeological sites in Mexico led to the proposal of a second domestication center in southern Mexico. Previous molecular studies with neutral markers were consistent with the former hypothesis. However, only two indigenous Mexican cultivars were included in these studies, and their provenance and genetic purity have been questioned. Therefore, we sequenced regions of the three candidate domestication genes containing SNPs diagnostic for domestication from large, newly collected samples of Mexican sunflower landraces and Mexican wild populations from a broad geographic range. The new germplasm also was genotyped for 12 microsatellite loci. Our evidence from multiple evolutionarily important loci and from neutral markers supports a single domestication event for extant cultivated sunflower in eastern North America.agriculture | Helianthus annuus | phylogeography M any genetic changes essential for crop evolution have been identified, and these alleles provide useful tools for inferring how, where, and when early societies transformed wild plants into agricultural staples (1, 2). Examining sequence diversity of these alleles in cultivated lineages, wild progenitors, and archaeological specimens can reveal critical information about the rate, timing, geography, and order of the domestication process (3). For instance, sequences of domestication loci obtained from archaeological maize cobs indicated that although domestication alleles for two traits became fixed early, fixation of domestication alleles for a third trait occurred several thousand years later (4). Patterns of sequence diversity around domestication alleles have yielded estimates of the strength of selection during domestication for several loci in rice and maize (5-7). In addition, the geographic distributions of domestication alleles in extant cultivated and wild germplasm have been used to assess how crops and crop alleles have spread from domestication centers and reveal whether convergent traits in independent lineages evolved from the same or unique suites of mutations (5,(8)(9)(10)(11).Here, we examine three genes that experienced selective sweeps during early domestication of sunflower, Helianthus annuus, to address a recent controversy about the number and location of sunflower domestication centers (12-17).

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Section: Methodsmentioning

confidence: 99%

Section: Selection On Gibberellin 2-oxidase Homolog Haga2ox During Earlymentioning

confidence: 99%

Section: Selection On Gibberellin 2-oxidase Homolog Haga2ox During Earlymentioning

confidence: 99%

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Sunflower domestication alleles support single domestication center in eastern North America

Blackman

Scascitelli

Kane

et al. 2011

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

105

View full text Add to dashboard Cite

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“…In Arabidopsis, under long days, GI acts earlier in the pathway than CONSTANS (CO) and FLOWERING TIME (FT), by increasing the CO and FT mRNA abundance. CO and FT were targets of selection during domestication of crops such as rice (Takahashi and Shimamoto, 2011;Wu et al, 2013) and sunflower (Helianthus annuus; Blackman et al, 2011). In pea (Pisum sativum), Hecht et al (2007) identified LATE BLOOMER1 (LATE1) as the pea ortholog of Arabidopsis GI and showed that LATE1 is necessary for the promotion of flowering, the production of a mobile flowering stimulus, and the induction of an FT homolog under long-day conditions.…”

Section: Selectionmentioning

confidence: 99%

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

et al. 2014

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ORCID ID: 0000-0001-9598-3131 (R.P.)Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ;190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (;60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.

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“…The TE-mediated duplication of the tomato SUN gene described above provides one such example. Another well documented instance involves paralogous copies of the flowering time gene FT ( FLOWERING LOCUS T) in sunflower and selection for changes in flowering time during domestication and later crop improvement (Blackman et al, 2010, 2011). FT genes function as positive regulators of reproductive meristem development, and Blackman and colleagues were able to identify four paralogous copies in sunflower, three of which appear to be functional and show evidence of having played a role in a shift toward later flowering time during sunflower domestication.…”

Section: Genetic Basis Of Domestication Phenotypesmentioning

confidence: 99%

Crop plants as models for understanding plant adaptation and diversification

Olsen¹,

Wendel²

2013

Front. Plant Sci.

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Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of “domestication syndrome” traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various “omics” involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution.

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Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

Cited by 82 publications

References 151 publications

Sunflower domestication alleles support single domestication center in eastern North America

Sunflower domestication alleles support single domestication center in eastern North America

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

Crop plants as models for understanding plant adaptation and diversification

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