Works (12)

Updated: July 26th, 2023 21:14

2009 journal article

Complex Rearrangements Lead to Novel Chimeric Gene Fusion Polymorphisms at the Arabidopsis thaliana MAF2-5 Flowering Time Gene Cluster

MOLECULAR BIOLOGY AND EVOLUTION, 26(3), 699–711.

author keywords: alternative splicing; gene origin; gene fusion; MADS-box; quantitative trait loci
MeSH headings : Arabidopsis / genetics; Arabidopsis Proteins / genetics; Flowers / genetics; Gene Fusion; Gene Rearrangement; Genes, Plant; MADS Domain Proteins / genetics; Multigene Family; Polymorphism, Genetic; Polymorphism, Single Nucleotide
TL;DR: The finding that complex rearrangements within gene clusters, such as those observed for MAF2, might play a role in the generation of ecologically important phenotypic variation, emphasize the need for emerging high throughput genotyping and sequencing techniques to correctly reconstruct gene chimeras and other complex polymorphisms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 article

Darwinian selection on a selfing locus (vol 306, pg 2081, 2004)

Science, Vol. 320, pp. 176–176.

By: K. Shimizu, J. Reininga, A. Caicedo, C. Mays, R. Moore, K. Olsen, S. Ruzsa, G. Coop, C. Bustamante, M. Purugganan

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field

AMERICAN NATURALIST, 169(5), E141–E157.

By: T. Korves, K. Schmid, A. Caicedo*, C. Mays*, J. Stinchcombe, M. Purugganan*, J. Schmitt

author keywords: epistasis; FLOWERING LOCUS C (FLC); population structure; vernalization; candidate gene association; heterogeneous selection
MeSH headings : Analysis of Variance; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Epistasis, Genetic; Evolution, Molecular; Flowers / genetics; Flowers / growth & development; Genetic Variation; Genetics, Population; Genotype; MADS Domain Proteins / genetics; Rhode Island; Seasons; Selection, Genetic; Survival Analysis
TL;DR: The results suggest that the combined effects of seasonally varying selection and epistasis could explain the maintenance of variation at FRI and, more generally, may be important in the evolution of genes underlying complex traits. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Genome-wide patterns of nucleotide polymorphism in domesticated rice

PLOS GENETICS, 3(9), 1745–1756.

By: A. Caicedo n, S. Williamson*, R. Hernandez*, A. Boyko*, A. Fledel-Alon*, T. York*, N. Polato*, K. Olsen n ...

MeSH headings : Alleles; Base Pairing; Base Sequence; Computer Simulation; Crops, Agricultural / genetics; Evolution, Molecular; Founder Effect; Gene Frequency; Genetic Variation; Genetics, Population; Genome, Plant; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Oryza / genetics; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Recombination, Genetic; Selection, Genetic; Sequence Analysis, DNA
TL;DR: It is found that a simple bottleneck model cannot explain the derived nucleotide polymorphism site frequency spectrum in rice, and a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow are more plausible explanations for patterns of variation in domesticated rice varieties. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

The extent of linkage disequilibrium in rice (Oryza sativa L.)

GENETICS, 177(4), 2223–2232.

By: K. Mather n, A. Caicedo n, N. Polato*, K. Olsen n, S. McCouch* & M. Purugganan n

MeSH headings : Base Sequence; Crops, Agricultural / genetics; Genetic Linkage; Genome, Plant; Linkage Disequilibrium; Molecular Sequence Data; Oryza / genetics; Polymorphism, Single Nucleotide; Recombination, Genetic
TL;DR: The feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs is demonstrated and variation in LD patterns among genomic regions is suggested. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Selection under domestication: Evidence for a sweep in the rice Waxy genomic region

GENETICS, 173(2), 975–983.

By: K. Olsen n, A. Caicedo n, N. Polato*, A. McClung, S. McCouch* & M. Purugganan n

MeSH headings : Agriculture; Amylose / metabolism; DNA, Plant / genetics; Evolution, Molecular; Genetic Variation; Genome, Plant; Mutation; Oryza / classification; Oryza / genetics; Oryza / metabolism; Plant Proteins / genetics; Selection, Genetic; Species Specificity; Starch Synthase / genetics
TL;DR: Findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2005 article

Comparative plant genomics. Frontiers and prospects

Caicedo, A. L., & Purugganan, M. D. (2005, June). PLANT PHYSIOLOGY, Vol. 138, pp. 545–547.

By: A. Caicedo n & M. Purugganan n

MeSH headings : Biological Evolution; Expressed Sequence Tags; Gene Expression Profiling; Genome, Plant; Genomic Library; Genomics / trends; Phylogeny
TL;DR: The availability of whole-genome sequences as well as other genomic resources (e.g. microarray methods, expressed sequence tag [EST] libraries) and comparisons have long been the cornerstone of studies that draw inferences about function and evolution at various levels of biological organization. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science; OpenAlex)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Vernalization sensitivity in Arabidopsis thaliana (brassicaceae): The effects of latitude and FLC variation

AMERICAN JOURNAL OF BOTANY, 92(10), 1701–1707.

author keywords: Brassicaceae; ecological genomics; FLC; flowering time; FRI; latitudinal cline; vernalization
TL;DR: A significant latitudinal cline in vernalization sensitivity was observed: southern accessions were more sensitive to vernnalization than northern accessions, and accessions that were late flowering in the absence of vernAlization were moresensitive to Vernalization cues. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 article

Darwinian selection on a selfing locus (Retracted Article. See vol 320, pg 176, 2008)

Shimizu, K. K., Cork, J. M., Caicedo, A. L., Mays, C. A., Moore, R. C., Olsen, K. M., … Purugganan, M. D. (2004, December 17). SCIENCE, Vol. 306, pp. 2081–2084.

By: K. Shimizu n, J. Cork n, A. Caicedo n, C. Mays n, R. Moore n, K. Olsen n, S. Ruzsa n, G. Coop n ...

MeSH headings : Alleles; Arabidopsis / genetics; Arabidopsis / physiology; Biological Evolution; Chromosome Mapping; Climate; DNA, Intergenic; Genes, Plant; Genetic Variation; Genome, Plant; Geography; Haplotypes; Likelihood Functions; Molecular Sequence Data; Open Reading Frames; Phylogeny; Plant Proteins; Pollen; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Protein Kinases / genetics; Protein Kinases / physiology; Pseudogenes; Recombination, Genetic; Selection, Genetic; Time
TL;DR: Coalescent simulations indicate that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response, and suggest that the post-Pleistocene expansion of A. thaliana from glacial refugia may have been associated with this adaptive event. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(44), 15670–15675.

author keywords: rosette leaf number; alternative splicing; linkage disequilibrium; epistatic selection; candidate gene association
MeSH headings : Alternative Splicing; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Base Sequence; DNA, Plant / genetics; Epistasis, Genetic; Evolution, Molecular; Flowers / growth & development; Genes, Plant; Genetics, Population; Genotype; Haplotypes; Linkage Disequilibrium; MADS Domain Proteins / genetics; Molecular Sequence Data; Polymorphism, Single Nucleotide; Sequence Homology, Nucleic Acid; Time Factors
TL;DR: It is suggested that developmental genetic pathways and networks provide the molecular basis for epistasis, contributing to ecologically important phenotypic variation in natural populations and to the process of evolutionary diversification. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(50), 17444–17449.

By: A. Caicedo* & B. Schaal*

author keywords: Cf-2 locus; evolution; plant disease-resistant genes
MeSH headings : Evolution, Molecular; Gene Dosage; Genes, Plant / genetics; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Polymorphism, Genetic / genetics; Selection, Genetic; Solanum / genetics
TL;DR: DNA sequence variation of Cf-2 homologs was surveyed in populations of Solanum pimpinellifolium, a wild relative of the cultivated tomato, involved in resistance to strains of the fungus Cladosporium fulvum, to illustrate the wealth of R gene diversity that exists in wild plant populations, as well as the complexity of interacting genetic and evolutionary processes that generate such diversity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene

MOLECULAR ECOLOGY, 13(7), 1871–1882.

By: A. Caicedo* & B. Schaal*

author keywords: gene genealogy; isolation by distance; lineage sorting; mating system; vacuolar invertase
MeSH headings : Analysis of Variance; Base Sequence; DNA Primers; Genetic Variation; Genetics, Population; Geography; Haplotypes / genetics; Models, Genetic; Molecular Sequence Data; Nuclear Proteins / genetics; Peru; Phylogeny; Sequence Alignment; Sequence Analysis, DNA; Solanum / genetics
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

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