Molecular Tools for Exploring Polyploid Genomes in Plants

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species

(2012) Daniel C. Ilut et al.   AMERICAN JOURNAL OF BOTANY

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

(2012) Thijs van Dijk et al.   BMC PLANT BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Advances in plant genome sequencing

(2012) John P. Hamilton et al.   PLANT JOURNAL

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics

(2011) Anthony Levasseur et al.   Biology Direct

Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

(2011) Yuanhong Han et al.   BMC GENOMICS

Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors

(2011) D W-K Ng et al.   HEREDITY

High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.)

(2011) Yuanhong Han et al.   MOLECULAR BREEDING

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing

(2011) Ian Bancroft et al.   NATURE BIOTECHNOLOGY

Transgenic maize plants expressing the Totivirus antifungal protein, KP4, are highly resistant to corn smut

(2011) Aron Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species

(2011) Sukhjiwan Kaur et al.   PLANT BIOTECHNOLOGY JOURNAL

cis- andtrans-Regulation of miR163 and Target Genes Confers Natural Variation of Secondary Metabolites in TwoArabidopsisSpecies and Their Allopolyploids

(2011) Danny W-K. Ng et al.   PLANT CELL

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.

(2011) R. E. Oliver et al.   THEORETICAL AND APPLIED GENETICS

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

(2011) Cyrille Saintenac et al.   GENOME BIOLOGY

Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton

(2010) Kai Wang et al.   CHROMOSOMA

Genetic and Epigenetic Dynamics of a Retrotransposon After Allopolyploidization of Wheat

(2010) Z. Kraitshtein et al.   GENETICS

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

(2010) Jeremy E. Coate et al.   Genome Biology and Evolution

Characterization of duplicate gene evolution in the recent natural allopolyploidTragopogon miscellusby next-generation sequencing and Sequenom iPLEX MassARRAY genotyping

(2010) RICHARD J. A. BUGGS et al.   MOLECULAR ECOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

The first meiosis of resynthesized Brassica napus, a genome blender

(2010) E. Szadkowski et al.   NEW PHYTOLOGIST

Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae)

(2010) Houda Chelaifa et al.   NEW PHYTOLOGIST

Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids

(2010) Véronique Chagué et al.   NEW PHYTOLOGIST

Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation

(2010) Anne Marmagne et al.   NEW PHYTOLOGIST

Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes in Brassica napus Allohaploids

(2010) M. Cifuentes et al.   PLANT CELL

Phenotypic and gene expression analyses of a ploidy series of maize inbred Oh43

(2010) Hong Yao et al.   PLANT MOLECULAR BIOLOGY

Impact of natural genetic variation on the transcriptome of autotetraploidArabidopsis thaliana

(2010) Zheng Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The CYCLIN-A CYCA1;2/TAM Is Required for the Meiosis I to Meiosis II Transition and Cooperates with OSD1 for the Prophase to First Meiotic Division Transition

(2010) Isabelle d'Erfurth et al.   PLoS Genetics

Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)

(2009) Bhupendra Chaudhary et al.   BMC GENOMICS

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

(2009) R J A Buggs et al.   HEREDITY

Along the speciation continuum in sticklebacks

(2009) A. P. Hendry et al.   JOURNAL OF FISH BIOLOGY

The allotetraploid Arabidopsis thaliana–Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants

(2009) Julien Beaulieu et al.   MOLECULAR GENETICS AND GENOMICS

Homoeologous nonreciprocal recombination in polyploid cotton

(2009) Armel Salmon et al.   NEW PHYTOLOGIST

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

(2009) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic Regulation of Meiotic Cross-Overs between Related Genomes in Brassica napus Haploids and Hybrids

(2009) S. D. Nicolas et al.   PLANT CELL

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

(2009) J. A. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus

(2009) Warren Albertin et al.   PROTEOMICS

Turning Meiosis into Mitosis

(2009) Isabelle d'Erfurth et al.   PLOS BIOLOGY

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis

(2009) Aleksandra Erilova et al.   PLoS Genetics

Origin and Early Evolution of Angiosperms

(2008) Douglas E. Soltis et al.   Annals of the New York Academy of Sciences

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)

(2008) M. L. Ainouche et al.   BIOLOGICAL INVASIONS

High-Resolution Melting Curve Analysis of Genomic and Whole-Genome Amplified DNA

(2008) M. H. Cho et al.   CLINICAL CHEMISTRY

Diploid/Polyploid Syntenic Shuttle Mapping and Haplotype-Specific Chromosome Walking Toward a Rust Resistance Gene (Bru1) in Highly Polyploid Sugarcane (2n   12x   115)

(2008) L. Le Cunff et al.   GENETICS

Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat

(2008) M. Pumphrey et al.   GENETICS

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

(2008) Elliott H. Margulies et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean

(2008) R. W. Innes et al.   PLANT PHYSIOLOGY

Replication of Nonautonomous Retroelements in Soybean Appears to Be Both Recent and Common

(2008) A. Wawrzynski et al.   PLANT PHYSIOLOGY

A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

(2008) E. Paux et al.   SCIENCE

Mutations in AtPS1 (Arabidopsis thaliana Parallel Spindle 1) Lead to the Production of Diploid Pollen Grains

(2008) Isabelle d'Erfurth et al.   PLoS Genetics