A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies

(2012) P Xu et al.   HEREDITY

The Origin of Spelt and Free-Threshing Hexaploid Wheat

(2012) J. Dvorak et al.   JOURNAL OF HEREDITY

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

Control of grain size, shape and quality by OsSPL16 in rice

(2012) Shaokui Wang et al.   NATURE GENETICS

Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum)

(2012) Aurora Díaz et al.   PLoS One

Evolution and Association Analysis of Ghd7 in Rice

(2012) Li Lu et al.   PLoS One

Evolution of Neutral and Flowering Genes along Pearl Millet (Pennisetum glaucum) Domestication

(2012) Ghayas Lakis et al.   PLoS One

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

(2012) C. Riedelsheimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular genetic basis of pod corn (Tunicate maize)

(2012) L. U. Wingen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1

(2012) Y. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical genomics of North American maize

(2012) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

(2012) H.-Y. Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maize genetic diversity and association mapping using transposable element insertion polymorphisms

(2012) Tatiana Zerjal et al.   THEORETICAL AND APPLIED GENETICS

New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

(2012) Amandine Cornille et al.   PLoS Genetics

Escape from Preferential Retention Following Repeated Whole Genome Duplications in Plants

(2012) James C. Schnable et al.   Frontiers in Plant Science

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

(2011) Eduard D Akhunov et al.   BMC GENOMICS

Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice

(2011) J. M. Flowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary History of Pearl Millet (Pennisetum glaucum [L.] R. Br.) and Selection on Flowering Genes since Its Domestication

(2011) J. Clotault et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1

(2011) Luke Ramsay et al.   NATURE GENETICS

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

(2011) Kristen L Kump et al.   NATURE GENETICS

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Natural variation in GS5 plays an important role in regulating grain size and yield in rice

(2011) Yibo Li et al.   NATURE GENETICS

Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels

(2011) J. P. Cook et al.   PLANT PHYSIOLOGY

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication

(2011) B.-F. Zhu et al.   PLANT PHYSIOLOGY

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

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

Cereal Domestication and Evolution of Branching: Evidence for Soft Selection in the Tb1 Orthologue of Pearl Millet (Pennisetum glaucum [L.] R. Br.)

(2011) Marie-Stanislas Remigereau et al.   PLoS One

Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium)

(2011) Y. Bao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

(2011) J. A. Poland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Artificial selection for a green revolution gene during japonica rice domestication

(2011) K. Asano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

(2011) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association mapping of agronomic traits in sugar beet

(2011) Tobias Würschum et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize

(2011) Patrick J. Brown et al.   PLoS Genetics

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication

(2010) Ryan A Rapp et al.   BMC BIOLOGY

Sequence variation and selection of small RNAs in domesticated rice

(2010) Yu Wang et al.   BMC EVOLUTIONARY BIOLOGY

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

(2010) Ertao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats

(2010) Kseniya A Golovnina et al.   BMC PLANT BIOLOGY

The Role of Recently Derived FT Paralogs in Sunflower Domestication

(2010) Benjamin K. Blackman et al.   CURRENT BIOLOGY

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

(2010) B. K. Blackman et al.   GENETICS

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Molecular Basis of the Waxy Endosperm Starch Phenotype in Broomcorn Millet (Panicum miliaceum L.)

(2010) H. V. Hunt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Soft selective sweep near a gene that increases plant height in wheat

(2010) A.-L. RAQUIN et al.   MOLECULAR ECOLOGY

Evidence of selection at theramosa1locus during maize domestication

(2010) BRANDI SIGMON et al.   MOLECULAR ECOLOGY

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Artificial selection for determinate growth habit in soybean

(2010) Z. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic signals of origin, spread, and introgression in a large sample of maize landraces

(2010) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice

(2010) K. Sugimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals

(2010) Andrea K. Knox et al.   THEORETICAL AND APPLIED GENETICS

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

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

Domestication of plants revisited - Darwin to the present day

(2009) BARBARA PICKERSGILL   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Domestication and plant genomes

(2009) Haibao Tang et al.   CURRENT OPINION IN PLANT BIOLOGY

Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet

(2009) A.-A. Saidou et al.   GENETICS

Evolutionary History of GS3 , a Gene Conferring Grain Length in Rice

(2009) Noriko Takano-Kai et al.   GENETICS

Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.)

(2009) Andrej Benjak et al.   Genome Biology and Evolution

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

(2009) A Fournier-Level et al.   HEREDITY

Waxy strains of three amaranth grains raised by different mutations in the coding region

(2009) Young-Jun Park et al.   MOLECULAR BREEDING

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa)

(2009) Briana L. Gross et al.   NEW PHYTOLOGIST

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

Post-Domestication Selection in the Maize Starch Pathway

(2009) Longjiang Fan et al.   PLoS One

The origin and evolution of fragrance in rice (Oryza sativa L.)

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

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

The Palomero Genome Suggests Metal Effects on Domestication

(2009) J.-P. Vielle-Calzada et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Molecular insights into the evolution of crop plants

(2008) Jutta C. Burger et al.   AMERICAN JOURNAL OF BOTANY

Evolutionary Genetics of Genome Merger and Doubling in Plants

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

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Parallel Domestication, Convergent Evolution and Duplicated Gene Recruitment in Allopolyploid Cotton

(2008) R. Hovav et al.   GENETICS

Breeding Designs for Recombinant Inbred Advanced Intercross Lines

(2008) Matthew V. Rockman et al.   GENETICS

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular evidence for post-domestication selection in the Waxy gene of Chinese waxy maize

(2008) Longjiang Fan et al.   MOLECULAR BREEDING

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication

(2008) Bin Cong et al.   NATURE GENETICS

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

(2008) Weiya Xue et al.   NATURE GENETICS

Control of a key transition from prostrate to erect growth in rice domestication

(2008) Lubin Tan et al.   NATURE GENETICS

Control of rice grain-filling and yield by a gene with a potential signature of domestication

(2008) Ertao Wang et al.   NATURE GENETICS

Genetic control of rice plant architecture under domestication

(2008) Jian Jin et al.   NATURE GENETICS

Deletion in a gene associated with grain size increased yields during rice domestication

(2008) Ayahiko Shomura et al.   NATURE GENETICS

Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication

(2008) Y. Yu et al.   PLANT CELL

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

(2008) M. A. Chapman et al.   PLANT CELL

Genetic and Molecular Characterization of the VRN2 Loci in Tetraploid Wheat

(2008) A. Distelfeld et al.   PLANT PHYSIOLOGY

The Evolution of Spinnable Cotton Fiber Entailed Prolonged Development and a Novel Metabolism

(2008) Ran Hovav et al.   PLoS Genetics

Genome-Wide Analysis of the “Cut-and-Paste” Transposons of Grapevine

(2008) Andrej Benjak et al.   PLoS One

Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway

(2008) S. Taketa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE