Connecting genome structural variation with complex traits in crop plants

Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

(2018) Aude Darracq et al.   BMC GENOMICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Finding invisible quantitative trait loci with missing data

(2018) Iulian Gabur et al.   PLANT BIOTECHNOLOGY JOURNAL

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

(2018) Bhavna Hurgobin et al.   PLANT BIOTECHNOLOGY JOURNAL

INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.)

(2018) Candy M. Taylor et al.   PLANT CELL AND ENVIRONMENT

Detecting de Novo Homoeologous Recombination Events in Cultivated Brassica napus Using a Genome-Wide SNP Array

(2018) Erin E. Higgins et al.   G3-Genes Genomes Genetics

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata

(2017) Jun Zou et al.   PLANT BIOTECHNOLOGY JOURNAL

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

(2017) Anna Stein et al.   PLANT BIOTECHNOLOGY JOURNAL

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

The pangenome of hexaploid bread wheat

(2017) Juan D. Montenegro et al.   PLANT JOURNAL

Copy number variations ofCBFgenes at theFr-A2locus are essential components of winter hardiness in wheat

(2017) Tobias Würschum et al.   PLANT JOURNAL

A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array

(2017) Annaliese S. Mason et al.   THEORETICAL AND APPLIED GENETICS

The soybean GmSNAP18 gene underlies two types of resistance to soybean cyst nematode

(2017) Shiming Liu et al.   Nature Communications

Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species

(2017) Birgit Samans et al.   Plant Genome

Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus

(2017) Ting Xiang Neik et al.   Frontiers in Plant Science

Targeted deep sequencing of flowering regulators in Brassica napus reveals extensive copy number variation

(2017) Sarah Schiessl et al.   Scientific Data

Post-polyploidisation morphotype diversification associates with gene copy number variation

(2017) Sarah Schiessl et al.   Scientific Reports

gsrc: an R package for genome structure rearrangement calling

(2016) Fabian Grandke et al.   BIOINFORMATICS

The impact and origin of copy number variations in the Oryza species

(2016) Zetao Bai et al.   BMC GENOMICS

Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

(2016) N Ali et al.   HEREDITY

Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus

(2016) Lunwen Qian et al.   Molecular Plant

Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings

(2016) Xianglan Wang et al.   NATURE GENETICS

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

(2016) A. S. Mason et al.   PLANT BIOLOGY

Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization

(2016) Zhesi He et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

(2016) Michael A. Hardigan et al.   PLANT CELL

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

(2016) Enrico Francia et al.   PLANT MOLECULAR BIOLOGY

Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat

(2016) Alisa-Naomi Sieber et al.   THEORETICAL AND APPLIED GENETICS

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

(2016) Miao Liu et al.   Scientific Reports

Putative interchromosomal rearrangements in the hexaploid wheat (Triticum aestivum L.) genotype ‘Chinese Spring’ revealed by gene locations on homoeologous chromosomes

(2015) Jian Ma et al.   BMC EVOLUTIONARY BIOLOGY

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat

(2015) Tobias Würschum et al.   BMC GENETICS

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

A decade of structural variants: description, history and methods to detect structural variation

(2015) Geòrgia Escaramís et al.   Briefings in Functional Genomics

Evolution and selection ofRhg1,a copy-number variant nematode-resistance locus

(2015) Tong Geon Lee et al.   MOLECULAR ECOLOGY

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

Understanding and utilizing crop genome diversity via high-resolution genotyping

(2015) Kai Voss-Fels et al.   PLANT BIOTECHNOLOGY JOURNAL

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

High-resolution genetic mapping of maize pan-genome sequence anchors

(2015) Fei Lu et al.   Nature Communications

Copy Number Variation of Cytokinin Oxidase Gene Tackx4 Associated with Grain Weight and Chlorophyll Content of Flag Leaf in Common Wheat

(2015) Cheng Chang et al.   PLoS One

Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads

(2014) Jan Schröder et al.   BIOINFORMATICS

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

(2014) Ke Lin et al.   BMC GENOMICS

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

(2014) Emma Mace et al.   BMC PLANT BIOLOGY

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

(2014) Wei Wang et al.   PLoS One

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

A Roadmap for Functional Structural Variants in the Soybean Genome

(2014) Justin E. Anderson et al.   G3-Genes Genomes Genetics

Copy Number Variation in the Horse Genome

(2014) Sharmila Ghosh et al.   PLoS Genetics

Strategies for transferring resistance into wheat: from wide crosses to GM cassettes

(2014) Brande B. H. Wulff et al.   Frontiers in Plant Science

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

Identification of structural variation in mouse genomes

(2014) Thomas M. Keane et al.   Frontiers in Genetics

Genome-wide copy number variations in Oryza sativa L.

(2013) Ping Yu et al.   BMC GENOMICS

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

(2013) Anna Esteve-Codina et al.   BMC GENOMICS

Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array

(2013) Jiasen Liu et al.   BMC GENOMICS

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions

(2013) Yusaku Uga et al.   NATURE GENETICS

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Copy number variation in potato - an asexually propagated autotetraploid species

(2013) Marina Iovene et al.   PLANT JOURNAL

Genomic DNA Enrichment Using Sequence Capture Microarrays: a Novel Approach to Discover Sequence Nucleotide Polymorphisms (SNP) in Brassica napus L

(2013) Wayne E. Clarke et al.   PLoS One

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

(2013) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Copy number polymorphism in plant genomes

(2013) Agnieszka Żmieńko et al.   THEORETICAL AND APPLIED GENETICS

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-Step Model of Paleohexaploidy

(2012) H. Tang et al.   GENETICS

Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time

(2012) Hidetaka Nishida et al.   MOLECULAR BREEDING

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency

(2012) Rico Gamuyao et al.   NATURE

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

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

A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation

(2012) Yiyuan Li et al.   NEW PHYTOLOGIST

Current analysis platforms and methods for detecting copy number variation

(2012) Wenli Li et al.   PHYSIOLOGICAL GENOMICS

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

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

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

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Insights from ANA-grade angiosperms into the early evolution of CUP-SHAPED COTYLEDON genes

(2011) Aurélie C. M. Vialette-Guiraud et al.   ANNALS OF BOTANY

Detection of copy number variations in rice using array-based comparative genomic hybridization

(2011) Ping Yu et al.   BMC GENOMICS

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Molecular Characterization of Rht-1 Dwarfing Genes in Hexaploid Wheat

(2011) S. Pearce et al.   PLANT PHYSIOLOGY

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

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

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Copy number variation in the bovine genome

(2010) João Fadista et al.   BMC GENOMICS

Karyotype and Identification of All Homoeologous Chromosomes of Allopolyploid Brassica napus and Its Diploid Progenitors

(2010) Z. Xiong 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

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

(2010) Jinsheng Lai et al.   NATURE GENETICS

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

(2010) W. J. Haun et al.   PLANT PHYSIOLOGY

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

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Association of copy number variation in the FCGR3B gene with risk of autoimmune diseases

(2009) M Mamtani et al.   GENES AND IMMUNITY

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

(2009) Yoko Hattori et al.   NATURE

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Mechanisms of change in gene copy number

(2009) P. J. Hastings et al.   NATURE REVIEWS GENETICS

Homoeologous recombination in allopolyploids: the polyploid ratchet

(2009) Robert T. Gaeta et al.   NEW PHYTOLOGIST

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

The flowering world: a tale of duplications

(2009) Yves Van de Peer et al.   TRENDS IN PLANT 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

Mapping translocation breakpoints by next-generation sequencing

(2008) W. Chen et al.   GENOME RESEARCH

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

(2008) Joshua M Korn et al.   NATURE GENETICS

MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings

(2008) Mitch McVey et al.   TRENDS IN GENETICS