Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot

(2020) Beatrice Corsi et al.   THEORETICAL AND APPLIED GENETICS

Genetic mapping using a wheat multi-founder population reveals a locus on chromosome 2A controlling resistance to both leaf and glume blotch caused by the necrotrophic fungal pathogen Parastagonospora nodorum

(2020) Min Lin et al.   THEORETICAL AND APPLIED GENETICS

Fine mapping and gene cloning in the post-NGS era: advances and prospects

(2020) Deepa Jaganathan et al.   THEORETICAL AND APPLIED GENETICS

Natural Selection Towards Wild-Type in Composite Cross Populations of Winter Wheat

(2020) Samuel Knapp et al.   Frontiers in Plant Science

Development of a multiparent advanced generation intercross (MAGIC) population for genetic exploitation of complex traits in Brassica juncea : Glucosinolate content as an example

(2020) Wei Yan et al.   PLANT BREEDING

Ten Years of the maize Nested Association Mapping Population: Impact, Limitations, and Future Directions

(2020) Joseph L. Gage et al.   PLANT CELL

Integrating genomics for chickpea improvement: achievements and opportunities

(2020) Manish Roorkiwal et al.   THEORETICAL AND APPLIED GENETICS

Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny

(2020) Chin Jian Yang et al.   G3-Genes Genomes Genetics

Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population

(2020) Kimberly Ponce et al.   Frontiers in Plant Science

Application of the cottonscope for determining fiber maturity and fineness of an upland cotton MAGIC population

(2020) Hee Jin Kim et al.   CROP SCIENCE

Effects of breeding history and crop management on the root architecture of wheat

(2020) N. Fradgley et al.   PLANT AND SOIL

Multi-parent multi-environment QTL analysis: an illustration with the EU-NAM Flint population

(2020) Vincent Garin et al.   THEORETICAL AND APPLIED GENETICS

Occurrence of the potent mutagens 2- nitrobenzanthrone and 3-nitrobenzanthrone in fine airborne particles

(2019) Aldenor G. Santos et al.   Scientific Reports

Impact of Host Plant Species and Whitefly Species on Feeding Behavior of Bemisia tabaci

(2019) Milan Milenovic et al.   Frontiers in Plant Science

A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton

(2019) Martin J. Wubben et al.   THEORETICAL AND APPLIED GENETICS

Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population

(2019) Marina Naoumkina et al.   BMC GENOMICS

Multi-Parental Advances Generation Inter-Cross Population, to Develop Organic Tomato Genotypes by Participatory Plant Breeding

(2019) Gabriele Campanelli et al.   Agronomy-Basel

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Development of a Multi-parent Population for Genetic Mapping and Allele Discovery in Six-Row Barley

(2019) Alex Ollhoff et al.   GENETICS

Unravelling the genetic basis of Fusarium seedling rot resistance in the MAGIC maize population: novel targets for breeding

(2019) Popi Septiani et al.   Scientific Reports

Evaluation of genomic selection methods for predicting fiber quality traits in Upland cotton

(2019) Md Sariful Islam et al.   MOLECULAR GENETICS AND GENOMICS

Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population

(2019) Zhongmin Han et al.   THEORETICAL AND APPLIED GENETICS

Mapping of resistance to corn borers in a MAGIC population of maize

(2019) José Cruz Jiménez-Galindo et al.   BMC PLANT BIOLOGY

TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

(2019) Qiuyue Chen et al.   GENETICS

Effect of epistasis and environment on flowering time in barley reveals a novel flowering-delaying QTL allele

(2019) Nazanin P Afsharyan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dissecting the genetics of cold tolerance in a multiparental maize population

(2019) Q. Yi et al.   THEORETICAL AND APPLIED GENETICS

Gene action governing the inheritance of drought tolerance and selected agronomic traits in Ugandan groundnut (Arachis hypogaea L.) lines under drought environment

(2019) R. Kakeeto et al.   EUPHYTICA

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea )

(2019) Sunil S. Gangurde et al.   PLANT BIOTECHNOLOGY JOURNAL

Four-Parent Maize (FPM) Population: Development and Phenotypic Characterization

(2018) Adam L. Mahan et al.   CROP SCIENCE

Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population

(2018) Ana M. Bossa-Castro et al.   PLANT BIOTECHNOLOGY JOURNAL

TEOSINTE BRANCHED1Regulates Inflorescence Architecture and Development in Bread Wheat (Triticum aestivum)

(2018) Laura E. Dixon et al.   PLANT CELL

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.)

(2018) Bao-Lam Huynh et al.   PLANT JOURNAL

The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

(2018) Katherine W. Jordan et al.   PLANT JOURNAL

Four Parent Maize (FPM) Population: Effects of Mating Designs on Linkage Disequilibrium and Mapping Quantitative Traits

(2018) Steven L. Anderson et al.   Plant Genome

Functional Mapping of Quantitative Trait Loci (QTLs) Associated With Plant Performance in a Wheat MAGIC Mapping Population

(2018) Anyela V. Camargo et al.   Frontiers in Plant Science

Metarhizium brunneum (Ascomycota; Hypocreales) Treatments Targeting Olive Fly in the Soil for Sustainable Crop Production

(2018) Meelad Yousef et al.   Frontiers in Plant Science

QTL Identification for Cooking and Eating Quality in indica Rice Using Multi-Parent Advanced Generation Intercross (MAGIC) Population

(2018) Kimberly S. Ponce et al.   Frontiers in Plant Science

Assessing European Wheat Sensitivities to Parastagonospora nodorum Necrotrophic Effectors and Fine-Mapping the Snn3-B1 Locus Conferring Sensitivity to the Effector SnTox3

(2018) Rowena C. Downie et al.   Frontiers in Plant Science

Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array

(2018) Qian You et al.   Frontiers in Plant Science

Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

(2018) Wiebke Sannemann et al.   BMC GENOMICS

Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence

(2018) Chaozhi Zheng et al.   GENETICS

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

(2018) et al.   SCIENCE

In situ immune response and mechanisms of cell damage in central nervous system of fatal cases microcephaly by Zika virus

(2018) Raimunda S. S. Azevedo et al.   Scientific Reports

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multi-parent Populations

(2018) Karl W. Broman et al.   GENETICS

A large nested association mapping (NAM) population for breeding and QTL mapping in Ethiopian durum wheat

(2018) Yosef Gebrehawaryat Kidane et al.   PLANT BIOTECHNOLOGY JOURNAL

QTLs for Resistance to Fusarium Ear Rot in a Multi-parent Advanced Generation Inter-cross (MAGIC) Maize Population

(2018) Ana Butron et al.   PLANT DISEASE

A multi-parent faba bean (Vicia faba L.) population for future genomic studies

(2018) Hamid Khazaei et al.   Plant Genetic Resources-Characterization and Utilization

Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.)

(2018) Gregory N. Thyssen et al.   THEORETICAL AND APPLIED GENETICS

Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population

(2017) Boby Mathew et al.   GENETICS

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

(2017) Martha Imprialou et al.   GENETICS

Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

(2017) Sophie Bouchet et al.   GENETICS

Wheat Landrace Genome Diversity

(2017) Luzie U. Wingen et al.   GENETICS

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

(2017) Bernardo J. Clavijo et al.   GENOME RESEARCH

Enhancing genomic prediction with genome-wide association studies in multiparental maize populations

(2017) Y Bian et al.   HEREDITY

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

DNA sequencing technologies: 2006–2016

(2017) Elaine R Mardis   Nature Protocols

Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum )

(2017) Amanda J. Burridge et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic Characterization of the Soybean Nested Association Mapping Population

(2017) Qijian Song et al.   Plant Genome

Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population

(2017) Boby Mathew et al.   GENETICS

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

(2017) Martha Imprialou et al.   GENETICS

Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

(2017) Sophie Bouchet et al.   GENETICS

Wheat Landrace Genome Diversity

(2017) Luzie U. Wingen et al.   GENETICS

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Locating rearrangement events in a phylogeny based on highly fragmented assemblies

(2016) Chunfang Zheng et al.   BMC GENOMICS

QTL mapping for agronomic traits using multi-parent advanced generation inter-cross (MAGIC) populations derived from diverse elite indica rice lines

(2016) Lijun Meng et al.   FIELD CROPS RESEARCH

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild x Cultivated Barley

(2016) L. M. Nice et al.   GENETICS

A multiple-phenotype imputation method for genetic studies

(2016) Andrew Dahl et al.   NATURE GENETICS

Rapid genotype imputation from sequence without reference panels

(2016) Robert W Davies et al.   NATURE GENETICS

A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments

(2016) Keith A. Gardner et al.   PLANT BIOTECHNOLOGY JOURNAL

Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

(2016) Prabin Bajgain et al.   PLoS One

Chromosome-level assembly ofArabidopsis thalianaLerreveals the extent of translocation and inversion polymorphisms

(2016) Luis Zapata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine mapping of a major QTL for awn length in barley using a multiparent mapping population

(2016) Corinna B. Liller et al.   THEORETICAL AND APPLIED GENETICS

Bandwagons I, too, have known

(2016) Rex Bernardo   THEORETICAL AND APPLIED GENETICS

The pangenome of an agronomically important crop plant Brassica oleracea

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

Dynamic response of RNA editing to temperature in Drosophila

(2015) Leila E Rieder et al.   BMC BIOLOGY

Modelling the genetic architecture of flowering time control in barley through nested association mapping

(2015) Andreas Maurer et al.   BMC GENOMICS

Association mapping for frost tolerance using multi-parent advanced generation inter-cross (MAGIC) population in faba bean (Vicia faba L.)

(2015) Ahmed Sallam et al.   GENETICA

Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data

(2015) C. A. Fragoso et al.   GENETICS

Reconstruction of Genome Ancestry Blocks in Multiparental Populations

(2015) Chaozhi Zheng et al.   GENETICS

Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept

(2015) Wiebke Sannemann et al.   MOLECULAR BREEDING

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidumssp.durum)

(2015) Sara Giulia Milner et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide Association of Carbon and Nitrogen Metabolism in the Maize Nested Association Mapping Population

(2015) Nengyi Zhang et al.   PLANT PHYSIOLOGY

MAGIC populations in crops: current status and future prospects

(2015) B. Emma Huang et al.   THEORETICAL AND APPLIED GENETICS

Allele mining and enhanced genetic recombination for rice breeding

(2015) Hei Leung et al.   Rice

Reconstruction of Genome Ancestry Blocks in Multiparental Populations

(2015) Chaozhi Zheng et al.   GENETICS

Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL

(2015) Jose M. Barrero et al.   GENOME BIOLOGY

Ppd-1 is a key regulator of inflorescence architecture and paired spikelet development in wheat

(2015) Scott A. Boden et al.   Nature Plants

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus

(2015) Thomas Schmutzer et al.   Scientific Data

Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants

(2015) Kelly Swarts et al.   Plant Genome

Efficient Imputation of Missing Markers in Low-Coverage Genotyping-by-Sequencing Data from Multiparental Crosses

(2014) B. Emma Huang et al.   GENETICS

Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat

(2014) Stéphanie Thépot et al.   GENETICS

Multiple Quantitative Trait Analysis Using Bayesian Networks

(2014) Marco Scutari et al.   GENETICS

The Genetic Architecture Of Maize Height

(2014) Jason A. Peiffer et al.   GENETICS

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

(2014) Sebastian Gnan et al.   GENETICS

Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

(2014) Laura Pascual et al.   PLANT BIOTECHNOLOGY JOURNAL

New Arabidopsis Advanced Intercross Recombinant Inbred Lines Reveal Female Control of Nonrandom Mating

(2014) J. N. Fitz Gerald et al.   PLANT PHYSIOLOGY

Genetic characterization of a multiparent recombinant inbred line of rice population

(2014) Zhixin Li et al.   RESEARCH ON CROPS

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

(2013) Mathilde Causse et al.   BMC GENOMICS

Development and evaluation of multi-genotype varieties of rice derived from MAGIC lines

(2013) Xiao-Fang Li et al.   EUPHYTICA

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

(2013) Amelie Baud et al.   NATURE GENETICS

Use of a large multiparent wheat mapping population in genomic dissection of coleoptile and seedling growth

(2013) Greg J. Rebetzke et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana

(2013) J. Agren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

(2013) E. S. Mace et al.   THEORETICAL AND APPLIED GENETICS

Intraspecific variation of recombination rate in maize

(2013) Eva Bauer et al.   GENOME BIOLOGY

Properties and Power of the Drosophila Synthetic Population Resource for the Routine Dissection of Complex Traits

(2012) Elizabeth G. King et al.   GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Maize HapMap2 identifies extant variation from a genome in flux

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

A multiparent advanced generation inter-cross population for genetic analysis in wheat

(2012) Bevan E. Huang et al.   PLANT BIOTECHNOLOGY JOURNAL

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Exploring and Exploiting Genetic Variation from Unadapted Sorghum Germplasm in a Breeding Program

(2011) D. R. Jordan et al.   CROP SCIENCE

Diversity arrays technology (DArT) markers in apple for genetic linkage maps

(2011) Henk J. Schouten et al.   MOLECULAR BREEDING

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

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

(2011) Feng Tian et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Joint QTL Linkage Mapping for Multiple-Cross Mating Design Sharing One Common Parent

(2011) Huihui Li et al.   PLoS One

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

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

Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population

(2011) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparative analysis of exome capture

(2011) Jennifer S Parla et al.   GENOME BIOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Efficient genome ancestry inference in complex pedigrees with inbreeding

(2010) E. Y. Liu et al.   BIOINFORMATICS

Detection and use of QTL for complex traits in multiple environments

(2010) Fred A van Eeuwijk et al.   CURRENT OPINION IN PLANT BIOLOGY

Insight into the genetic bases of climatic adaptation in experimentally evolving wheat populations

(2010) BÉNÉDICTE RHONÉ et al.   MOLECULAR ECOLOGY

Genetic Properties of the Maize Nested Association Mapping Population

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

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

(2009) Paula X. Kover et al.   PLoS Genetics

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Missing data imputation and haplotype phase inference for genome-wide association studies

(2008) Sharon R. Browning   HUMAN GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One