Understanding and utilizing crop genome diversity via high-resolution genotyping

Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling

(2015) Trevor W Rife et al.   BMC GENOMICS

Patterns of genomic changes with crop domestication and breeding

(2015) Junpeng Shi et al.   CURRENT OPINION IN PLANT BIOLOGY

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

(2015) Noah Fahlgren et al.   CURRENT OPINION IN PLANT BIOLOGY

Breeding-assisted genomics

(2015) Jesse Poland   CURRENT OPINION IN PLANT BIOLOGY

Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change

(2015) Marta S. Lopes et al.   JOURNAL OF EXPERIMENTAL BOTANY

Widely distributed hot and cold spots in meiotic recombination as shown by the sequencing of rice F2plants

(2015) Weina Si et al.   NEW PHYTOLOGIST

Heterotic Haplotype Capture: precision breeding for hybrid performance

(2015) Rod J. Snowdon et al.   TRENDS IN PLANT SCIENCE

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

(2015) Fei Lu et al.   Nature Communications

Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

(2015) Xuehui Huang et al.   Nature Communications

Subgenomic Diversity Patterns Caused by Directional Selection in Bread Wheat Gene Pools

(2015) Kai Voss-Fels et al.   Plant Genome

Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome

(2015) Lunwen Qian et al.   BMC GENOMICS

Genotyping by sequencing for genomic prediction in a soybean breeding population

(2014) Diego Jarquín et al.   BMC GENOMICS

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

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

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

High-resolution molecular karyotyping uncovers pairing between ancestrally relatedBrassicachromosomes

(2014) Annaliese S. Mason et al.   NEW PHYTOLOGIST

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

(2014) Shichen Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Selection Strategies for the Development of Maize Introgression Populations

(2014) Eva Herzog et al.   PLoS One

Predicting hybrid performance in rice using genomic best linear unbiased prediction

(2014) S. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genomic selection in crops, trees and forages: a review

(2014) Z. Lin et al.   Crop & Pasture Science

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

(2014) Rajeev K. Varshney et al.   PLOS BIOLOGY

Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus

(2014) Sarah Schiessl et al.   Frontiers in Plant Science

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Plant genome sequencing — applications for crop improvement

(2013) Marie E Bolger et al.   CURRENT OPINION IN BIOTECHNOLOGY

A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

(2013) Haodong Chen et al.   Molecular Plant

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Crossover rate between homologous chromosomes and interference are regulated by the addition of specific unpaired chromosomes inBrassica

(2013) Loreto Suay et al.   NEW PHYTOLOGIST

High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array

(2013) Wubishet A. Bekele et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2013) Martin Mascher et al.   PLANT JOURNAL

Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean

(2013) Qijian Song et al.   PLoS One

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

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

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

(2013) Z.-Y. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

(2013) C. R. Cavanagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

(2013) Jennifer Spindel et al.   THEORETICAL AND APPLIED GENETICS

Field high-throughput phenotyping: the new crop breeding frontier

(2013) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

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

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

Exome versus transcriptome sequencing in identifying coding region variants

(2012) Chee-Seng Ku et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Field-based phenomics for plant genetics research

(2012) Jeffrey W. White et al.   FIELD CROPS RESEARCH

Large SNP arrays for genotyping in crop plants

(2012) Martin W Ganal et al.   JOURNAL OF BIOSCIENCES

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Associative transcriptomics of traits in the polyploid crop species Brassica napus

(2012) Andrea L Harper et al.   NATURE BIOTECHNOLOGY

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

(2012) Jordi Comadran et al.   NATURE GENETICS

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants

(2012) Mahmood Gholami et al.   PLANT BIOTECHNOLOGY JOURNAL

Accessing complex crop genomes with next-generation sequencing

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

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Single nucleotide polymorphism discovery in elite north american potato germplasm

(2011) John P Hamilton et al.   BMC GENOMICS

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

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

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

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

Selection strategies for marker-assisted backcrossing with high-throughput marker systems

(2011) Eva Herzog 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

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Making the most of ‘omics’ for crop breeding

(2010) Peter Langridge et al.   TRENDS IN BIOTECHNOLOGY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS