Designing Future Crops: Genomics-Assisted Breeding Comes of Age

An Integrated Framework Reinstating the Environmental Dimension for GWAS and Genomic Selection in Crops

(2021) Xianran Li et al.   Molecular Plant

The genetic basis of cytoplasmic male sterility and fertility restoration in wheat

(2021) Joanna Melonek et al.   Nature Communications

Need for speed: manipulating plant growth to accelerate breeding cycles

(2021) Madhav Bhatta et al.   CURRENT OPINION IN PLANT BIOLOGY

Systems biology for crop improvement

(2021) Lekha T. Pazhamala et al.   Plant Genome

Recurrent genomic selection for wheat grain fructans

(2020) Lynn D. Veenstra et al.   CROP SCIENCE

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

(2020) Sibin Yu et al.   THEORETICAL AND APPLIED GENETICS

Counting on Crossovers: Controlled Recombination for Plant Breeding

(2020) Ella Taagen et al.   TRENDS IN PLANT SCIENCE

Enhancing Hybrid Prediction in Pearl Millet Using Genomic and/or Multi-Environment Phenotypic Information of Inbreds

(2020) Diego Jarquin et al.   Frontiers in Genetics

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

(2020) Pallavi Sinha et al.   PLANT BIOTECHNOLOGY JOURNAL

PANOMICS meets germplasm

(2020) Wolfram Weckwerth et al.   PLANT BIOTECHNOLOGY JOURNAL

Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea ( Cajanus cajan L.)

(2020) Pallavi Sinha et al.   PLANT BIOTECHNOLOGY JOURNAL

Speed breeding short-day crops by LED-controlled light schemes

(2020) Felix Jähne et al.   THEORETICAL AND APPLIED GENETICS

A platinum standard pan-genome resource that represents the population structure of Asian rice

(2020) Yong Zhou et al.   Scientific Data

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

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

(2020) Michael F. Scott et al.   HEREDITY

BrassicaEDB: A Gene Expression Database for Brassica Crops

(2020) Haoyu Chao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mobilizing Crop Biodiversity

(2020) Susan McCouch et al.   Molecular Plant

Applications of CRISPR–Cas in agriculture and plant biotechnology

(2020) Haocheng Zhu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genomic interventions for sustainable agriculture

(2020) Abhishek Bohra et al.   PLANT BIOTECHNOLOGY JOURNAL

Soybean ( Glycine max ) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics

(2020) Davoud Torkamaneh et al.   PLANT BIOTECHNOLOGY JOURNAL

The barley pan-genome reveals the hidden legacy of mutation breeding

(2020) Murukarthick Jayakodi et al.   NATURE

BnaGVD: A Genomic Variation Database of Rapeseed (Brassica napus)

(2020) Tao Yan et al.   PLANT AND CELL PHYSIOLOGY

A haplotype-led approach to increase the precision of wheat breeding

(2020) Jemima Brinton et al.   Communications Biology

High-Throughput Estimation of Crop Traits: A Review of Ground and Aerial Phenotyping Platforms

(2020) Xiuliang Jin et al.   IEEE Geoscience and Remote Sensing Magazine

Optimal Designs for Genomic Selection in Hybrid Crops

(2019) Tingting Guo et al.   Molecular Plant

From genome to phenome: genome-wide association studies and other approaches that bridge the genotype to phenotype gap

(2019) Alisdair R. Fernie et al.   PLANT JOURNAL

Review: New sensors and data-driven approaches—A path to next generation phenomics

(2019) Thomas Roitsch et al.   PLANT SCIENCE

Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions

(2019) Narinder Singh et al.   Scientific Reports

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

(2019) Zhenchang Liang et al.   Nature Communications

Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains

(2019) Ragavendran Abbai et al.   PLANT BIOTECHNOLOGY JOURNAL

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

(2019) Sanu Arora et al.   NATURE BIOTECHNOLOGY

De Novo Domestication: An Alternative Route toward New Crops for the Future

(2019) Alisdair R. Fernie et al.   Molecular Plant

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

(2019) Rajeev K. Varshney et al.   NATURE GENETICS

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

Hybrid Breeding of Rice via Genomic Selection

(2019) Yanru Cui et al.   PLANT BIOTECHNOLOGY JOURNAL

Development and evaluation of improved lines with broad-spectrum resistance to rice blast using nine resistance genes

(2019) Haichao Jiang et al.   Rice

Breeding crops to feed 10 billion

(2019) Lee T. Hickey et al.   NATURE BIOTECHNOLOGY

Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding

(2019) Martin Mascher et al.   NATURE GENETICS

Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification

(2019) Qian You et al.   THEORETICAL AND APPLIED GENETICS

­­­­Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays

(2019) Karl A. G. Kremling et al.   G3-Genes Genomes Genetics

Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics

(2019) Philomin Juliana et al.   NATURE GENETICS

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

(2019) Aamir W. Khan et al.   TRENDS IN PLANT SCIENCE

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays)

(2018) Baobao Wang et al.   BMC PLANT BIOLOGY

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield

(2018) Zhiying Ma et al.   NATURE GENETICS

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

(2018) Qiang Zhao et al.   NATURE GENETICS

The rice genome revolution: from an ancient grain to Green Super Rice

(2018) Rod A. Wing et al.   NATURE REVIEWS GENETICS

Incorporation of the novel bacterial blight resistance gene Xa38 into the genetic background of elite rice variety Improved Samba Mahsuri

(2018) Arra Yugander et al.   PLoS One

Translating High-Throughput Phenotyping into Genetic Gain

(2018) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

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

(2018) et al.   SCIENCE

Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice

(2018) Gitishree Das et al.   Scientific Reports

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

(2018) Jason G. Wallace et al.   Annual Review of Genetics

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

(2018) Dezhi Wu et al.   Molecular Plant

Domestication of wild tomato is accelerated by genome editing

(2018) Tingdong Li et al.   NATURE BIOTECHNOLOGY

De novo domestication of wild tomato using genome editing

(2018) Agustin Zsögön et al.   NATURE BIOTECHNOLOGY

Genebank genomics highlights the diversity of a global barley collection

(2018) Sara G. Milner et al.   NATURE GENETICS

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

(2018) Sreya Ghosh et al.   Nature Protocols

An Updated Gene Atlas for Maize Reveals Organ‐Specific and Stress‐Induced Genes

(2018) Genevieve M Hoopes et al.   PLANT JOURNAL

Toward the sequence-based breeding in legumes in the post-genome sequencing era

(2018) Rajeev K. Varshney et al.   THEORETICAL AND APPLIED GENETICS

Breaking the curse of dimensionality to identify causal variants in Breeding 4

(2018) Guillaume P. Ramstein et al.   THEORETICAL AND APPLIED GENETICS

Molecular introgression of leaf rust resistance gene Lr34 validates enhanced effect on resistance to spot blotch in spring wheat

(2017) Neeraj Kumar Vasistha et al.   EUPHYTICA

Marker-assisted breeding to develop the drought-tolerant version of Sabitri, a popular variety from Nepal

(2017) Shalabh Dixit et al.   EUPHYTICA

Registration of Conventional Soybean Germplasm JTN-4307 with Resistance to Nematodes and Fungal Diseases

(2017) Prakash R. Arelli et al.   Journal of Plant Registrations

Development of a maize 55 K SNP array with improved genome coverage for molecular breeding

(2017) Cheng Xu et al.   MOLECULAR BREEDING

Genomic innovation for crop improvement

(2017) Michael W. Bevan et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat

(2017) Yong Jiang et al.   NATURE GENETICS

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

(2017) Lei Fang et al.   NATURE GENETICS

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

(2017) Rajeev K Varshney et al.   NATURE GENETICS

A study of allelic diversity underlying flowering-time adaptation in maize landraces

(2017) J Alberto Romero Navarro et al.   NATURE GENETICS

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

(2017) Xia Wang et al.   NATURE GENETICS

The pangenome of hexaploid bread wheat

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

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Development and Evaluation of a Barley 50k iSelect SNP Array

(2017) Micha M. Bayer et al.   Frontiers in Plant Science

Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

(2017) Manish K. Pandey et al.   Scientific Reports

SorGSD: a sorghum genome SNP database

(2016) Hong Luo et al.   Biotechnology for Biofuels

A practical, rapid generation-advancement system for rice breeding using simplified biotron breeding system

(2016) Junichi Tanaka et al.   BREEDING SCIENCE

Marker assisted introgression of blast (Pi-2 and Pi-54) genes in to the genetic background of elite, bacterial blight resistant indica rice variety, Improved Samba Mahsuri

(2016) K. Ratna Madhavi et al.   EUPHYTICA

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

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

(2016) David John Bertioli et al.   NATURE GENETICS

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

(2016) Kenji Yano et al.   NATURE GENETICS

Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum)

(2016) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Cytoplasmic male sterility (CMS) in hybrid breeding in field crops

(2016) Abhishek Bohra et al.   PLANT CELL REPORTS

Time to flowering of temperate pulses in vivo and generation turnover in vivo–in vitro of narrow-leaf lupin accelerated by low red to far-red ratio and high intensity in the far-red region

(2016) Janine S. Croser et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Molecular breeding for introgression of fatty acid desaturase mutant alleles ( ahFAD2A and ahFAD2B ) enhances oil quality in high and low oil containing peanut genotypes

(2016) Pasupuleti Janila et al.   PLANT SCIENCE

Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding

(2016) Ranjith K. Ellur et al.   PLANT SCIENCE

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

(2016) Wayne E. Clarke et al.   THEORETICAL AND APPLIED GENETICS

Crop Diversity: An Unexploited Treasure Trove for Food Security

(2016) Festo Massawe et al.   TRENDS IN PLANT SCIENCE

Genomic Prediction of Gene Bank Wheat Landraces

(2016) José Crossa et al.   G3-Genes Genomes Genetics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Marker-assisted backcrossing: a useful method for rice improvement

(2015) Muhammad Mahmudul Hasan et al.   BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT

WheatExp: an RNA-seq expression database for polyploid wheat

(2015) Stephen Pearce et al.   BMC PLANT BIOLOGY

Study on Essential Derivation in Maize: III. Selection and Evaluation of a Panel of Single Nucleotide Polymorphism Loci for Use in European and North American Germplasm

(2015) Yves Rousselle et al.   CROP SCIENCE

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

(2015) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Development, validation and genetic analysis of a large soybean SNP genotyping array

(2015) Yun-Gyeong Lee et al.   PLANT JOURNAL

Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding

(2015) Yusheng Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Redesigning photosynthesis to sustainably meet global food and bioenergy demand

(2015) Donald R. Ort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice

(2015) Apurva Khanna et al.   THEORETICAL AND APPLIED GENETICS

Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice

(2015) Nisha Singh et al.   Scientific Reports

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

(2015) Qijian Song et al.   G3-Genes Genomes Genetics

A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection

(2015) Nonoy Bandillo et al.   Plant Genome

An RNA-Seq based gene expression atlas of the common bean

(2014) Jamie A O’Rourke 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

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

(2014) Nadia Shakoor et al.   BMC PLANT BIOLOGY

Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

(2014) Yanpeng Wang et al.   NATURE BIOTECHNOLOGY

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

(2014) Wei Chen et al.   NATURE GENETICS

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Insights into the Maize Pan-Genome and Pan-Transcriptome

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

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

(2014) B. Chalhoub et al.   SCIENCE

Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

(2014) Rajeev K. Varshney et al.   THEORETICAL AND APPLIED GENETICS

Assessing the utility of intermediate phenotypes for genetic mapping of psychiatric disease

(2014) Jonathan Flint et al.   TRENDS IN NEUROSCIENCES

Marker-Assisted Backcrossing to Introgress Resistance to Fusarium Wilt Race 1 and Ascochyta Blight in C 214, an Elite Cultivar of Chickpea

(2014) R. K. Varshney et al.   Plant Genome

Genomic selection in sugar beet breeding populations

(2013) Tobias Würschum et al.   BMC GENETICS

A procedure allowing up to eight generations of wheat and nine generations of barley per annum

(2013) Z. Zheng et al.   EUPHYTICA

Feeding the future

(2013) Susan McCouch et al.   NATURE

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

(2013) Trupti Joshi et al.   NUCLEIC ACIDS RESEARCH

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

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

A whole-genome SNP array (RICE6K) for genomic breeding in rice

(2013) Huihui Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

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

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

Can genomics boost productivity of orphan crops?

(2012) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

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

Genomic prediction of sunflower hybrid performance

(2012) Jochen C. Reif et al.   PLANT BREEDING

Development of genome-wide SNP assays for rice

(2011) Susan R. McCouch et al.   BREEDING SCIENCE

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

Marker-Assisted Selection to Pyramid Nematode Resistance and the High Oleic Trait in Peanut

(2011) Y. Chu et al.   Plant Genome

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

(2010) Chih-Wei Tung et al.   Rice

Marker assisted backcross breeding to improve cooking quality traits in Myanmar rice cultivar Manawthukha

(2009) Myint Yi et al.   FIELD CROPS RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A dynamic gene expression atlas covering the entire life cycle of rice

(2009) Lei Wang et al.   PLANT JOURNAL

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable 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

Inheritance of resistance in soybean PI 567516C to LY1 nematode population infecting cv. Hartwig

(2008) Prakash R. Arelli et al.   EUPHYTICA

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS