Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing

Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map

(2020) E. Carrillo-Perdomo et al.   Scientific Reports

Density enhancement of a faba bean genetic linkage map ( Vicia faba ) based on simple sequence repeats markers

(2019) Tao Yang et al.   PLANT BREEDING

Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus )

(2019) Xiaolong Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize

(2019) Zifeng Guo et al.   MOLECULAR BREEDING

A high-throughput SNP discovery strategy for RNA-seq data

(2019) Yun Zhao et al.   BMC GENOMICS

Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm

(2019) Vera Vendramin et al.   BMC GENOMICS

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley

(2019) Camilla Beate Hill et al.   Scientific Data

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

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

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

A 55 K SNP array-based genetic map and its utilization in QTL mapping for productive tiller number in common wheat

(2018) Jiajun Liu et al.   THEORETICAL AND APPLIED GENETICS

Enhancing faba bean (Vicia faba L.) genome resources

(2017) James W. Cooper et al.   JOURNAL OF EXPERIMENTAL BOTANY

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

(2017) Awais Rasheed et al.   Molecular Plant

Development and evaluation of high-density Axiom® CicerSNP  Array for high-resolution genetic mapping and breeding applications in chickpea

(2017) Manish Roorkiwal et al.   PLANT BIOTECHNOLOGY JOURNAL

Saturation mapping of regions determining resistance to Ascochyta blight and broomrape in faba bean using transcriptome-based SNP genotyping

(2017) S. Ocaña-Moral et al.   THEORETICAL AND APPLIED GENETICS

Molecular Breeding for Ascochyta Blight Resistance in Lentil: Current Progress and Future Directions

(2017) Matthew S. Rodda et al.   Frontiers in Plant Science

Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway

(2017) Irma Terracciano et al.   Scientific Reports

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

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

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

(2015) Anne Webb et al.   PLANT BIOTECHNOLOGY JOURNAL

Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map

(2015) Nadim Tayeh et al.   PLANT JOURNAL

Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history

(2015) Peter G. Vos et al.   THEORETICAL AND APPLIED GENETICS

Transcriptome characterization and large-scale identification of SSR/SNPmarkers in symbiotic nitrogen fixation crop faba bean (Vicia faba L.)

(2015) Sundan SURESH et al.   Turkish Journal of Agriculture and Forestry

Estimating variability in grain legume yields across Europe and the Americas

(2015) Charles Cernay et al.   Scientific Reports

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

(2015) Modhumita Ghosh Dasgupta et al.   PLoS One

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Recent progress on molecular breeding of rice in China

(2014) Yuchun Rao et al.   PLANT CELL REPORTS

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

(2014) Camila Campos Mantello et al.   PLoS One

High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets

(2014) Allan F. Brown et al.   THEORETICAL AND APPLIED GENETICS

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

(2013) Haodong Chen et al.   Molecular Plant

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Development of an expressed gene catalogue and molecular markers from thede novoassembly of short sequence reads of the lentil (Lens culinarisMedik.) transcriptome

(2013) Priyanka Verma et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2013) Huihui Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic linkage map of Chinese native variety faba bean (Vicia fabaL.) based on simple sequence repeat markers

(2013) Yu Ma et al.   PLANT BREEDING

SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance

(2013) Sukhjiwan Kaur et al.   PLANT SCIENCE

De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)

(2012) Jianan Zhang et al.   BMC GENOMICS

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

High-throughput novel microsatellite marker of faba bean via next generation sequencing

(2012) Tao Yang et al.   BMC GENOMICS

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

(2012) Jialei Duan et al.   BMC GENOMICS

Current state-of-art of sequencing technologies for plant genomics research

(2012) M. Thudi et al.   Briefings in Functional Genomics

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

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

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

Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers

(2011) Hai-fei Wang et al.   THEORETICAL AND APPLIED GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Molecular variation among Chinese and global germplasm in spring faba bean areas

(2010) X. Zong et al.   PLANT BREEDING

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Faba bean in cropping systems

(2009) Erik S. Jensen et al.   FIELD CROPS RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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