MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)

Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections

(2021) Hiromi Kajiya-Kanegae et al.   DNA RESEARCH

Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di)

(2021) Sota Yoshikawa et al.   MARINE BIOTECHNOLOGY

QTL analysis of crown gall disease resistance in apple: first plant R gene candidates effective against Rhizobium rhizogenes (Ti)

(2021) Shigeki Moriya et al.   Tree Genetics & Genomes

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population

(2021) Giriraj Kumawat et al.   Frontiers in Genetics

Geographical distribution and adaptive variation of VRN-A3 alleles in worldwide polyploid wheat (Triticum spp.) species collection

(2021) Kazusa Nishimura et al.   PLANTA

Complementary combination of multiplex high‐throughput DNA sequencing for molecular phylogeny

(2021) Yoshihisa Suyama et al.   ECOLOGICAL RESEARCH

The genotype-dependent phenotypic landscape of quinoa in salt tolerance and key growth traits

(2020) Nobuyuki Mizuno et al.   DNA RESEARCH

Multiple wheat genomes reveal global variation in modern breeding

(2020) Sean Walkowiak et al.   NATURE

Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112

(2020) Yan Yang et al.   PLoS One

GRAS-Di system facilitates high-density genetic map construction and QTL identification in recombinant inbred lines of the wheat progenitor Aegilops tauschii

(2020) Yuka Miki et al.   Scientific Reports

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

(2018) Xiao-Ting Wang et al.   Insect Science

The Rosa genome provides new insights into the domestication of modern roses

(2018) Olivier Raymond et al.   NATURE GENETICS

The early flowering trait of an emmer wheat accession (Triticum turgidum L. ssp. dicoccum) is associated with the cis-element of the Vrn-A3 locus

(2018) Kazusa Nishimura et al.   THEORETICAL AND APPLIED GENETICS

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

(2018) et al.   SCIENCE

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

(2017) Waseem Hussain et al.   Scientific Reports

Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice

(2017) Gopal Misra et al.   Scientific Reports

Characterization of a mini core collection of Japanese wheat varieties using single-nucleotide polymorphisms generated by genotyping-by-sequencing

(2016) Fuminori Kobayashi et al.   BREEDING SCIENCE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform

(2015) Yoshihisa Suyama et al.   Scientific Reports

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

An improved 2b-RAD approach (I2b-RAD) offering genotyping tested by a rice (Oryza sativa L.) F2 population

(2014) Yu Guo et al.   BMC GENOMICS

Draft Sequences of the Radish (Raphanus sativus L.) Genome

(2014) Hiroyasu Kitashiba et al.   DNA RESEARCH

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

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

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

Coevolution between simple sequence repeats (SSRs) and virus genome size

(2012) Xiangyan Zhao et al.   BMC GENOMICS

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

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.)

(2008) Edward P. Wilhelm et al.   THEORETICAL AND APPLIED GENETICS