High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum × G. barbadense in response to Verticillium dahliae infection

(2019) Peng-tao Li et al.   BMC PLANT BIOLOGY

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

(2019) Yan Hu et al.   NATURE GENETICS

Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

(2019) Jun Zou et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic Introgression from to Soybean to Increase Seed Yield

(2018) A. Akpertey et al.   CROP SCIENCE

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

(2018) Zhiying Ma et al.   NATURE GENETICS

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum )

(2018) Tianwang Wen et al.   PLANT BIOTECHNOLOGY JOURNAL

Quantitative Trait Locus Mapping and Candidate Gene Analysis for Verticillium Wilt Resistance Using Gossypium barbadense Chromosomal Segment Introgressed Line

(2018) Jun Zhao et al.   Frontiers in Plant Science

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang 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

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Genetic and phenotypic effects of chromosome segments introgressed from Gossypium barbadense into Gossypium hirsutum

(2017) Weiwu Song et al.   PLoS One

Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

(2016) Baosheng Dai et al.   BMC GENETICS

Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species

(2016) M. Ulloa et al.   GENETICA

Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

(2016) N Ali et al.   HEREDITY

Expanding Maize Genetic Resources with Predomestication Alleles: Maize–Teosinte Introgression Populations

(2016) Zhengbin Liu et al.   Plant Genome

Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing

(2016) Xin Ma et al.   Scientific Reports

Genetic structure ofMiscanthus sinensisandMiscanthus sacchariflorusin Japan indicates a gradient of bidirectional but asymmetric introgression

(2015) Lindsay V. Clark et al.   JOURNAL OF EXPERIMENTAL BOTANY

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

(2015) Sen Wang et al.   GENOME BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Contemporary ecotypic divergence during a recent range expansion was facilitated by adaptive introgression

(2014) K. Lucek et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptomic Analysis of Fiber Strength in Upland Cotton Chromosome Introgression Lines Carrying Different Gossypium barbadense Chromosomal Segments

(2014) Lei Fang et al.   PLoS One

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

(2014) Chris S. Clarkson et al.   Nature Communications

A standardized method for quantifying unidirectional genetic introgression

(2014) Sten Karlsson et al.   Ecology and Evolution

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication

(2010) Ryan A Rapp et al.   BMC BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

Fast model-based estimation of ancestry in unrelated individuals

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Reconstructing Indian population history

(2009) David Reich et al.   NATURE