Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq)

[1]  R. Varshney,et al.  Genetic Mapping and Quantitative Trait Loci Analysis for Disease Resistance Using F2 and F5 Generation‐based Genetic Maps Derived from ‘Tifrunner’ × ‘GT‐C20’ in Peanut , 2013 .

[2]  Songnian Hu,et al.  Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus , 2013, BMC Genomics.

[3]  S. Tabata,et al.  Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes , 2013, DNA research : an international journal for rapid publication of reports on genes and genomes.

[4]  A. Meyer,et al.  A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes (Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq) , 2013, G3: Genes | Genomes | Genetics.

[5]  Robert J. Elshire,et al.  Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol , 2013, PLoS genetics.

[6]  Sylvie Cloutier,et al.  SNP Discovery through Next-Generation Sequencing and Its Applications , 2012, International journal of plant genomics.

[7]  Zechen Chong,et al.  Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads , 2012, Bioinform..

[8]  S. Yuan,et al.  Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata) , 2012, BMC Genomics.

[9]  H. T. Stalker,et al.  A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut , 2012, BMC Genomics.

[10]  S. N. Nigam,et al.  An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.) , 2012, PloS one.

[11]  Manabu Watanabe,et al.  In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut , 2012, BMC Plant Biology.

[12]  H. Hoekstra,et al.  Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species , 2012, PloS one.

[13]  Xinfa Wang,et al.  Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed , 2012, PloS one.

[14]  Wei Hua,et al.  Development and application of single nucleotide polymorphism markers in the polyploid Brassica napus by 454 sequencing of expressed sequence tags , 2012 .

[15]  Mukesh Jain,et al.  NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data , 2012, PloS one.

[16]  B. Rosen,et al.  Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.) , 2012, BMC Plant Biology.

[17]  Qian Qian,et al.  Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm , 2011, Nature Genetics.

[18]  S. N. Nigam,et al.  Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.) , 2011, Molecular Breeding.

[19]  H. L. Nadaf,et al.  Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.) , 2011, Molecular Breeding.

[20]  S. Knapp,et al.  An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations , 2011, Theoretical and Applied Genetics.

[21]  Detlef Weigel,et al.  Paired-end RAD-seq for de novo assembly and marker design without available reference , 2011, Bioinform..

[22]  M. Trick,et al.  Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing , 2011, Nature Biotechnology.

[23]  Y. Chu,et al.  Marker‐Assisted Selection to Pyramid Nematode Resistance and the High Oleic Trait in Peanut , 2011 .

[24]  Eric A. Johnson,et al.  Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne , 2011, Theoretical and Applied Genetics.

[25]  M. Rubenfield,et al.  Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology , 2011, BMC Genomics.

[26]  Patrick M Hayes,et al.  Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley , 2011, BMC Genomics.

[27]  A. Kilian,et al.  Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley , 2010, Molecular Genetics and Genomics.

[28]  Qi Feng,et al.  Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing , 2010, Proceedings of the National Academy of Sciences.

[29]  Xiaoping Chen,et al.  A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome , 2010, BMC Plant Biology.

[30]  Steven B Cannon,et al.  High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence , 2010, BMC Genomics.

[31]  B. Courtois,et al.  Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid , 2009, BMC Plant Biology.

[32]  K. Kristiansen,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[33]  Xuehui Huang,et al.  High-throughput genotyping by whole-genome resequencing. , 2009, Genome research.

[34]  Yan Long,et al.  Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. , 2009, Plant biotechnology journal.

[35]  S. N. Nigam,et al.  The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.) , 2009, Theoretical and Applied Genetics.

[36]  P. Etter,et al.  Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers , 2008, PloS one.

[37]  Matthew J. Huentelman,et al.  IDENTIFICATION OF GENETIC VARIANTS USING BARCODED MULTIPLEXED SEQUENCING , 2008, Nature Methods.

[38]  C. Kvien,et al.  Registration of ‘Tifguard’ Peanut , 2008 .

[39]  B. Courtois,et al.  Identification and mapping of AFLP markers linked to peanut (Arachis hypogaea L.) resistance to the aphid vector of groundnut rosette disease , 2004, Theoretical and Applied Genetics.

[40]  R. Bernardo,et al.  Chromosomal regions associated with segregation distortion in maize , 2002, Theoretical and Applied Genetics.

[41]  A. Paterson,et al.  Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species. , 2001, Genetics.

[42]  H. T. Stalker,et al.  Molecular Markers of Arachis and Marker-Assisted Selection , 2001 .

[43]  I. Leitch,et al.  Nuclear DNA Amounts in Angiosperms and their Modern Uses—807 New Estimates , 2000 .

[44]  J. Seabrook,et al.  Linkage analysis of anther-derived monoploids showing distorted segregation of molecular markers , 2000, Theoretical and Applied Genetics.

[45]  A. Brookes.  The essence of SNPs. , 1999, Gene.

[46]  R. Sederoff,et al.  Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. , 1994, Genetics.

[47]  R. Varshney,et al.  Genetic Mapping and Quantitative Trait Loci Analysis for Disease Resistance Using F 2 and F 5 Generation-based Genetic Maps Derived from ‘ Tifrunner ’ × ‘ GTC 20 ’ in Peanut , 2013 .

[48]  H. T. Stalker,et al.  Genomics and Genetic Enhancement of Peanut , 2004 .

[49]  R. Voorrips.  MapChart: software for the graphical presentation of linkage maps and QTLs. , 2002, The Journal of heredity.

[50]  Roeland E. Voorrips,et al.  Software for the calculation of genetic linkage maps , 2001 .