Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.; Chapman, Jarrod; Schmutz, Jeremy; Barry, Kerrie; Muñoz-Amatriaín, María; Close, Timothy J.; Wise, Roger P.; Schulman, Alan H.; Himmelbach, Axel; Mayer, Klaus F. X.; Scholz, Uwe; Poland, Jesse A.; Stein, Nils; Waugh, Robbie

doi:10.1111/tpj.12319

Title: Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Journal Article · Thu Oct 10 00:00:00 EDT 2013 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.12319· OSTI ID:1625934

Mascher, Martin ^[1]; Muehlbauer, Gary J. ^[2]; Rokhsar, Daniel S. ^[3]; Chapman, Jarrod ^[4]; Schmutz, Jeremy ^[5]; Barry, Kerrie ^[4]; Muñoz-Amatriaín, María ^[6]; Close, Timothy J. ^[7]; Wise, Roger P. ^[8]; Schulman, Alan H. ^[9]; Himmelbach, Axel ^[1]; Mayer, Klaus F. X. ^[10]; Scholz, Uwe ^[1]; Poland, Jesse A. ^[11]; Stein, Nils ^[1]; Waugh, Robbie ^[12]

Leibniz Inst. of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany)
Univ. of Minnesota, St Paul, MN (United States). Dept. of Agronomy and Plant Genetics; Univ. of Minnesota, St Paul, MN (United States). Dept. Plant Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Molecular and Cell Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
Univ. of Minnesota, St Paul, MN (United States). Dept. of Agronomy and Plant Genetics
Univ. of California, Riverside, CA (United States). Dept. of Botany & Plant Sciences
US Dept. of Agriculture (USDA)., Ames, IA (United States). Agricultural Research Service (ARS). Iowa State Univ.
Univ. of Helsinki (Finland). MTT Agrifood Research. Inst. of Biotechnology
Helmholtz Zentrum München, Neuherberg (Germany). Munich Information Center for Protein Sequences. Inst. of Bioinformatics and Systems Biology
Kansas State Univ., Manhattan, KS (United States). US Dept. of Agriculture. Agricultural Research Service (ARS). Hard Winter Wheat Genetics Research Unit. Dept. of Agronomy
Univ. of Dundee (United Kingdom). The James Hutton Inst. Division of Plant Sciences

Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625934

Journal Information:: The Plant Journal, Vol. 76, Issue 4; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (33)

Multiplexed shotgun genotyping for rapid and efficient genetic mapping Andolfatto, P.; Davison, D.; Erezyilmaz, D. Genome Research, Vol. 21, Issue 4 https://doi.org/10.1101/gr.115402.110	journal	January 2011
Analysis of the bread wheat genome using whole-genome shotgun sequencing Brenchley, Rachel; Spannagl, Manuel; Pfeifer, Matthias Nature, Vol. 491, Issue 7426 https://doi.org/10.1038/nature11650	journal	November 2012
The Maize Genome Sequencing Project Chandler, Vicki L.; Brendel, Volker Plant Physiology, Vol. 130, Issue 4 https://doi.org/10.1104/pp.015594	journal	December 2002
An Integrated Physical and Genetic Map of the Rice Genome Chen, Mingsheng; Presting, Gernot; Barbazuk, W. Brad The Plant Cell, Vol. 14, Issue 3 https://doi.org/10.1105/tpc.010485	journal	March 2002
Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley Comadran, Jordi; Kilian, Benjamin; Russell, Joanne Nature Genetics, Vol. 44, Issue 12 https://doi.org/10.1038/ng.2447	journal	November 2012
Integrating cereal genomics to support innovation in the Triticeae Feuillet, C.; Stein, N.; Rossini, L. Functional & Integrative Genomics, Vol. 12, Issue 4 https://doi.org/10.1007/s10142-012-0300-5	journal	November 2012
High-quality draft assemblies of mammalian genomes from massively parallel sequence data Gnerre, S.; MacCallum, I.; Przybylski, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 4 https://doi.org/10.1073/pnas.1017351108	journal	December 2010
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions Guo, Shaogui; Zhang, Jianguo; Sun, Honghe Nature Genetics, Vol. 45, Issue 1 https://doi.org/10.1038/ng.2470	journal	November 2012
Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content: GenomeZipper analysis of wheat chromosome 4A Hernandez, Pilar; Martis, Mihaela; Dorado, Gabriel The Plant Journal, Vol. 69, Issue 3 https://doi.org/10.1111/j.1365-313X.2011.04808.x	journal	November 2011
High-throughput genotyping by whole-genome resequencing Huang, X.; Feng, Q.; Qian, Q. Genome Research, Vol. 19, Issue 6 https://doi.org/10.1101/gr.089516.108	journal	May 2009
Genome-wide association studies of 14 agronomic traits in rice landraces Huang, Xuehui; Wei, Xinghua; Sang, Tao Nature Genetics, Vol. 42, Issue 11 https://doi.org/10.1038/ng.695	journal	October 2010
De novo assembly and genotyping of variants using colored de Bruijn graphs Iqbal, Zamin; Caccamo, Mario; Turner, Isaac Nature Genetics, Vol. 44, Issue 2 https://doi.org/10.1038/ng.1028	journal	January 2012
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly Lam, Ernest T.; Hastie, Alex; Lin, Chin Nature Biotechnology, Vol. 30, Issue 8 https://doi.org/10.1038/nbt.2303	journal	July 2012
Genomic mapping by fingerprinting random clones: A mathematical analysis Lander, Eric S.; Waterman, Michael S. Genomics, Vol. 2, Issue 3 https://doi.org/10.1016/0888-7543(88)90007-9	journal	April 1988
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data Li, H. Bioinformatics, Vol. 27, Issue 21 https://doi.org/10.1093/bioinformatics/btr509	journal	September 2011
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population Manickavelu, Alagu; Kawaura, Kanako; Imamura, Hisako Euphytica, Vol. 177, Issue 2 https://doi.org/10.1007/s10681-010-0217-9	journal	July 2010
Sequencing the maize genome Martienssen, Robert A.; Rabinowicz, Pablo D.; O’Shaughnessy, Andrew Current Opinion in Plant Biology, Vol. 7, Issue 2 https://doi.org/10.1016/j.pbi.2004.01.010	journal	April 2004
Molecular mapping of wheat. Homoeologous group 3 Nelson, James C.; Deynze, Allen E. Van; Sorrells, Mark E. Genome, Vol. 38, Issue 3 https://doi.org/10.1139/g95-068	journal	June 1995
A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B Paux, E.; Sourdille, P.; Salse, J. Science, Vol. 322, Issue 5898 https://doi.org/10.1126/science.1161847	journal	October 2008
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach Poland, Jesse A.; Brown, Patrick J.; Sorrells, Mark E. PLoS ONE, Vol. 7, Issue 2 https://doi.org/10.1371/journal.pone.0032253	journal	February 2012
A window into third-generation sequencing Schadt, E. E.; Turner, S.; Kasarskis, A. Human Molecular Genetics, Vol. 19, Issue R2 https://doi.org/10.1093/hmg/ddq416	journal	September 2010
The B73 Maize Genome: Complexity, Diversity, and Dynamics Schnable, P. S.; Ware, D.; Fulton, R. S. Science, Vol. 326, Issue 5956, p. 1112-1115 https://doi.org/10.1126/science.1178534	journal	November 2009
Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History Wei, Fusheng; Coe, Ed; Nelson, William PLoS Genetics, Vol. 3, Issue 7 https://doi.org/10.1371/journal.pgen.0030123	journal	July 2007
Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph Wu, Yonghui; Bhat, Prasanna R.; Close, Timothy J. PLoS Genetics, Vol. 4, Issue 10 https://doi.org/10.1371/journal.pgen.1000212	journal	October 2008
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing Xie, W.; Feng, Q.; Yu, H. Proceedings of the National Academy of Sciences, Vol. 107, Issue 23 https://doi.org/10.1073/pnas.1005931107	journal	May 2010
The draft genome of sweet orange (Citrus sinensis) Xu, Qiang; Chen, Ling-Ling; Ruan, Xiaoan Nature Genetics, Vol. 45, Issue 1 https://doi.org/10.1038/ng.2472	journal	November 2012
A Greedy Algorithm for Aligning DNA Sequences Zhang, Zheng; Schwartz, Scott; Wagner, Lukas Journal of Computational Biology, Vol. 7, Issue 1-2 https://doi.org/10.1089/10665270050081478	journal	February 2000
A window into third generation sequencing Schadt, E. E.; Turner, S.; Kasarskis, A. Human Molecular Genetics, Vol. 20, Issue 4 https://doi.org/10.1093/hmg/ddq481	journal	December 2010
Aquabacterium terrae sp. nov., isolated from soil Dahal, Ram Hari; Han, Ji Yeon; Lee, Hyosun Archives of Microbiology, Vol. 203, Issue 6 https://doi.org/10.1007/s00203-021-02269-8	journal	April 2021
Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors Lemos, Danilo; Stuart, Jackson B.; Louie, William Journal of Virology, Vol. 94, Issue 24 https://doi.org/10.1128/jvi.01605-20	journal	September 2020
Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History Wei, Fusheng; Coe, Ed; Nelson, William PLoS Genetics, Vol. preprint, Issue 2007 https://doi.org/10.1371/journal.pgen.0030123.eor	journal	January 2005
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data Li, Heng arXiv https://doi.org/10.48550/arxiv.1203.6372	text	January 2012

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Genetics of Tillering in Rice and Barley Hussien, Ahmed; Tavakol, Elahe; Horner, David S. The Plant Genome, Vol. 7, Issue 1 https://doi.org/10.3835/plantgenome2013.10.0032	journal	January 2014
A High‐Density, Sequence‐Enriched Genetic Map of Hordeum bulbosum and Its Collinearity to H. vulgare Wendler, Neele; Mascher, Martin; Himmelbach, Axel The Plant Genome, Vol. 10, Issue 3 https://doi.org/10.3835/plantgenome2017.06.0049	journal	November 2017
Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques Åhman, Inger; Bengtsson, Therése Theoretical and Applied Genetics, Vol. 132, Issue 5 https://doi.org/10.1007/s00122-019-03287-3	journal	February 2019
Analysis of early-flowering genes at barley chromosome 2H expands the repertoire of mutant alleles at the Mat-c locus Matyszczak, Izabela; Tominska, Marta; Zakhrabekova, Shakhira Plant Cell Reports, Vol. 39, Issue 1 https://doi.org/10.1007/s00299-019-02472-4	journal	September 2019
Genome-wide association studies of net form of net blotch resistance at seedling and adult plant stages in spring barley collection Amezrou, Reda; Verma, Ramesh Pal Singh; Chao, Shiaoman Molecular Breeding, Vol. 38, Issue 5 https://doi.org/10.1007/s11032-018-0813-2	journal	April 2018
Identifying a novel powdery mildew resistance gene in a barley landrace from Morocco Piechota, Urszula; Czembor, Paweł C.; Słowacki, Piotr Journal of Applied Genetics, Vol. 60, Issue 3-4 https://doi.org/10.1007/s13353-019-00505-y	journal	July 2019
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data Alaux, Michael; Rogers, Jane; Letellier, Thomas Genome Biology https://doi.org/10.1101/363259	posted_content	January 2018
Targeted resequencing reveals genomic signatures of barley domestication Pankin, Artem; Altmüller, Janine; Becker, Christian New Phytologist, Vol. 218, Issue 3 https://doi.org/10.1111/nph.15077	journal	March 2018
Unlocking the secondary gene‐pool of barley with next‐generation sequencing Wendler, Neele; Mascher, Martin; Nöh, Christiane Plant Biotechnology Journal, Vol. 12, Issue 8 https://doi.org/10.1111/pbi.12219	journal	July 2014
High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool Winfield, Mark O.; Allen, Alexandra M.; Burridge, Amanda J. Plant Biotechnology Journal, Vol. 14, Issue 5 https://doi.org/10.1111/pbi.12485	journal	October 2015
Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application Scheben, Armin; Batley, Jacqueline; Edwards, David Plant Biotechnology Journal, Vol. 15, Issue 2 https://doi.org/10.1111/pbi.12645	journal	January 2017
A high-resolution einkorn ( Triticum monococcum L.) linkage map involving wild, domesticated and feral einkorn genotypes Marino, Rosanna; Volante, Andrea; Brandolini, Andrea Plant Breeding, Vol. 137, Issue 5 https://doi.org/10.1111/pbr.12637	journal	September 2018
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome Mayer, K. F. X.; Rogers, J.; Dole el, J. Science, Vol. 345, Issue 6194 https://doi.org/10.1126/science.1251788	journal	July 2014
Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae Bernhardt, Nadine; Brassac, Jonathan; Kilian, Benjamin BMC Evolutionary Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12862-017-0989-9	journal	June 2017
Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits Fan, Yun; Shabala, Sergey; Ma, Yanling BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1243-8	journal	February 2015
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Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress Kochevenko, Andriy; Jiang, Yong; Seiler, Christiane BMC Plant Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12870-018-1323-4	journal	June 2018
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High Resolution Mapping of a Hordeum bulbosum-Derived Powdery Mildew Resistance Locus in Barley Using Distinct Homologous Introgression Lines Hoseinzadeh, Parastoo; Ruge-Wehling, Brigitte; Schweizer, Patrick Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00225	journal	March 2020
Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley Surdonja, Korana; Eggert, Kai; Hajirezaei, Mohammad-Reza Epigenomes, Vol. 1, Issue 2 https://doi.org/10.3390/epigenomes1020009	journal	June 2017
transPLANT Resources for Triticeae Genomic Data Spannagl, Manuel; Alaux, Michael; Lange, Matthias The Plant Genome, Vol. 9, Issue 1 https://doi.org/10.3835/plantgenome2015.06.0038	journal	March 2016
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools Monat, Cécile; Padmarasu, Sudharsan; Lux, Thomas BioMed Central https://doi.org/10.5167/uzh-198645	text	January 2019
Genome-Wide Association Study Reveals a New QTL for Salinity Tolerance in Barley (Hordeum vulgare L.) Fan, Yun; Zhou, Gaofeng; Shabala, Sergey Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00946	journal	June 2016
A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance Pavy, Nathalie; Lamothe, Manuel; Pelgas, Betty The Plant Journal, Vol. 90, Issue 1 https://doi.org/10.1111/tpj.13478	journal	March 2017
A chromosome conformation capture ordered sequence of the barley genome Mascher, Martin; Gundlach, Heidrun; Al, Et Nature Publishing Group https://doi.org/10.5167/uzh-149295	text	January 2017
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools Monat, Cécile; Padmarasu, Sudharsan; Lux, Thomas Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1899-5	journal	December 2019
High resolution mapping of a Hordeum bulbosum -derived powdery mildew resistance locus in barley using distinct homologous introgression lines Hoseinzadeh, Parastoo; Ruge-Wehling, Brigitte; Schweizer, Patrick Frontiers in Plant Science https://doi.org/10.1101/867960	posted_content	January 2019
Advances in genome studies in plants and animals Appels, R.; Nystrom-Persson, J.; Keeble-Gagnere, G. Functional & Integrative Genomics, Vol. 14, Issue 1 https://doi.org/10.1007/s10142-014-0364-5	journal	March 2014
GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley – A review Alqudah, Ahmad M.; Sallam, Ahmed; Stephen Baenziger, P. Journal of Advanced Research, Vol. 22 https://doi.org/10.1016/j.jare.2019.10.013	journal	March 2020
Resolve barley domestication Lyu, Jun Nature Plants, Vol. 4, Issue 4 https://doi.org/10.1038/s41477-018-0135-8	journal	March 2018
POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat Suchecki, Radosław; Watson-Haigh, Nathan S.; Baumann, Ute Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-14591-7	journal	October 2017
Improvement of barley genome annotations by deciphering the Haruna Nijo genome Sato, Kazuhiro; Tanaka, Tsuyoshi; Shigenobu, Shuji DNA Research https://doi.org/10.1093/dnares/dsv033	journal	November 2015
Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping Maurer, Andreas; Draba, Vera; Pillen, Klaus Journal of Experimental Botany, Vol. 67, Issue 8 https://doi.org/10.1093/jxb/erw070	journal	March 2016
Answering a four decade-old question on epicuticular wax biosynthesis Kosma, Dylan K.; Rowland, Owen Journal of Experimental Botany, Vol. 67, Issue 9 https://doi.org/10.1093/jxb/erw144	journal	April 2016
The role of epistasis and its interaction with environment in fine-tuning heading time in barley Christov, Nikolai K. Journal of Experimental Botany, Vol. 71, Issue 3 https://doi.org/10.1093/jxb/erz503	journal	January 2020
Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome Munoz-Amatriain, Maria; Lonardi, S.; Lou, M. C. Semantic Scholar https://doi.org/10.1101/018978	journal	May 2015
Targeted re-sequencing reveals the genomic signatures of multiple barley domestications Pankin, Artem; Altmuller, Janine; Becker, Christain New Phytologist https://doi.org/10.1101/070078	journal	August 2017
Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes Beier, Sebastian; Himmelbach, Axel; Schmutzer, Thomas Plant Biotechnology Journal, Vol. 14, Issue 7 https://doi.org/10.1111/pbi.12511	journal	January 2016
Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A Poursarebani, Naser; Nussbaumer, Thomas; Šimková, Hana The Plant Journal, Vol. 79, Issue 2 https://doi.org/10.1111/tpj.12550	journal	June 2014
Genetic Dissection of Photoperiod Response Based on GWAS of Pre-Anthesis Phase Duration in Spring Barley Alqudah, Ahmad M.; Sharma, Rajiv; Pasam, Raj K. PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0113120	journal	November 2014
A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family Houston, Kelly; Burton, Rachel A.; Sznajder, Beata PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0130890	journal	July 2015
Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-qi PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0133161	journal	July 2015
Identification and Fine Mapping of a White Husk Gene in Barley (Hordeum vulgare L.) Hua, Wei; Zhang, Xiao-Qi; Zhu, Jinghuan PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0152128	journal	March 2016
Genetic Diversity and Genome Wide Association Study of β-Glucan Content in Tetraploid Wheat Grains Marcotuli, Ilaria; Houston, Kelly; Schwerdt, Julian G. PLOS ONE, Vol. 11, Issue 4 https://doi.org/10.1371/journal.pone.0152590	journal	April 2016
Mapping of quantitative trait loci associated with resistance to net form net blotch (Pyrenophora teres f. teres) in a doubled haploid Norwegian barley population Wonneberger, Ronja; Ficke, Andrea; Lillemo, Morten PLOS ONE, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pone.0175773	journal	April 2017
Fast and Cost-Effective Genetic Mapping in Apple Using Next-Generation Sequencing Gardner, Kyle M.; Brown, Patrick; Cooke, Thomas F. G3 Genes\|Genomes\|Genetics, Vol. 4, Issue 9 https://doi.org/10.1534/g3.114.011023	journal	September 2014
Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid Wheat Edae, Erena A.; Bowden, Robert L.; Poland, Jesse G3 Genes\|Genomes\|Genetics, Vol. 5, Issue 12 https://doi.org/10.1534/g3.115.020362	journal	December 2015
Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus Richards, Jonathan; Chao, Shiaoman; Friesen, Timothy G3 Genes\|Genomes\|Genetics, Vol. 6, Issue 7 https://doi.org/10.1534/g3.116.028902	journal	July 2016
Genetic anchoring of whole-genome shotgun assemblies Mascher, Martin; Stein, Nils Frontiers in Genetics, Vol. 5 https://doi.org/10.3389/fgene.2014.00208	journal	July 2014
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools Fierst, Janna L. Frontiers in Genetics, Vol. 6 https://doi.org/10.3389/fgene.2015.00220	journal	June 2015
The Genetic Architecture of Barley Plant Stature Alqudah, Ahmad M.; Koppolu, Ravi; Wolde, Gizaw M. Frontiers in Genetics, Vol. 7 https://doi.org/10.3389/fgene.2016.00117	journal	June 2016
A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A Balcárková, Barbora; Frenkel, Zeev; Škopová, Monika Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.02063	journal	January 2017
Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes Dreissig, Steven; Fuchs, Jörg; Himmelbach, Axel Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01620	journal	September 2017
Pyramiding rpg4- and Rpg1-Mediated Stem Rust Resistance in Barley Requires the Rrr1 Gene for Both to Function Sharma Poudel, Roshan; Al-Hashel, Abdullah F.; Gross, Thomas Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01789	journal	December 2018
Genetic Dissection of Root System Architectural Traits in Spring Barley Jia, Zhongtao; Liu, Ying; Gruber, Benjamin D. Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00400	journal	April 2019
Strategies for Sequence Assembly of Plant Genomes Deschamps, Stéphane; Llaca, Victor Plant Genomics https://doi.org/10.5772/61927	book	July 2016
A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat Adamski, Nikolai M.; Borrill, Philippa; Brinton, Jemima eLife, Vol. 9 https://doi.org/10.7554/elife.55646	journal	March 2020

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