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The Plant Genome | First Look

the plant genome coverArticles are posted here immediately following acceptance to provide faster publication and better access to the newest research. These articles have not been professionally edited and do not appear as they will in the final journal issue. Finalized manuscripts will be compiled in the next issue of The Plant Genome.

Online ISSN: 1940-3372

Citation | Articles posted here may be cited by the doi. Ex. Joseph, B., J.A. Schlueter, J.Du, M.A. Graham, J. Ma, and R.C. Shoemaker. 2009. Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution. Plant Gen., 10.3835/plantgenome2009.01.0001.

  The Plant Genome is an open-access journal.

 

 

Original Research

Using RNA-seq and in silico Subtraction to Identify Resistance Gene Analog Markers for Lr16 in Wheat
Nicole Rezac Harrison, Allan K. Fritz, Jarret I. Glasscock, Sara Ahmed, David N. Messina, Paul St. Amand, and John P. Fellers
doi: 10.3835/plantgenome2014.08.0040; Posted 27 Feb. 2015
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Natural Antisense Transcripts Associated with Salinity Response in Alfalfa
O.A. Postnikova and L.G. Nemchinov
doi: 10.3835/plantgenome2014.09.0057; Posted 27 Feb. 2015
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Genome-wide Responses to Selection and Genetic Networks Underlying Submergence Tolerance in Rice (Oryza sativa L.)
Wensheng Wang, Binying Fu, Jauhar Ali, Jianlong Xu, Yongming Gao, Tianqing Zheng, Fan Zhang, and Zhikang Li
doi: 10.3835/plantgenome2014.10.0066; Posted 27 Feb. 2015
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A Long-read Transcriptome Assembly of Cotton (Gossypium hirsutum) and Intraspecific SNP Discovery
Hamid Ashrafi, Amanda M. Hulse-Kemp, Fei Wang, S. Samuel Yang, Xueying Guan, Don C. Jones, Marta Matvienko, Keithanne Mockaitis, Z. Jeffrey Chen, David M. Stelly, and Allen Van Deynze
doi: 10.3835/plantgenome2014.10.0068; Posted 27 Feb. 2015
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Marker Imputation Before Genomewide Selection in Biparental Maize Populations
Amy Jacobson, Lian Lian, Shengqiang Zhong, and Rex Bernardo
doi: 10.3835/plantgenome2014.10.0078; Posted 27 Feb. 2015
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Identification of a New Chromosomal Region Involved in the Genetic Control of Resistance to Anthracnose in Common Bean
Noemí Trabanco, Ana Campa, Juan José Ferreira
doi: 10.3835/plantgenome2014.10.0079; Posted 27 Feb. 2015
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Association Mapping for Fusarium Wilt Resistance in Chinese Asparagus Bean Germplasm
Xinyi Wu, Xiaohua Wu, Pei Xu, Baogen Wang, Zhongfu Lu, and Guojing Li
doi: 10.3835/plantgenome2014.11.0082; Posted 27 Feb. 2015
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A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in Gossypium raimondii
Lei Gong, Rick E. Masonbrink, Corrinne E. Grover, Simon Renny-Byfield, and Jonathan F. Wendel
doi: 10.3835/plantgenome2014.11.0088; Posted 27 Feb. 2015
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Candidate Gene Identification of Flowering Time Genes in Cotton (Gossypium)
Corrinne E Grover, Joseph P Gallagher, and Jonathan F Wendel
doi: 10.3835/plantgenome2014.12.0098; Posted 27 Feb. 2015
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De Novo Assembly and Characterization of Tall fescue [Lolium arundinaceum (Schreb.) Darbysh.] Transcriptome under Water Stress
S.K. Talukder, P. Azhaguvel, S. Mukherjee, C.A. Young, T. Yuhong, N. Krom, and M.C. Saha
doi: 10.3835/plantgenome2014.09.0050; Posted 9 Feb. 2015
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Genetic Gain from Phenotypic and Genomic Selection for Quantitative Resistance to Stem Rust of Wheat
J. Rutkoski, R. P. Singh, J. Huerta-Espino, S. Bhavani, J. Poland, J.-L. Jannink, and M. E. Sorrells
doi: 10.3835/plantgenome2014.10.0074; Posted 9 Feb. 2015
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Discovery of Conservation and Diversification of miR171 Genes by Phylogenetic Analysis Based on Global Genomes
Xudong Zhu, Xiangpeng Leng, Xin Sun, Qian Mu, Baoju Wang, Xiaopeng Li, Chen Wang, and Jinggui Fang
doi: 10.3835/plantgenome2014.10.0076; Posted 9 Feb. 2015
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Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet (SS) Parent and an Elite Parent
Morgan Echeverry-Solarte, Ajay Kumar, Shahryar Kianian, Eder E. Mantovani, Phillip E. McClean, Edward L. Deckard, Elias Elias, Senay Simsek, Mohammed S. Alamri, Justin Hegstad, Blaine Schatz, and Mohamed Mergoum
doi: 10.3835/plantgenome2014.12.0089; Posted 9 Feb. 2015
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Genomic Characterization of Interspecific Hybrids and an Admixture Population Derived from Panicum amarum x P. virgatum
Christopher Heffelfinger, Adam P. Deresienski, Kimberly A. Nelson, Maria A. Moreno, Joel P Hague, Stephen L. Dellaporta, and Albert P. Kausch
doi: 10.3835/plantgenome2015.01.0001; Posted 9 Feb. 2015
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Marker-assisted Backcrossing (MABC) Using CMS-specific, SSR and ISSR markers to Develop an Elite CMS Line in Rice
Asadollah Ahmadikhah, Mehdi Mirarab, Mohammad Hadi Pahlevani, and Leila Nayyeripasand
doi: 10.3835/plantgenome2014.07.0031; Posted 20 Jan. 2015
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Linkage Maps of a Mediterranean x Continental Tall Fescue (Festuca arundinacea) Population and Their Comparative Analysis with Other Poaceae Species
Ryan Dierking, Perumal Azhaguvel, Robert Kallenbach, Malay Saha, Joseph Bouton, Konstantin Chekhovskiy, David Kopecký, and Andrew Hopkins
doi: 10.3835/plantgenome2014.07.0032; Posted 20 Jan. 2015
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Comparative Transcriptional Profiling of Contrasting Genotypes of Rice (Oryza sativa L.) in Response to Arsenic Exposure Reveals Different Mechanisms of Stress Perception and Tolerance
Arti Rai, Archana Bhardwaj, Prashant Misra, Sumit K. Bag, Bijan Adhikari, Rudra D. Tripathi, Prabodh K. Trivedi, and Debasis Chakrabarty
doi: 10.3835/plantgenome2014.09.0054; Posted 20 Jan. 2015
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Genomic SSR Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame
Ay┼če Özgür Uncu, Visam Gultekin, Jens Allmer, Anne Frary, and Sami Doganlar
doi: 10.3835/plantgenome2014.11.0087; Posted 20 Jan. 2015
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Faba bean (Vicia faba L.): Transcriptome Analysis from Etiolated Seedling and Developing Seed Coat of Key Cultivars for Synthesis of Proanthocyanidins, Phytate, Raffinose-family Oligosaccharides, Vicine and Convicine
Heather Ray, Cheryl Bock, and Fawzy Georges
doi: 10.3835/plantgenome2014.07.0028; Posted 8 Jan. 2015
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Dissecting a QTL into Candidate Genes Highlighted the Key Role of Pectinestarases in Regulating the Ascorbic Acid Content in Tomato Fruit
Valentino Ruggieri, Adriana Sacco, Roberta Calafiore, Luigi Frusciante, and Amalia Barone
doi: 10.3835/plantgenome2014.08.0038; Posted 8 Jan. 2015
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Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near-Isogenic Lines
Meixia Zhao, Chunmei Cai, Jixian Zhai, Feng Lin, Linghong Li, Jacob Shreve, Jyothi Thimmapuram, Teresa J. Hughes, Blake C. Meyers, and Jianxin Ma
doi: 10.3835/plantgenome2014.09.0044; Posted 8 Jan. 2015
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Efficient Use of Historical Data for Genomic Selection: A Case Study of Stem Rust Resistance in Wheat
J. Rutkoski, R.P. Singh, J. Huerta-Espino, S. Bhavani, J. Poland, J.-L. Jannink, and M.E. Sorrells
doi: 10.3835/plantgenome2014.09.0046; Posted 8 Jan. 2015
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Natural Variation in Synthesis and Catabolism Genes Influences Dhurrin Content in Sorghum (Sorghum bicolor L. Moench)
Chad M. Hayes, Gloria B. Burow, Patrick J. Brown, Carrie Thurber, Zhanguo Xin, and John J. Burke
doi: 10.3835/plantgenome2014.09.0048; Posted 8 Jan. 2015
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SimpleMap: A Pipeline to Streamline High Density Linkage Map Construction
Abdulqader Jighly, Reem Joukhadar, and Manickavelu Alagu
doi: 10.3835/plantgenome2014.09.0056; Posted 8 Jan. 2015
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Genotyping-by-Sequencing Enabled Mapping and Marker Development for the By-2 Potyvirus Resistance Allele in Common Bean
John P. Hart and Phillip D. Griffiths
doi: 10.3835/plantgenome2014.09.0058; Posted 8 Jan. 2015
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The Genetic Makeup of a Global Barnyard Millet Germplasm Collection
Jason G. Wallace, Hari D. Upadhyaya, M. Vetriventhan, Edward S. Buckler, C. Tom Hash, and Punna Ramu
doi: 10.3835/plantgenome2014.10.0067; Posted 8 Jan. 2015
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HtStuf: High-throughput Sequencing to Locate unknown DNA Junction Fragments
Lisa B. Kanizay, Thomas B. Jacobs, Kevin Gillespie, Jade A. Newsome, Brittany N. Spaid, and Wayne A. Parrott
doi: 10.3835/plantgenome2014.10.0070; Posted 8 Jan. 2015
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Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis
Desalegn D. Serba, Srinivasa Rao Uppalapati, Shreyartha Mukherjee, Nick Krom, Yuhong Tang, Kirankumar S. Mysore, and Malay C. Saha
doi: 10.3835/plantgenome2014.10.0075; Posted 8 Jan. 2015
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Genome-wide Mapping and Analysis of Grapevine MicroRNAs and Their Potential Target Genes
Songtao Jiu, Xudong Zhu, Jian Wang, Cheng Zhang, Qian Mu, Chen Wang, and Jinggui Fang
doi: 10.3835/plantgenome2014.12.0091; Posted 8 Jan. 2015
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Optimizing Transcriptome Assemblies for Eleusine indica Leaf and Seedling by Combining Multiple Assemblies from Three De Novo Assemblers
Shu Chen, J. Scott McElroy, Fenny Dane, and Eric Peatman
doi: 10.3835/plantgenome2014.10.0064; Posted online 4 Dec. 2014
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Phytic Acid and Inorganic Phosphate Composition in Soybean Lines with Independent IPK1 Mutations
Jennifer A. Vincent, Minviluz Stacey, Gary Stacey, and Kristin D. Bilyeu
doi: 10.2135/plantgenome2014.10.0077; Posted online 4 Dec. 2014
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Characterization of the Granule-Bound Starch Synthase I Gene in Chenopodium

Douglass C. Brown, Veronica Cepeda-Cornejo, Peter J. Maughan, and Eric N. Jellen
doi: 10.3835/plantgenome2014.09.0051; Posted online 17 Nov. 2014
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A Transcriptome Profile for Developing Seed of Polyploid Cotton (Gossypium hirsutum)

Ran Hovav, Adi Faigenboim-Doron, Noa Kadmon, Guanjing Hu, Xia Zhang, Joseph P. Gallagher, and Jonathan F. Wendel
doi: 10.3835/plantgenome2014.08.0041; Posted online 24 Oct 2014
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Taxonomy and Genetic Differentiation Among Wild and Cultivated Germplasm of Solanum sect. Petota

Michael A. Hardigan, John Bamberg, C. Robin Buell, and David S. Douches
doi: 10.3835/plantgenome2014.06.0025; Posted online 25 Sept. 2014
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Detection, Validation and Application of Genotyping-by-Sequencing Based Single Nucleotide Polymorphisms in Upland Cotton (Gossypium hirsutum L.)
Md. Sariful Islam, Gregory N. Thyssen, Johnie N. Jenkins, and David D. Fang
doi: 10.3835/plantgenome2014.07.0034; Posted online 25 Sept. 2014
Full Text | Supplement 1 | Supplement 2 | Supplement 3 | Supplement 4 | Supplement 5 | Supplement 6 | Supplement 7 | Supplement 8 (PDF)  OPEN ACCESS

Structure, Organization and Expression of the Alpha Prolamin Multigenic Family Bring New Insights into the Evolutionary Relationships among Grasses

Rafael Soares Correa de Souza, Tiago Santana Balbuena, and Paulo Arruda
doi: 10.3835/plantgenome2014.06.0027; Posted online 5 Sept. 2014
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Assessing Genomic Selection Prediction Accuracy in a Dynamic Barley Breeding Population
A. H. Sallam, J. B. Endelman, J.-L. Jannink, and K. P. Smith
doi: 10.3835/plantgenome2014.05.0020; Posted online 5 Sept. 2014
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