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Volume 9 Issue 3, November 2016



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  • RESEARCH HIGHLIGHTS up

  • ORIGINAL RESEARCH up

    • Cheng Zhang, Haifeng Jia, Jingjue Zeng, Tariq Perraiz, Zhenqiang Xie, Xudong Zhu and Chen Wang
      Fertilization of Grapevine Based on Gene Expression
      Core Ideas
      • This approach is more accurate and reliable than traditional fertilization strategies.
      • This study verified the feasibility and workability of gene expression-based fertilization strategies.
      • The specific nutritional requirements of grapevine at different developmental stages were depicted in the level of gene expression.
      doi:10.3835/plantgenome2015.09.0083
      The Plant Genome 2016 9:
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    • Huifen Cao, Erli Pang and Kui Lin
      Hierarchical Map of Orthologous Genomic Regions Reconstructed from Two Closely Related Genomes: Cucumber Case Study
      Core Ideas
      • A strategy for reconstructing a hierarchical map of orthologous genomic regions from two genomes.
      • Both large- and small-scale genomic changes could be more accurately detected from this map.
      • Many large-scale genomic changes are inferred between two cucumber subspecies diverged shortly.
      doi:10.3835/plantgenome2015.10.0099
      The Plant Genome 2016 9:
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    • Dario Fè, Bilal H. Ashraf, Morten G. Pedersen, Luc Janss, Stephen Byrne, Niels Roulund, Ingo Lenk, Thomas Didion, Torben Asp, Christian S. Jensen and Just Jensen
      Accuracy of Genomic Prediction in a Commercial Perennial Ryegrass Breeding Program
      Core Ideas
      • High accuracies for genomic prediction in a perennial ryegrass breeding program
      • The additive genetic variance can be traced by genotyping assays
      • Predictions work across different generations and in different traits
      • Good prospects for the implementation of genomic selection in perennial ryegrass
      doi:10.3835/plantgenome2015.11.0110
      The Plant Genome 2016 9:
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    • Brenda A. Peterson, Sarah H. Holt, F. Parker E. Laimbeer, Andreas G. Doulis, Joseph Coombs, David S. Douches, Michael A. Hardigan, C. Robin Buell and Richard E. Veilleux
      Self-Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single-Nucleotide Polymorphism Array
      Core Ideas
      • Self-fertility in diploid potato is independent of self-compatibility
      • SNP genotyping may be confounded by copy number variation
      • Genomic regions of a highly heterozygous species resist homozygosity during inbreeding
      doi:10.3835/plantgenome2016.01.0003
      The Plant Genome 2016 9:
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    • Meriem Aoun, Matthew Breiland, M. Kathryn Turner, Alexander Loladze, Shiaoman Chao, Steven S. Xu, Karim Ammar, James A. Anderson, James A. Kolmer and Maricelis Acevedo
      Genome-Wide Association Mapping of Leaf Rust Response in a Durum Wheat Worldwide Germplasm Collection
      Core Ideas
      • Thirteen durum wheat accessions showed resistance to all Puccinia triticina races tested
      • GWAS revealed 88 SNPs (37 loci) associated with leaf rust response in durum wheat
      • Associations were identified on all chromosomes except 1B and 7B
      • GWAS revealed 14 previously uncharacterized loci for leaf rust resistance
      doi:10.3835/plantgenome2016.01.0008
      The Plant Genome 2016 9:
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    • Rodrigo R. Amadeu, Catherine Cellon, James W. Olmstead, Antonio A. F. Garcia, Marcio F. R. Resende Jr. and Patricio R. Muñoz
      AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example
      Core Ideas
      • We developed an R package for autopolyploids to construct the relationship matrix.
      • We estimated the level and effect of double reduction in blueberry.
      • The package is unique as it can create A-matrices for different levels of ploidy.
      • The package can create A-matrices for different levels of double reduction
      doi:10.3835/plantgenome2016.01.0009
      The Plant Genome 2016 9:
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    • Samira Mafi Moghaddam, Sujan Mamidi, Juan M. Osorno, Rian Lee, Mark Brick, James Kelly, Phillip Miklas, Carlos Urrea, Qijian Song, Perry Cregan, Jane Grimwood, Jeremy Schmutz and Phillip E. McClean
      Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean
      doi:10.3835/plantgenome2016.02.0012
      The Plant Genome 2016 9:
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    • Anne-Michelle Faux, Gregor Gorjanc, R. Chris Gaynor, Mara Battagin, Stefan M. Edwards, David L. Wilson, Sarah J. Hearne, Serap Gonen and John M. Hickey
      AlphaSim: Software for Breeding Program Simulation
      Core Ideas
      • AlphaSim allows breeders and researchers to simulate genomic data with specific user criteria.
      • AlphaSim is flexible, computationally efficient, and easy to use for a wide range of possible scenarios.
      • AlphaSim can also be used in animal breeding, human genetics, and population genetics.
      doi:10.3835/plantgenome2016.02.0013
      The Plant Genome 2016 9:
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    • Štěpán Stočes, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldán-Ruiz, Tomasz Książczyk, Elodie Rey, Jaroslav Doležel and David Kopecký
      Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery
      Core Ideas
      • Transcriptomes of F. pratensis and L. multiflorum were sequenced and assembled
      • We present a catalogue of SNPs for ancestry analysis and future breeding of grasses
      • We defined interspecific SNPs to study parental-genome specific gene expression in hybrids
      • We positioned SNPs on linkage groups for high-resolution genome constitution analysis
      doi:10.3835/plantgenome2016.02.0017
      The Plant Genome 2016 9:
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    • Anthony T. Slater, Noel O.I. Cogan, John W. Forster, Benjamin J. Hayes and Hans D. Daetwyler
      Improving Genetic Gain with Genomic Selection in Autotetraploid Potato
      Core Ideas
      • Progress in conventional potato breeding can be complex and slow.
      • Genomic selection can be applied to autotetraploid potato.
      • A number of factors that will affect genomic selection need to be considered.
      • Genomic selection will accelerate genetic gain in potato.
      doi:10.3835/plantgenome2016.02.0021
      The Plant Genome 2016 9:
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    • Jaime Cuevas, José Crossa, Víctor Soberanis, Sergio Pérez-Elizalde, Paulino Pérez-Rodríguez, Gustavo de los Campos, O. A. Montesinos-López and Juan Burgueño
      Genomic Prediction of Genotype × Environment Interaction Kernel Regression Models
      doi:10.3835/plantgenome2016.03.0024
      The Plant Genome 2016 9:
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    • Li Song, Dhruv S. Shankar and Liliana Florea
      Rascaf: Improving Genome Assembly with RNA Sequencing Data
      Core Ideas
      • Rascaf simultaneously improves an assembly and its gene annotations
      • Rascaf finds thousands of new contig connections in draft Fragaria genomes
      • Rascaf is a highly accurate, efficient, and practical tool for plant genome sequencing projects
      doi:10.3835/plantgenome2016.03.0027
      The Plant Genome 2016 9:
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    • Jinping Cheng, Yongqi He, Chengfang Zhan, Bin Yang, Enshun Xu, Hongsheng Zhang and Zhoufei Wang
      Identification and Characterization of Quantitative Trait Loci for Shattering in Japonica Rice Landrace Jiucaiqing from Taihu Lake Valley, China
      doi:10.3835/plantgenome2016.03.0034
      The Plant Genome 2016 9:
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    • Zahirul I. Talukder, Gerald J. Seiler, Qijian Song, Guojia Ma and Lili Qi
      SNP Discovery and QTL Mapping of Sclerotinia Basal Stalk Rot Resistance in Sunflower using Genotyping-by-Sequencing
      doi:10.3835/plantgenome2016.03.0035
      The Plant Genome 2016 9:
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    • Jeffrey D. Wolt, Kan Wang, Dipali Sashital and Carolyn J. Lawrence-Dill
      Achieving Plant CRISPR Targeting that Limits Off-Target Effects
      Core Ideas
      • Plant CRISPR-Cas9 genome editing may generate unintended off-target mutation.
      • Potential for off-target mutation is an important regulatory question for genome-edited plants.
      • Validated design approaches to discriminate target and potential off-target edits are needed.
      doi:10.3835/plantgenome2016.05.0047
      The Plant Genome 2016 9:
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    • Genqiao Li, Xiangyang Xu, Guihua Bai, Brett F. Carver, Robert Hunger, J. Michael Bonman, James Kolmer and Hongxu Dong
      Genome-Wide Association Mapping Reveals Novel QTL for Seedling Leaf Rust Resistance in a Worldwide Collection of Winter Wheat
      Core Ideas
      • The association panel used in this study may represent the largest in wheat GWAS
      • Three pathotypes, including a bulked races collected in the field, were used
      • A total of 14 QTL for leaf rust resistance were identified at a FDR of 0.01.
      • Six QTL identified in this study are novel loci in bread wheat
      • Thirty-one additional QTL were significant at a FDR of 0.05.
      doi:10.3835/plantgenome2016.06.0051
      The Plant Genome 2016 9:
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    • Kenta Shirasawa, Chikara Kuwata, Manabu Watanabe, Masanobu Fukami, Hideki Hirakawa and Sachiko Isobe
      Target Amplicon Sequencing for Genotyping Genome-Wide Single Nucleotide Polymorphisms Identified by Whole-Genome Resequencing in Peanut
      doi:10.3835/plantgenome2016.06.0052
      The Plant Genome 2016 9:
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  • ERRATA up


    • Fast-Track Introgression of “ QTL-hotspot ” for Root Traits and Other Drought Tolerance Traits in JG 11, an Elite and Leading Variety of Chickpea
      doi:10.3835/plantgenome2013.07.0022er
      The Plant Genome 2016 9:
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    • The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly
      doi:10.3835/plantgenome2015.07.0062er
      The Plant Genome 2016 9:
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