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Volume 9 Issue 2, July 2016



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  • RESEARCH HIGHLIGHTS up

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    • Victoria C. Blake, Clay Birkett, David E. Matthews, David L. Hane, Peter Bradbury and Jean-Luc Jannink
      The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding
      doi:10.3835/plantgenome2014.12.0099
      The Plant Genome 2016 9:
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    • Ying-hui Li, Xue-hui Shi, Hui-hui Li, Jochen C. Reif, Jia-jun Wang, Zhang-xiong Liu, Sang He, Bai-shuang Yu and Li-juan Qiu
      Dissecting the Genetic Basis of Resistance to Soybean Cyst Nematode Combining Linkage and Association Mapping
      Core Ideas
      • SCN3-11 (closest paralog of rhg1-b) explained 5.8% phenotypic variance for SCN resistance
      • The combination of rhg1-b and SCN3-11 provides a high level of SCN resistance
      • Joint LM-AM approach can aid in revealing the genetic basis of a complex trait
      doi:10.3835/plantgenome2015.04.0020
      The Plant Genome 2016 9:
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    • Jing Zhao, Maria B. Mantilla Perez, Jieyun Hu and Maria G. Salas Fernandez
      Genome-Wide Association Study for Nine Plant Architecture Traits in Sorghum
      doi:10.3835/plantgenome2015.06.0044
      The Plant Genome 2016 9:
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    • Manohar Chakrabarti, Randy D. Dinkins and Arthur G. Hunt
      De novo Transcriptome Assembly and Dynamic Spatial Gene Expression Analysis in Red Clover
      Core Ideas
      • De novo transcriptome assembly of red clover (Trifolium pratense L.)
      • Functional annotation of the assembled transcriptome
      • Global identification of red clover transcripts encoding putative transcription factors
      • Identification of tissue-enriched gene coexpression clusters
      doi:10.3835/plantgenome2015.06.0048
      The Plant Genome 2016 9:
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    • Anil Kumar, Divya Sharma, Apoorv Tiwari, J.P. Jaiswal, N.K. Singh and Salej Sood
      Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins
      Core Ideas
      • GBS analysis generated 33 GB of data with 160 million raw reads.
      • Population structure analysis revealed three subpopulations among the finger millet accessions.
      • A total of 1128 GO terms were assigned to SNP carrying genes.
      • GBS analysis would be useful for future marker-assisted breeding applications.
      doi:10.3835/plantgenome2015.07.0058
      The Plant Genome 2016 9:
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    • Keith Rincker, Alexander E. Lipka and Brian W. Diers
      Genome-Wide Association Study of Brown Stem Rot Resistance in Soybean across Multiple Populations
      Core Ideas
      • GWAS narrowed chromosome 16 interval containing a BSR resistance QTL to 0.3 Mb
      • SNPs identified provide new targets for marker-assisted selection of BSR resistance
      • GWAS of public BSR resistance data failed to identify three separate resistance genes
      doi:10.3835/plantgenome2015.08.0064
      The Plant Genome 2016 9:
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    • Lise L. Mahoney, Daniel J. Sargent, F. Abebe-Akele, Dave J. Wood, Judson A. Ward, Nahla V. Bassil, James F. Hancock, Kevin M. Folta and Thomas M. Davis
      A High-Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae , Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing
      doi:10.3835/plantgenome2015.08.0071
      The Plant Genome 2016 9:
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    • Matthew Herritt, Arun Prabhu Dhanapal and Felix B. Fritschi
      Identification of Genomic Loci Associated with the Photochemical Reflectance Index by Genome-Wide Association Study in Soybean
      doi:10.3835/plantgenome2015.08.0072
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    • Umesh R. Rosyara, Walter S. De Jong, David S. Douches and Jeffrey B. Endelman
      Software for Genome-Wide Association Studies in Autopolyploids and Its Application to Potato
      doi:10.3835/plantgenome2015.08.0073
      The Plant Genome 2016 9:
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    • Ludmila Tyler, Scott J. Lee, Nelson D. Young, Gregory A. DeIulio, Elena Benavente, Michael Reagon, Jessica Sysopha, Riccardo M. Baldini, Angelo Troìa, Samuel P. Hazen and Ana L. Caicedo
      Population Structure in the Model Grass Brachypodium distachyon Is Highly Correlated with Flowering Differences across Broad Geographic Areas
      Core Ideas
      • Genotyping diverse Brachypodium accessions expands research tools for grasses.
      • The B. hybridum genome is a mosaic of B. distachyon- and B. stacei-like sequences.
      • Three distinct, genetically defined populations of B. distachyon were identified.
      • Flowering time, more than geography, distinguishes B. distachyon populations.
      • Results support the feasibility of genome-wide association studies in a model grass.
      doi:10.3835/plantgenome2015.08.0074
      The Plant Genome 2016 9:
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    • Maxime Gotté, Magalie Bénard, Marie-Christine Kiefer-Meyer, Rim Jaber, John P. Moore, Maïté Vicré-Gibouin and Azeddine Driouich
      Endoplasmic Reticulum Body–Related Gene Expression in Different Root Zones of Arabidopsis Isolated by Laser-Assisted Microdissection
      Core Ideas
      • ER body–related genes are specifically regulated in different root zones
      • Methyl jasmonate induces ER body formation in Arabidopsis root
      • Methyl jasmonate induces the overexpression of ER body–related genes in the root
      • Primary root zones can be easily microdissected without any chemical treatment
      doi:10.3835/plantgenome2015.08.0076
      The Plant Genome 2016 9:
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    • A. J. Ji, H. M. Luo, Z. C. Xu, X. Zhang, Y. J. Zhu, B. S. Liao, H. Yao, J. Y. Song and S. L. Chen
      Genome-Wide Identification of the AP2/ERF Gene Family Involved in Active Constituent Biosynthesis in Salvia miltiorrhiza
      doi:10.3835/plantgenome2015.08.0077
      The Plant Genome 2016 9:
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    • Yakup Bakir, Vahap Eldem, Gokmen Zararsiz and Turgay Unver
      Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves
      Core Ideas
      • Hyperhydricity is a morphophysiological disorder of plants in tissue culture
      • RNA-seq showed more than 300 transcripts notably responsive to hyperhydricity
      • Expression of Laccase 3 involved in lignin polymerization related to hyperhydricity
      doi:10.3835/plantgenome2015.09.0080
      The Plant Genome 2016 9:
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    • Ying Huang, Bao-Long Zhang, Sheng Sun, Guo-Ming Xing, Feng Wang, Meng-Yao Li, Yong-Sheng Tian and Ai-Sheng Xiong
      AP2/ERF Transcription Factors Involved in Response to Tomato Yellow Leaf Curly Virus in Tomato
      Core Ideas
      • SlAP2/ERF factors respond to the TYLCV infection.
      • GCC-box binding ability of SlERF factors was different in tomato cultivars.
      • SlERFs interact with other proteins in tomato.
      • The defense mechanism to TYLCV is a complicated network.
      doi:10.3835/plantgenome2015.09.0082
      The Plant Genome 2016 9:
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    • Junchao Liang, Bisheng Fu, Wenbin Tang, Nasr U. Khan, Na Li and Zhengqiang Ma
      Fine Mapping of Two Wheat Powdery Mildew Resistance Genes Located at the Pm1 Cluster
      Core Ideas
      • High-resolution maps were constructed for both Mlm2033 and Mlm80.
      • Mlm2033, Mlm80, and MlIW172 are different powdery mildew resistance genes in the Pm1 cluster.
      • New markers tightly linked to Mlm2033 were developed.
      doi:10.3835/plantgenome2015.09.0084
      The Plant Genome 2016 9:
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    • Florian Leplat, Just Jensen and Per Madsen
      Genomic Prediction of Manganese Efficiency in Winter Barley
      Core Ideas
      • The prediction accuracies of the G-BLUP model clearly outperformed the BLUP model
      • Greenhouse experiments are useful information for Mn efficiency
      • Prediction accuracies are more accurate than
      • Genomic prediction is a promising tool for plant breeding for nutrition traits
      doi:10.3835/plantgenome2015.09.0085
      The Plant Genome 2016 9:
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    • N. R. Redekar, E. M. Clevinger, M. A. Laskar, R. M. Biyashev, T. Ashfield, R. V. Jensen, S. C. Jeong, S. A. Tolin and M. A. Saghai Maroof
      Candidate Gene Sequence Analyses toward Identifying Rsv3 -Type Resistance to Soybean Mosaic Virus
      Core Ideas
      • Rsv3 locus confers strain-specific resistance to Soybean mosaic virus
      • The Rsv3 locus contains a cluster of five NB-LRR resistance genes
      • Comprehensive study of five Rsv3 candidate NB-LRR gene sequences was conducted
      • Comparisons were done between Rsv3-type resistant vs. rsv-type susceptible soybeans
      • Glyma14g38533 gene was identified as the most likely candidate gene for Rsv3
      doi:10.3835/plantgenome2015.09.0088
      The Plant Genome 2016 9:
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    • Santoshkumar M. Shetty, Maria Ulfa Md Shah, Kavyashree Makale, Yusmin Mohd-Yusuf, Norzulaani Khalid and Rofina Yasmin Othman
      Complete Chloroplast Genome Sequence of Musa balbisiana Corroborates Structural Heterogeneity of Inverted Repeats in Wild Progenitors of Cultivated Bananas and Plantains
      Core Ideas
      • First structural description of complete nucleotide sequence of M. balbisiana chloroplast genome
      • Evolutionarily conserved IRa-SSC expansion events in the genus Musa and Zingiberales species
      • Existence of infrageneric fluctuations in the IRb-SSC junction expansion among wild Musa species
      • M. balbisiana and M. textilis share close evolutionary relationship albeit variable IRb-SSC expansion
      • A significant addition to a growing body of Musa genomics resources
      doi:10.3835/plantgenome2015.09.0089
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    • Ling Zhou, Longhai Luo, Jian-Fang Zuo, Linfeng Yang, Li Zhang, Xuanmin Guang, Yuan Niu, Jianbo Jian, Qing-Chun Geng, Liping Liang, Qijian Song, Jim M. Dunwell, Zhenzhen Wu, Jia Wen, Yu-Qin Liu and Yuan-Ming Zhang
      Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean
      doi:10.3835/plantgenome2015.09.0090
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    • Richard E. Boyles, Elizabeth A. Cooper, Matthew T. Myers, Zachary Brenton, Bradley L. Rauh, Geoffrey P. Morris and Stephen Kresovich
      Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm
      Core Ideas
      • Association mapping elucidated the genetic basis of sorghum grain yield components.
      • GWAS results suggest yield component traits may be manipulated independently.
      • The yield component loci identified may be targeted for grain sorghum improvement.
      doi:10.3835/plantgenome2015.09.0091
      The Plant Genome 2016 9:
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    • Sujan Mamidi, Phillip N. Miklas, Jennifer Trapp, Erin Felicetti, Jane Grimwood, Jeremy Schmutz, Rian Lee and Phillip E. McClean
      Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean
      Core Ideas
      • Sequenced-based introgression mapping rapidly maps QTL to a physical location
      • A highly polymorphic candidate gene associated with apoptosis maps in the WM7.1 QTL
      • A highly polymorphic gene associated with effector recognition maps in the WM8.3 QTL
      doi:10.3835/plantgenome2015.09.0092
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    • Carlos P. Cantalapiedra, Bruno Contreras-Moreira, Cristina Silvar, Dragan Perovic, Frank Ordon, María Pilar Gracia, Ernesto Igartua and Ana M. Casas
      A Cluster of Nucleotide-Binding Site–Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL
      doi:10.3835/plantgenome2015.10.0101
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    • Ashley S. Chaffin, Yung-Fen Huang, Scott Smith, Wubishet A. Bekele, Ebrahiem Babiker, Belaghihalli N. Gnanesh, Bradley J. Foresman, Steven G. Blanchard, Jeremy J. Jay, Robert W. Reid, Charlene P. Wight, Shiaoman Chao, Rebekah Oliver, Emir Islamovic, Frederic L. Kolb, Curt McCartney, Jennifer W. Mitchell Fetch, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Tim Langdon, Catherine J. Howarth, Cory R. Brouwer, Eric N. Jellen, Kathy Esvelt Klos, Jesse A. Poland, Tzung-Fu Hsieh, Ryan Brown, Eric Jackson, Jessica A. Schlueter and Nicholas A. Tinker
      A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement
      Core Ideas
      • We constructed a hexaploid oat consensus map from 12 populations representing 19 parents.
      • The map represents the most common physical chromosome arrangements in oat.
      • Deviations from the consensus map may indicate physical rearrangements.
      • Large chromosomal translocations vary among different varieties.
      • There is regional synteny with rice but considerable subgenome rearrangement.
      doi:10.3835/plantgenome2015.10.0102
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    • Kathy Esvelt Klos, Yung-Fen Huang, Wubishet A. Bekele, Don E. Obert, Ebrahiem Babiker, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Martin L. Carson, Shiaoman Chao, Belaghihalli N. Gnanesh, Irene Griffiths, Stephen A. Harrison, Catherine J. Howarth, Gongshe Hu, Amir Ibrahim, Emir Islamovic, Eric W. Jackson, Jean-Luc Jannink, Frederic L. Kolb, Michael S. McMullen, Jennifer Mitchell Fetch, J. Paul Murphy, Herbert W. Ohm, Howard W. Rines, Brian G. Rossnagel, Jessica A. Schlueter, Mark E. Sorrells, Charlene P. Wight, Weikai Yan and Nicholas A. Tinker
      Population Genomics Related to Adaptation in Elite Oat Germplasm
      Core Ideas
      • An oat association-mapping panel contributed by active breeding programs worldwide.
      • Characterized population structure and found subdivisions related to adaptation
      • Characterized genome-wide and chromosome-specific linkage disequilibrium
      • Performed association-mapping and post hoc modeling of heading date
      • Found several consistently associated QTL
      doi:10.3835/plantgenome2015.10.0103
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    • Paolo Annicchiarico, Nelson Nazzicari, Acharya Ananta, Maria Carelli, Yanling Wei and E. Charles Brummer
      Assessment of Cultivar Distinctness in Alfalfa: A Comparison of Genotyping-by-Sequencing, Simple-Sequence Repeat Marker, and Morphophysiological Observations
      doi:10.3835/plantgenome2015.10.0105
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    • Somashekhar M. Punnuri, Jason G. Wallace, Joseph E. Knoll, Katie E. Hyma, Sharon E. Mitchell, Edward S. Buckler, Rajeev K. Varshney and Bharat P. Singh
      Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers
      Core Ideas
      • Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is an important forage and grain crop in many parts of the world but genomic resources for this species are needed to facilitate crop improvement.
      • The reference genetic map developed using 150 recombinant inbred lines contained 16,650 single-nucleotide polymorphisms and 333,567 sequence tags spread across all seven chromosomes.
      • This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community.
      • Genome mapping studies are a prerequisite for tagging agronomically important traits.
      • Genotyping-by-sequencing markers can be used to build high-density linkage maps, even in species lacking a reference genome.
      doi:10.3835/plantgenome2015.10.0106
      The Plant Genome 2016 9:
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    • Bushra Saeed, Vinay K. Baranwal and Paramjit Khurana
      Identification and Expression Profiling of the Lectin Gene Superfamily in Mulberry
      Core Ideas
      • Identification of lectin catalogues in Morus notabilis genome
      • Genome-wide expression profiling of lectins
      • Role of lectins in stress responses in mulberry
      doi:10.3835/plantgenome2015.10.0107
      The Plant Genome 2016 9:
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    • Lijun Meng, Longbiao Guo, Kimberly Ponce, Xiangqian Zhao and Guoyou Ye
      Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification
      Core Ideas
      • Three rice MAGIC populations were developed to better integrate QTL identification and breeding.
      • MAGIC populations are valuable for QTL identification, 8-way populations being more powerful.
      • QTL (2 and 3) were identified for heading date and plant height, respectively.
      • One novel QTL for PH was identified on chromosome 12 using the 8-way population.
      doi:10.3835/plantgenome2015.10.0109
      The Plant Genome 2016 9:
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    • Zoë Migicovsky, Kyle M. Gardner, Daniel Money, Jason Sawler, Joshua S. Bloom, Peter Moffett, C. Thomas Chao, Heidi Schwaninger, Gennaro Fazio, Gan-Yuan Zhong and Sean Myles
      Genome to Phenome Mapping in Apple Using Historical Data
      doi:10.3835/plantgenome2015.11.0113
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    • Xufeng Bai, Hu Zhao, Yong Huang, Weibo Xie, Zhongmin Han, Bo Zhang, Zilong Guo, Lin Yang, Haijiao Dong, Weiya Xue, Guangwei Li, Gang Hu, Yong Hu and Yongzhong Xing
      Genome-Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between Indica and Japonica Rice
      Core Ideas
      • Thirty loci for panicle size were identified by genome-wide association analysis.
      • Ghd7 and DST were specifically associated with panicle length in indica and japonica rice.
      • Different gene networks regulate panicle architecture in indica and japonica rice.
      doi:10.3835/plantgenome2015.11.0115
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    • Marnin D. Wolfe, Ismail Y. Rabbi, Chiedozie Egesi, Martha Hamblin, Robert Kawuki, Peter Kulakow, Roberto Lozano, Dunia Pino Del Carpio, Punna Ramu and Jean-Luc Jannink
      Genome-Wide Association and Prediction Reveals Genetic Architecture of Cassava Mosaic Disease Resistance and Prospects for Rapid Genetic Improvement
      Core Ideas
      • Cassava mosaic disease resistance has a narrow genetic basis in breeding germplasm.
      • Evidence suggests two possibly epistatic loci and/or multiple resistance alleles exist at the major QTL.
      • Genomic prediction is accurate both for selecting parents and identifying highly CMD-resistant clones as varieties.
      doi:10.3835/plantgenome2015.11.0118
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    • You Tang, Xiaolei Liu, Jiabo Wang, Meng Li, Qishan Wang, Feng Tian, Zhongbin Su, Yuchun Pan, Di Liu, Alexander E. Lipka, Edward S. Buckler and Zhiwu Zhang
      GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction
      Core Ideas
      • Genome-wide association study
      • Genomic prediction
      • Simulation and experimental design
      doi:10.3835/plantgenome2015.11.0120
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    • Sarah D. Battenfield, Carlos Guzmán, R. Chris Gaynor, Ravi P. Singh, Roberto J. Peña, Susanne Dreisigacker, Allan K. Fritz and Jesse A. Poland
      Genomic Selection for Processing and End-Use Quality Traits in the CIMMYT Spring Bread Wheat Breeding Program
      Core Ideas
      • Genomic selection applied for wheat quality in CIMMYT spring bread wheat breeding program.
      • All wheat quality traits predicted and validated using forward genomic selection.
      • Dough and loaf traits have moderately high predictive ability in CIMMYT breeding program.
      • Genomic selection genetic gain 1.4 to 2.7 times higher than phenotypic selection.
      doi:10.3835/plantgenome2016.01.0005
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    • Dan Chang, Yanqi Wu, Linglong Liu, Shuiyi Lu-Thames, Hongxu Dong, Carla Goad, Shiqie Bai, Shiva Makaju and Tilin Fang
      Quantitative Trait Loci Mapping for Tillering-Related Traits in Two Switchgrass Populations
      Core Ideas
      • Phenotypic data for six tillering traits related to biomass yield in two populations were assessed in two field trials.
      • Associations between phenotypic data and two preexisting linkage maps were analyzed.
      • Twenty QTL were identified in a hybrid population.
      • Twenty-six QTL were identified in a selfed population.
      • Two significant QTL were stably expressed in multiple environments in the two populations.
      doi:10.3835/plantgenome2016.01.0010
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    • Norman Philipp, Guozheng Liu, Yusheng Zhao, Sang He, Monika Spiller, Gunther Stiewe, Klaus Pillen, Jochen C. Reif and Zuo Li
      Genomic Prediction of Barley Hybrid Performance
      doi:10.3835/plantgenome2016.02.0016
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    • Rex Bernardo and Addie M. Thompson
      Germplasm Architecture Revealed through Chromosomal Effects for Quantitative Traits in Maize
      Core Ideas
      • Germplasm architecture reveals the distribution of favorable alleles in germplasm.
      • Germplasm architecture for quantitative traits in maize is unknown.
      • Lines with chromosomes deficient in favorable alleles are targets for improvement.
      doi:10.3835/plantgenome2016.03.0028
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