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Volume 10 Issue 2, July 2017



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    • Jose R. Lopez, John E. Erickson, Patricio Munoz, Ana Saballos, Terry J. Felderhoff and Wilfred Vermerris
      QTLs Associated with Crown Root Angle, Stomatal Conductance, and Maturity in Sorghum
      Core Ideas
      • QTLs for crown root angle, stomatal conductance, and maturity were identified in two field studies through the construction of a high-density bin map.
      • The QTL for stomatal conductance was associated with reduced leaf transpiration but not reduced net assimilation rate.
      • Candidate genes are proposed based on the physical location of the QTLs and the function of known genes in those locations.
      doi:10.3835/plantgenome2016.04.0038
      The Plant Genome 2017 10:
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    • Nonoy B. Bandillo, Aaron J. Lorenz, George L. Graef, Diego Jarquin, David L. Hyten, Randall L Nelson and James E. Specht
      Genome-wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection
      Core Ideas
      • Genome-wide association (GWA) is usually aimed at quantitative (but not so much at qualitative) traits.
      • Germplasm collections have extensive data on qualitatively inherited descriptor traits.
      • Positional location of classical genes is lacking in most crop genome sequence maps.
      • Genome-wide association easily generates high-resolution genome sequence map positions for classical loci.
      • Genome-wide association-based gene positions are attainable even for traits governed by digenic epistasis.
      doi:10.3835/plantgenome2016.06.0054
      The Plant Genome 2017 10:
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    • Malachy T. Campbell, Qian Du, Kan Liu, Chris J. Brien, Bettina Berger, Chi Zhang and Harkamal Walia
      A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice ( Oryza sativa )
      Core Ideas
      • Functional mapping uncovers the genetic architecture of shoot growth dynamics.
      • Gibberellic acid is an underlying component for natural variation for shoot growth dynamics in rice.
      • Genomic prediction is effective for improving early growth dynamics.
      doi:10.3835/plantgenome2016.07.0064
      The Plant Genome 2017 10:
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    • Shiaoman Chao, Matthew N. Rouse, Maricelis Acevedo, Agnes Szabo-Hever, Harold Bockelman, J. Michael Bonman, Elias Elias, Daryl Klindworth and Steven Xu
      Evaluation of Genetic Diversity and Host Resistance to Stem Rust in USDA NSGC Durum Wheat Accessions
      Core Ideas
      • Characterized the utility of a core subset of USDA–NSGC worldwide durum wheat accessions
      • The durum core subset captured a considerable amount of genetic diversity
      • Identified accessions’ resistance to wheat stem rust pathogen races
      • Assessed genome-wide LD present in the durum core subset
      doi:10.3835/plantgenome2016.07.0071
      The Plant Genome 2017 10:
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    • Paolo Annicchiarico, Nelson Nazzicari, Luciano Pecetti, Massimo Romani, Barbara Ferrari, Yanling Wei and E. Charles Brummer
      GBS-Based Genomic Selection for Pea Grain Yield under Severe Terminal Drought
      Core Ideas
      • GBS-based genomic predictions of pea grain yield and phenology are accurate and cost-efficient.
      • Genomic areas related to high yield and early flowering colocate under severe terminal drought.
      • Cross-population genomic predictions have quite variable predictive ability.
      doi:10.3835/plantgenome2016.07.0072
      The Plant Genome 2017 10:
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    • Philomin Juliana, Ravi P. Singh, Pawan K. Singh, Jose Crossa, Jessica E. Rutkoski, Jesse A. Poland, Gary C. Bergstrom and Mark E. Sorrells
      Comparison of Models and Whole-Genome Profiling Approaches for Genomic-Enabled Prediction of Septoria Tritici Blotch, Stagonospora Nodorum Blotch, and Tan Spot Resistance in Wheat
      doi:10.3835/plantgenome2016.08.0082
      The Plant Genome 2017 10:
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    • Paulino Pérez-Rodríguez, José Crossa, Jessica Rutkoski, Jesse Poland, Ravi Singh, Andrés Legarra, Enrique Autrique, Gustavo de los Campos, Juan Burgueño and Susanne Dreisigacker
      Single-Step Genomic and Pedigree Genotype × Environment Interaction Models for Predicting Wheat Lines in International Environments
      Core Ideas
      • Genomic prediction accuracy models have been commonly used in plant breeding but only in reduced datasets comprising a few hundred genotyped individual plants.
      • In this study we used pedigree and genomic data from 58,798 wheat lines evaluated in different environments.
      • We use pedigree and genomic information in a model that incorporates genotype × environment interactions to predict wheat line performance in environments in South Asia.
      doi:10.3835/plantgenome2016.09.0089
      The Plant Genome 2017 10:
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    • Surbhi Grewal, Laura-Jayne Gardiner, Barbora Ndreca, Emilie Knight, Graham Moore, Ian P. King and Julie King
      Comparative Mapping and Targeted-Capture Sequencing of the Gametocidal Loci in Aegilops sharonensis
      doi:10.3835/plantgenome2016.09.0090
      The Plant Genome 2017 10:
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    • Junping Chen, Ratan Chopra, Chad Hayes, Geoffrey Morris, Sandeep Marla, John Burke, Zhanguo Xin and Gloria Burow
      Genome-Wide Association Study of Developing Leaves’ Heat Tolerance during Vegetative Growth Stages in a Sorghum Association Panel
      Core Ideas
      • Sorghum could serve as a vital resource of heat tolerance DNA markers.
      • Natural variation of leaf traits provides understanding of heat tolerance in sorghum.
      • GWAS reveals 14 SNPs with two heat stress responsive traits in sorghum leaves.
      doi:10.3835/plantgenome2016.09.0091
      The Plant Genome 2017 10:
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    • Shiliang Cao, Alexander Loladze, Yibing Yuan, Yongsheng Wu, Ao Zhang, Jiafa Chen, Gordon Huestis, Jingsheng Cao, Vijay Chaikam, Michael Olsen, Boddupalli M. Prasanna, Felix San Vicente and Xuecai Zhang
      Genome-Wide Analysis of Tar Spot Complex Resistance in Maize Using Genotyping-by-Sequencing SNPs and Whole-Genome Prediction
      Core Ideas
      • Association and linkage mapping are effective for dissecting genetic architecture of complex traits in maize.
      • TSC resistance in maize is controlled by a major QTL and several minor QTL.
      • Major QTL on bin 8.03 confirmed by association and linkage mapping.
      • TSC resistance in tropical maize could be improved by MAS and GS individually or stepwise.
      doi:10.3835/plantgenome2016.10.0099
      The Plant Genome 2017 10:
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    • Yaopeng Zhou, Benjamin Conway, Daniela Miller, David Marshall, Aaron Cooper, Paul Murphy, Shiaoman Chao, Gina Brown-Guedira and José Costa
      Quantitative Trait Loci Mapping for Spike Characteristics in Hexaploid Wheat
      Core Ideas
      • A high-density wheat genetic map was generated using GBS and the 9K iSelect Array.
      • Spike characteristics were mainly determined by additive effects.
      • Major QTL of spike characteristics were identified on chromosomes 1A, 2B, and 5A.
      doi:10.3835/plantgenome2016.10.0101
      The Plant Genome 2017 10:
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    • Kathy Esvelt Klos, Belayneh A. Yimer, Ebrahiem M. Babiker, Aaron D. Beattie, J. Michael Bonman, Martin L. Carson, James Chong, Stephen A. Harrison, Amir M.H. Ibrahim, Frederic L. Kolb, Curt A. McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J. Paul Murphy and Nicholas A. Tinker
      Genome-Wide Association Mapping of Crown Rust Resistance in Oat Elite Germplasm
      Core Ideas
      • Multienvironment genome-wide association study of reaction to crown rust in elite oat
      • Oat response to inoculation with 10 well-characterized Puccinia coronata isolates evaluated
      • Adult plant response to crown rust assessed in 10 location–years
      • Patterns of association compared against genotypes of differential gene stocks
      • QTL placed in the context of current literature
      doi:10.3835/plantgenome2016.10.0107
      The Plant Genome 2017 10:
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    • Qijian Song, Long Yan, Charles Quigley, Brandon D. Jordan, Edward Fickus, Steve Schroeder, Bao-Hua Song, Yong-Qiang Charles An, David Hyten, Randall Nelson, Katy Rainey, William D Beavis, Jim Specht, Brian Diers and Perry Cregan
      Genetic Characterization of the Soybean Nested Association Mapping Population
      Core Ideas
      • 40 NAM families were developed and 5600 RILs in the families were characterized.
      • The linkage maps for each family and a composite linkage map were constructed.
      • More than a half million high-confidence SNPs were identified and annotated.
      • Segregation distortion in most families favored alleles from the female parent.
      • The REs in the soybean genome is low.
      doi:10.3835/plantgenome2016.10.0109
      The Plant Genome 2017 10:
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    • Jin Sun, Jessica E. Rutkoski, Jesse A. Poland, José Crossa, Jean-Luc Jannink and Mark E. Sorrells
      Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield
      Core Ideas
      • HTP platforms used to measure secondary traits across time
      • Longitudinal data of secondary traits evaluated by SR, MT, and RR models, separately
      • BLUPs of secondary traits used in the multivariate pedigree and genomic prediction
      • Grain yield predictive ability was improved by 70%
      doi:10.3835/plantgenome2016.11.0111
      The Plant Genome 2017 10:
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    • Stefano Pavan, Concetta Lotti, Angelo R. Marcotrigiano, Rosa Mazzeo, Nicoletta Bardaro, Valentina Bracuto, Francesca Ricciardi, Francesca Taranto, Nunzio D’Agostino, Adalgisa Schiavulli, Claudio De Giovanni, Cinzia Montemurro, Gabriella Sonnante and Luigi Ricciardi
      A Distinct Genetic Cluster in Cultivated Chickpea as Revealed by Genome-wide Marker Discovery and Genotyping
      Core Ideas
      • Genotyping-by-sequencing analysis in cultivated chickpea generated 3187 high-quality single nucleotide polymorphisms.
      • Analysis of genetic diversity supports the identification of three subpopulations.
      • Accessions traditionally grown in Italy form a clearly distinct genetic cluster.
      • We identified genomic regions putatively resulting from directional selection.
      • Our findings are of interest for chickpea conservation genetics and breeding.
      doi:10.3835/plantgenome2016.11.0115
      The Plant Genome 2017 10:
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    • Rex Bernardo
      Prospective Targeted Recombination and Genetic Gains for Quantitative Traits in Maize
      doi:10.3835/plantgenome2016.11.0118
      The Plant Genome 2017 10:
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    • Cai-yun Zhu, Wei Liu, Li-Fang Kang, Qin Xu, Shi-Lai Xing, Yang-Yang Fan, Zhi-Hong Song, Juan Yan, Jian-Qiang Li and Tao Sang
      Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments
      Core Ideas
      • A new method based on allele frequency to detect selection is proposed.
      • Haplotypes were inferred from transcriptomes of 80 individuals.
      • In total, 401 and 52 genes were targets of positive and negative selection respectively.
      • Abiotic-related and photosynthesis-related genes were enriched in targeted genes.
      doi:10.3835/plantgenome2016.11.0119
      The Plant Genome 2017 10:
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    • Vidyasagar Sathuvalli, Shawn A. Mehlenbacher and David C. Smith
      High-Resolution Genetic and Physical Mapping of the Eastern Filbert Blight Resistance Region in ‘Jefferson’ Hazelnut ( Corylus avellana L.)
      Core Ideas
      • Resistance to EFB from ‘Gasaway’ hazelnut is controlled by a single dominant locus.
      • Map-based cloning is a feasible approach for gene identification in tree crops.
      • Chromosome walking results in high-resolution genetic and physical mapping.
      doi:10.3835/plantgenome2016.12.0123
      The Plant Genome 2017 10:
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    • Bettina Lado, Sarah Battenfield, Carlos Guzmán, Martín Quincke, Ravi P. Singh, Susanne Dreisigacker, R. Javier Peña, Allan Fritz, Paula Silva, Jesse Poland and Lucía Gutiérrez
      Strategies for Selecting Crosses Using Genomic Prediction in Two Wheat Breeding Programs
      Core Ideas
      • Cross prediction strategies for grain yield and baking quality traits were compared.
      • Crosses for all parent combinations were obtained via genomic prediction models.
      • Mid-parent selection was similar to accounting for variance when selecting yield.
      • The variance had a larger impact in cross predictions for quality traits.
      doi:10.3835/plantgenome2016.12.0128
      The Plant Genome 2017 10:
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    • Diego Jarquín, Cristiano Lemes da Silva, R. Chris Gaynor, Jesse Poland, Allan Fritz, Reka Howard, Sarah Battenfield and Jose Crossa
      Increasing Genomic-Enabled Prediction Accuracy by Modeling Genotype × Environment Interactions in Kansas Wheat
      Core Ideas
      • Incorporating environmental covariates increases genomic selection accuracy.
      • G × E models can impute known lines into known environments with good accuracy.
      • Breeding programs may exploit genomic selection cross-validation schemes in trial designs.
      doi:10.3835/plantgenome2016.12.0130
      The Plant Genome 2017 10:
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    • Paul D. Mihalyov, Virginia A. Nichols, Peter Bulli, Matthew N. Rouse and Michael O. Pumphrey
      Multi-Locus Mixed Model Analysis Of Stem Rust Resistance In Winter Wheat
      Core Ideas
      • Multi-locus association mapping outperforms single-locus genome scans in polyploid species.
      • Single nucleotide polymorphism marker IWA435 reliably detects the 1BL.1RS rye translocation in diverse germplasm.
      • Markers linked to three novel stem rust resistance loci were identified.
      doi:10.3835/plantgenome2017.01.0001
      The Plant Genome 2017 10:
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    • Hamid Khazaei, Rajib Podder, Carolyn T. Caron, Shudhangshu S. Kundu, Marwan Diapari, Albert Vandenberg and Kirstin E. Bett
      Marker–Trait Association Analysis of Iron and Zinc Concentration in Lentil ( Lens culinaris Medik.) Seeds
      Core Ideas
      • First study to provide knowledge on genetics of biofortification in lentils.
      • SNP markers associated with seed Fe and Zn concentration were identified in lentils.
      • MAS to enhance breeding programs aiming to fight global micronutrient malnutrition.
      doi:10.3835/plantgenome2017.02.0007
      The Plant Genome 2017 10:
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    • A. J. Oiestad, J. M. Martin, J. Cook, A. C. Varella and M. J. Giroux
      Identification of Candidate Genes Responsible for Stem Pith Production Using Expression Analysis in Solid-Stemmed Wheat
      Core Ideas
      • Wheat stem solidness is associated with gene expression changes
      • A wheat stem solidness candidate gene is involved in lignin biosynthesis
      • Candidate genes can be identified via linked markers relatively easily.
      doi:10.3835/plantgenome2017.02.0008
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    • Lore Eggermont, Bruno Verstraeten and Els J.M. Van Damme
      Genome-Wide Screening for Lectin Motifs in Arabidopsis thaliana
      Core Ideas
      • More than 200 lectin genes were identified in Arabidopsis thaliana.
      • The biological role(s) of proteins containing lectin motifs was discussed.
      • Evolutionary relationships of several lectin motifs were investigated.
      doi:10.3835/plantgenome2017.02.0010
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    • Kateřina Holušová, Jan Vrána, Jan Šafář, Hana Šimková, Barbora Balcárková, Zeev Frenkel, Benoit Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel and Jan Bartoš
      Physical Map of the Short Arm of Bread Wheat Chromosome 3D
      Core Ideas
      • We developed and ordered the physical map of bread wheat chromosome arm 3DS.
      • Comparisons with related genomes provided information about gene movement.
      • The physical map is rich in anchored sequences and is ready for marker development.
      doi:10.3835/plantgenome2017.03.0021
      The Plant Genome 2017 10:
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