cran: rrBLUP | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giz028

Rice Galaxy: an open resource for plant science
Cited by: 13
Author(s): Venice Margarette Juanillas, Alexis Dereeper, Nicolas Beaume, Gaëtan Droc, Joshua Gregor A. Dizon, J. Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay R. Triplett, Jillian M. Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael J. Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar, Ramil Mauleon
Software Mentions: 18
Published: over 5 years ago

10.1534/g3.119.400728

Efficient Estimation of Marker Effects in Plant Breeding
Cited by: 10
Author(s): Alencar Xavier
Software Mentions: 13
Published: about 5 years ago

10.1038/s42003-021-02463-w

Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment
Cited by: 18
Author(s): Kauê de Sousa, Jacob van Etten, Jesse Poland, Carlo Fadda, Jean‐Luc Jannink, Yosef Gebrehawaryat Kidane, Basazen Fantahun, Deȷene K. Mengistu, Mario Enrico Pè, Svein Øivind Solberg, Matteo Dell’Acqua
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0156744

Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer
Cited by: 408
Author(s): Giovanny Covarrubias‐Pazaran
Software Mentions: 9
Published: over 8 years ago

10.1186/s13059-019-1697-0

WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants
Cited by: 10
Author(s): Laurent Gentzbittel, Cécile Ben, Mélanie Mazurier, Min-Gyoung Shin, Todd C. Lorenz, Martina Rickauer, Paul Marjoram, Sergey V. Nuzhdin, Tatiana V. Tatarinova
Software Mentions: 9
Published: over 5 years ago

10.1534/g3.120.401193

MoBPS - Modular Breeding Program Simulator
Cited by: 33
Author(s): Torsten Pook, Martin Schlather, Henner Simianer
Software Mentions: 9
Published: over 4 years ago

10.1007/s00122-021-03882-3

Genomic signatures of selection for resistance to stripe rust in Austrian winter wheat
Cited by: 2
Author(s): Laura Morales, Sebastian Michel, Christian Ametz, Hermann Gregor Dallinger, Franziska Löschenberger, Anton Neumayer, Simone Zimmerl, Hermann Buerstmayr
Software Mentions: 8
Published: over 3 years ago

10.1534/g3.119.400373

isqg: A Binary Framework forin SilicoQuantitative Genetics
Cited by: 1
Author(s): Fernando H. Toledo, Paulino Pérez‐Rodríguez, J. Crossa, Juan Burgueño
Software Mentions: 8
Published: over 5 years ago

10.1007/s00122-017-3030-1

Predictive ability of genomic selection models in a multi-population perennial ryegrass training set using genotyping-by-sequencing
Cited by: 49
Author(s): Marty J. Faville, Siva Ganesh, Mingshu Cao, M. Z. Z. Jahufer, Timothy P. Bilton, H. S. Easton, Douglas L. Ryan, Jason A. K. Trethewey, M. P. Rolston, Andrew G. Griffiths, Roger Moraga, Casey Flay, Joana Schmidt, Rachel Tan, Brent Barrett
Software Mentions: 8
Published: almost 7 years ago

10.1534/g3.114.010298

Parametric and Nonparametric Statistical Methods for Genomic Selection of Traits with Additive and Epistatic Genetic Architectures
Cited by: 132
Author(s): Réka Howard, Alicia L. Carriquiry, William D. Beavis
Software Mentions: 8
Published: over 10 years ago

10.3389/fgene.2021.680569

lme4GS: An R-Package for Genomic Selection
Cited by: 8
Author(s): Diana Caamal-Pat, Paulino Pérez‐Rodríguez, José Crossa, Ciro Velasco‐Cruz, Sergio Pérez-Elizalde, Mario Alberto Vázquez-Peña
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pgen.1008984

Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model
Cited by: 16
Author(s): Huimin Na, Stefan Zdraljevic, Robyn E. Tanny, Albertha J.M. Walhout, Erik C. Andersen
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0224920

Cassava yield traits predicted by genomic selection methods
Cited by: 31
Author(s): Luciano Rogério Braatz de Andrade, Massáine Bandeira e Sousa, E. J. de Oliveira, Marcos Deon Vilela de Resende, Camila Ferreira Azevedo
Software Mentions: 7
Published: about 5 years ago

10.1007/s10994-019-05848-5

An evaluation of machine-learning for predicting phenotype: studies in yeast, rice, and wheat
Cited by: 79
Author(s): Nastasiya F. Grinberg, Oghenejokpeme I. Orhobor, Ross D. King
Software Mentions: 7
Published: about 5 years ago

10.3390/plants10010029

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils
Cited by: 6
Author(s): Arfang Badji, Lewis Machida, Daniel Bomet Kwemoi, Frank Kumi, Dennis Okii, Natasha Mwila, Symphorien Agbahoungba, Angele Ibanda, Astère Bararyenya, Selma Ndapewa Nghituwamhata, Thomas Odong, Peter Wasswa, Michael Otim, Mildred Ochwo-Ssemakula, Herbert Talwana, Godfrey Asea, Samuel Kyamanywa, Patrick Rubaihayo
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12864-019-6275-z

Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance
Cited by: 29
Author(s): Waltram Ravelombola, Jun Qin, Ainong Shi, Liana Nice, Yong Bao, Aaron J. Lorenz, J. H. Orf, Nevin D. Young, Senyu Chen
Software Mentions: 7
Published: about 5 years ago

10.1534/g3.118.200913

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Cited by: 59
Author(s): Lindsay V. Clark, Alexander E. Lipka, Erik J. Sacks
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0119425

Genome Wide Analysis of Flowering Time Trait in Multiple Environments via High-Throughput Genotyping Technique in Brassica napus L.
Cited by: 27
Author(s): Lun Li, Yan Long, Libin Zhang, Jessica Dalton‐Morgan, Jacqueline Batley, Liang Yu, Jianghong Meng, Maoteng Li
Software Mentions: 6
Published: almost 10 years ago

10.1186/s12284-018-0223-4

Genomic selection of agronomic traits in hybrid rice using an NCII population
Cited by: 59
Author(s): Yongsheng Xu, Xin Wang, Xiaowen Ding, Xianwei Zheng, Zefeng Yang, Chenwu Xu, Zhongli Hu
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0222733

BWGS: A R package for genomic selection and its application to a wheat breeding programme
Cited by: 30
Author(s): Gilles Charmet, Louis-Gautier Tran, Jérôme Auzanneau, Renaud Rincent, Sophie Bouchet
Software Mentions: 6
Published: over 4 years ago

10.1111/mpp.12964

A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress
Cited by: 22
Author(s): Nathalie Aoun, Henri Desaint, Léa Boyrie, Maxime Bonhomme, Laurent Deslandes, Richard Berthomé, Fabrice Roux
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-020-1942-6

A framework for transcriptome-wide association studies in breast cancer in diverse study populations
Cited by: 60
Author(s): Arjun Bhattacharya, Montserrat García‐Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love
Software Mentions: 6
Published: almost 5 years ago

10.1534/g3.120.401491

High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenneL.)
Cited by: 20
Author(s): Thomas Keep, Jean‐Paul Sampoux, José Luis Blanco‐Pastor, Klaus J. Dehmer, Matthew J. Hegarty, Thomas Ledauphin, Isabelle Litrico, Hilde Muylle, Isabel Roldán‐Ruiz, Anna M. Roschanski, Tom Ruttink, Fabien Surault, E. Willner, Philippe Barré
Software Mentions: 6
Published: over 4 years ago

10.3389/fpls.2020.570871

Genomic Selection for Prediction of Fruit-Related Traits in Pepper (Capsicum spp.)
Cited by: 15
Author(s): Ju-Pyo Hong, Na-Young Ro, Hea-Young Lee, Geon Woo Kim, Jae-Hoon Kwon, Eiji Yamamoto, Byoung-Cheorl Kang
Software Mentions: 5
Published: about 4 years ago

10.1534/g3.113.007807

Increased Genomic Prediction Accuracy in Wheat Breeding Through Spatial Adjustment of Field Trial Data
Cited by: 75
Author(s): Bettina Lado, Iván Matus, Alejandra Rodríguez, Luis Inostroza, Jesse Poland, François Belzile, Alejandro del Pozo, Martín Quincke, Marina Castro, Jarislav von Zitzewitz
Software Mentions: 5
Published: about 11 years ago

10.1038/srep19244

Evaluation of the 2b-RAD method for genomic selection in scallop breeding
Cited by: 57
Author(s): Jun Dou, Xue Li, Qiang Fu, Wenqian Jiao, Yangping Li, Tianqi Li, Yangfan Wang, Xiaoli Hu, Shi Wang, Zhenmin Bao
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-017-03232-8

Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
Cited by: 14
Author(s): Stephen Byrne, Philip G. Conaghan, Susanne Barth, Sai Krishna Arojju, Michael D. Casler, Thibauld Michel, Janaki Velmurugan, Dan Milbourne
Software Mentions: 5
Published: over 7 years ago

10.1534/g3.119.400968

Multi-trait Genomic Prediction Model Increased the Predictive Ability for Agronomic and Malting Quality Traits in Barley (Hordeum vulgare L.)
Cited by: 54
Author(s): Madhav Bhatta, Lucı́a Gutiérrez, Lorena Cammarota, Fernanda Cardozo, Silvia Germán, Blanca Gómez-Guerrero, María Fernanda Pardo, Valeria Lanaro, Mercedes Sayas, Ariel J. Castro
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2018.01322

Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar)
Cited by: 13
Author(s): Yuichiro Hiraoka, Eitaro Fukatsu, Kentaro Mishima, Tomonori Hirao, Kenjiro Teshima, Miho Tamura, Miyoko Tsubomura, Taiichi Iki, Masayuki Kurita, Makoto Takahashi, Atsushi Watanabe
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-015-2212-y

Accuracy of genomic selection for alfalfa biomass yield in different reference populations
Cited by: 100
Author(s): Paolo Annicchiarico, Nelson Espinoza N., Xuehui Li, Yanling Wei, L. Pecetti, E. Charles Brummer
Software Mentions: 5
Published: about 9 years ago

10.1534/g3.120.401452

Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
Cited by: 10
Author(s): Mariem Nsibi, Barbara Gouble, Sylvie Bureau, Timothée Flutre, Christopher Sauvage, Jean‐Marc Audergon, Jean‐Luc Regnard
Software Mentions: 5
Published: about 4 years ago

10.1534/genetics.120.303038

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0227826

Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour
Cited by: 16
Author(s): Alison Lovegrove, Luzie U. Wingen, A.M. Plummer, A. Wood, Diana Passmore, Ondřej Kosík, J. Freeman, Rachel Mitchell, Kirsty L. Hassall, Mehmet Ülker, Karolina Tremmel-Bede, Marianna Rakszegi, Z. Bedő, Marie-Reine Perretant, Gilles Charmet, Caroline Pont, Jérôme Salse, Michelle Leverington Waite, Simon Orford, Amanda Burridge, Till K. Pellny, Peter R. Shewry, Simon Griffiths
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2017.02185

Morphometrics Reveals Complex and Heritable Apple Leaf Shapes
Cited by: 43
Author(s): Zoë Migicovsky, Mao Li, Daniel H. Chitwood, Sean Myles
Software Mentions: 5
Published: almost 7 years ago

10.7717/peerj.11580

Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach
Cited by: 0
Author(s): Siroj Bakoev, Aleksei Traspov, Lyubov Getmantseva, А. А. Белоус, Т. В. Карпушкина, Olga Kostyunina, А. В. Усатов, Tatiana V. Tatarinova
Software Mentions: 5
Published: over 3 years ago

10.3389/fpls.2015.00941

Genomic Prediction in Pea: Effect of Marker Density and Training Population Size and Composition on Prediction Accuracy
Cited by: 72
Author(s): Nadim Tayeh, Anthony Klein, Marie‐Christine Le Paslier, Françoise Jacquin, Hervé Houtin, Céline Rond, Marianne Chabert-Martinello, Jean-Bernard Magnin-Robert, Pascal Marget, Grégoire Aubert, Judith Burstin
Software Mentions: 5
Published: about 9 years ago

10.7554/eLife.35471

Genetics of trans-regulatory variation in gene expression
Cited by: 133
Author(s): Frank W. Albert, Joshua S. Bloom, Jake J. Siegel, Laura Day, Leonid Kruglyak
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-017-3920-2

Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus
Cited by: 59
Author(s): Bárbara S. F. Müller, Leandro G. Neves, Janeo Eustáquio de Almeida Filho, M. D. V. de Resende, Patricio Muñoz, P. E. T. dos Santos, E. Paludzyszyn Filho, Matias Kirst, Dário Grattapaglia
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2164-15-1048

Genomic selection accuracies within and between environments and small breeding groups in white spruce
Cited by: 86
Author(s): Jean Beaulieu, Trevor Doerksen, John Mackay, André Rainville, Jean Bousquet
Software Mentions: 5
Published: almost 11 years ago

10.1186/s13059-021-02416-w

MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits
Cited by: 21
Author(s): Daniel E. Runcie, Jiayi Qu, Hao Cheng, Lorin Crawford
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-020-03804-y

simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes
Cited by: 7
Author(s): Samuel B. Fernandes, Alexander E. Lipka
Software Mentions: 5
Published: about 4 years ago

10.3389/fgene.2019.01091

Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean
Cited by: 71
Author(s): Yang Liu, Duolin Wang, Fei He, Juexin Wang, Trupti Joshi, Dong Xu
Software Mentions: 5
Published: about 5 years ago

10.1007/s00122-020-03759-x

Multi-omics-based prediction of hybrid performance in canola
Cited by: 19
Author(s): Dominic Knoch, Christian R. Werner, Rhonda C. Meyer, David Riewe, Amine Abbadi, Sophie Lücke, Rod J. Snowdon, Thomas Altmann
Software Mentions: 5
Published: almost 4 years ago

10.1093/g3journal/jkaa017

AlphaSimR: an R package for breeding program simulations
Cited by: 88
Author(s): R. Chris Gaynor, Gregor Gorjanc, John M. Hickey
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0235089

Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation
Cited by: 26
Author(s): Waltram Ravelombola, Jun Qin, Ainong Shi, Liana Nice, Yong Bao, Aaron J. Lorenz, J. H. Orf, Nevin D. Young, Senyu Chen
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-38348-y

Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies
Cited by: 0
Author(s): Walid Korani, Justin N. Vaughn
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-018-30089-2

Predictive ability of genome-assisted statistical models under various forms of gene action
Cited by: 34
Author(s): Mehdi Momen, Ahmad Ayatollahi Mehrgardi, Ayyub Sheikhi, Andreas Kranis, Llibertat Tusell, Gota Morota, Guilherme J. M. Rosa, Daniel Gianola
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0218552

SNP-based mixed model association of growth- and yield-related traits in popcorn
Cited by: 9
Author(s): Gabrielle Sousa Mafra, Antônio Teixeira do Amaral Júnior, Janeo Eustáquio de Almeida Filho, Marcelo Vivas, Pedro Henrique Araújo Diniz Santos, Juliana Saltires Santos, Guilherme Ferreira Pena, Valter Jário de Lima, Samuel Henrique Kamphorst, Fábio Tomaz de Oliveira, Yure Pequeno de Souza, Ismael Albino Schwantes, Talles de Oliveira Santos, Rosimeire Barbosa Bispo, Carlos Maldonado, Freddy Mora
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-017-1059-6

Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F1 hybrids
Cited by: 86
Author(s): Beiping Tan, Dário Grattapaglia, Gustavo Salgado Martins, Karina Zamprogno Ferreira, Björn Sundberg, Pär K. Ingvarsson
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-020-02676-x

Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize
Cited by: 11
Author(s): Yixin An, Lin Chen, Yongxiang Li, Chunhui Li, Yunsu Shi, Dengfeng Zhang, Li Yu, Tianyu Wang
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.ppat.1007226

Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles
Cited by: 79
Author(s): Steffen Hahnel, Stefan Zdraljevic, Briana Rodriguez, Yuehui Zhao, Patrick T. McGrath, Erik C. Andersen
Software Mentions: 4
Published: about 6 years ago

10.1038/s41438-020-00370-5

Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple
Cited by: 31
Author(s): Morgane Roth, Hélène Muranty, Mario Di Guardo, Walter Guerra, Andrea Patocchi, Fabrizio Costa
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2019.00009

Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii
Cited by: 37
Author(s): Narinder Singh, Shuangye Wu, Vijay K. Tiwari, Sunish K. Sehgal, John Raupp, Duane Wilson, Mehraj Abbasov, Bikram S. Gill, Jesse Poland
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1004982

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines
Cited by: 378
Author(s): Jennifer Spindel, Hamida Begum, Deniz Akdemir, P. S. Virk, B. C. Y. Collard, Edilberto D. Redoña, G. N. Atlin, Jean‐Luc Jannink, Susan R. McCouch
Software Mentions: 4
Published: almost 10 years ago

10.3389/fpls.2021.697688

Multi-Locus Genome-Wide Association Study and Genomic Selection of Kernel Moisture Content at the Harvest Stage in Maize
Cited by: 5
Author(s): Guangfei Zhou, Qiuli Zhu, Yuxiang Mao, Guoqing Chen, Li Xue, Hailiang Lu, Mei Shi, Zhenliang Zhang, Xiaokai Song, Huimin Zhang, Dejun Hao
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-95268-0

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons
Cited by: 4
Author(s): Taishin Nomura, Yosuke Seki, Makoto Matsuoka, Kenji Yano, Koki Chigira, Shunsuke Adachi, Francisco J Piñera-Chávez, Matthew Reynolds, Shuichi Ohkubo, Taiichiro Ookawa
Software Mentions: 4
Published: over 3 years ago

10.2135/cropsci2018.01.0060

Genetic Variation and Trait Correlations in an East African Cassava Breeding Population for Genomic Selection
Cited by: 14
Author(s): Alfred Ozimati, R. Kawuki, Williams Esuma, Siraj Ismail Kayondo, Anthony Pariyo, Marnin D. Wolfe, Jean‐Luc Jannink
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2021.658267

Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review
Cited by: 11
Author(s): Roberto Fritsche‐Neto, Giovanni Galli, Karina Lima Reis Borges, Germano Costa‐Neto, Filipe Couto Alves, Felipe Sabadin, Danilo Hottis Lyra, Pedro Patric Pinho Morais, Luciano Rogério Braatz de Andrade, Ítalo Stefanine Correia Granato, José Crossa
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-15-246

Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations
Cited by: 55
Author(s): José Luis Gualdrón Duarte, Rodolfo Juan Carlos Cantet, R. O. Bates, Catherine W. Ernst, Nancy E. Raney, Juan P. Steibel
Software Mentions: 4
Published: over 10 years ago

10.1534/g3.120.401132

Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny
Cited by: 8
Author(s): Chin Jian Yang, Rajiv Sharma, Gregor Gorjanc, Sarah Hearne, W. Powell, Ian Mackay
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0233951

Predicting biomass of rice with intermediate traits: Modeling method combining crop growth models and genomic prediction models
Cited by: 14
Author(s): Yusuke Toda, Hitomi Wakatsuki, Toru Aoike, Hiromi Kajiya‐Kanegae, Mariko Yamasaki, Takuma Yoshioka, Kaworu Ebana, Takeshi Hayashi, Hiroshi Nakagawa, Toshihiro Hasegawa, Hiroyoshi Iwata
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0239609

Advancing crested wheatgrass [Agropyron cristatum (L.) Gaertn.] breeding through genotyping-by-sequencing and genomic selection
Cited by: 4
Author(s): Kiran Baral, Bruce Coulman, Bill Biligetu, Yong‐Bi Fu
Software Mentions: 4
Published: about 4 years ago

10.1534/genetics.119.302757

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection
Cited by: 26
Author(s): Marnin D. Wolfe, Guillaume Bauchet, A. M. C. Chan, Roberto Lozano, Punna Ramu, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0173368

Breeding Jatropha curcas by genomic selection: A pilot assessment of the accuracy of predictive models
Cited by: 15
Author(s): Leonardo de Azevedo Peixoto, Bruno Galvêas Laviola, Alexandre Alonso Alves, Tatiana Barbosa Rosado, Leonardo Lopes Bhering
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0169234

Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits
Cited by: 94
Author(s): Elisa Biazzi, Nelson Espinoza N., L. Pecetti, E. Charles Brummer, Alberto Palmonari, Aldo Tava, Paolo Annicchiarico
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0212200

Estimation of physiological genomic estimated breeding values (PGEBV) combining full hyperspectral and marker data across environments for grain yield under combined heat and drought stress in tropical maize (Zea mays L.)
Cited by: 12
Author(s): Samuel Trachsel, Thanda Dhliwayo, Lorena González Pérez, José Alberto Mendoza Lugo, Mathias Trachsel
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400617

Population Selection and Sequencing ofCaenorhabditis elegansWild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance
Cited by: 21
Author(s): Amy K. Webster, Anthony Hung, Brad T. Moore, Ryan Guzman, James M. Jordan, Rebecca E. W. Kaplan, Jonathan D. Hibshman, Robyn E. Tanny, Daniel E. Cook, Erik C. Andersen, L. Ryan Baugh
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.116.032532

Optimizing Training Population Data and Validation of Genomic Selection for Economic Traits in Soft Winter Wheat
Cited by: 46
Author(s): Amber Hoffstetter, Antonio G. Cabrera, Mao Fang Huang, Clay Sneller
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.116.033332

Marker-Based Estimates Reveal Significant Nonadditive Effects in Clonally Propagated Cassava (Manihot esculenta): Implications for the Prediction of Total Genetic Value and the Selection of Varieties
Cited by: 31
Author(s): Marnin D. Wolfe, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2021.676326

Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding
Cited by: 18
Author(s): Luís Felipe Ventorim Ferrão, Rodrigo R. Amadeu, Juliana Benevenuto, Ivone de Bem Oliveira, Patricio Muñoz
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.117.041426

The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster
Cited by: 47
Author(s): Elizabeth G. King, Anthony D. Long
Software Mentions: 4
Published: over 7 years ago

10.1007/s00122-018-3186-3

Resource allocation optimization with multi-trait genomic prediction for bread wheat (Triticum aestivum L.) baking quality
Cited by: 77
Author(s): Bettina Lado, Daniel Vázquez, Martín Quincke, Paula Silva, Ignácio Aguilar, Lucı́a Gutiérrez
Software Mentions: 4
Published: about 6 years ago

10.1007/s00122-020-03666-1

Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)
Cited by: 11
Author(s): Jared Crain, Steve Larson, Kevin M. Dorn, Traci Hagedorn, Lee R. DeHaan, Jesse Poland
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0224695

Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology
Cited by: 13
Author(s): Lisa Sakamoto, Hiromi Kajiya‐Kanegae, Koji Noshita, Hideki Takanashi, Mariko Kobayashi, Toru Kudo, Kentarô Yano, Tsuyoshi Tokunaga, Nobuhiro Tsutsumi, Hiroyoshi Iwata
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0073056

Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle
Cited by: 96
Author(s): Elizabeth M. Ross, Peter J. Moate, L. C. Marett, Ben Cocks, Ben J. Hayes
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-019-55338-w

Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)
Cited by: 17
Author(s): Hilal Betül Kaya, Deniz Akdemir, Roberto Lozano, Öznur Çetin, Hulya Sozer Kaya, Mustafa Şahi̇n, Jenny L. Smith, Bahattin Tanyolaç, Jean‐Luc Jannink
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-020-07188-4

Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine
Cited by: 31
Author(s): Ainhoa Calleja-Rodríguez, Peng Jin, Tomáš Funda, Zhiqiang Chen, John Baison, Fikret Isik, Sara Abrahamsson, Harry X. Wu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-69381-5

Prospects of GWAS and predictive breeding for European winter wheat’s grain protein content, grain starch content, and grain hardness
Cited by: 37
Author(s): Quddoos H. Muqaddasi, Jonathan Brassac, Erhard Ebmeyer, Sonja Kollers, Viktor Korzun, O. Argillier, Gunther Stiewe, Jörg Plieske, Martin W. Ganal, Marion S. Röder
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2019.01337

Genetic Dissection of Snow Mold Tolerance in US Pacific Northwest Winter Wheat Through Genome-Wide Association Study and Genomic Selection
Cited by: 17
Author(s): Dennis N. Lozada, Jayfred Godoy, Timothy Murray, Brian P. Ward, Arron H. Carter
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2016.02065

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture
Cited by: 10
Author(s): Vincent Migault, Benoît Pallas, Evelyne Costes
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-22657-3

Haplotype-based allele mining in the Japan-MAGIC rice population
Cited by: 23
Author(s): Daisuke Ogawa, Eiji Yamamoto, Toshikazu Ohtani, Noriko Kanno, Hiroshi Tsunematsu, Yasunori Nonoue, Masahiro Yano, Tetsuro Yamamoto, Jun‐ichi Yonemaru
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-82437-4

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm
Cited by: 38
Author(s): Jéssica Delfini, Vânia Moda-Cirino, José dos Santos Neto, Paulo Maurício Ruas, Gustavo César Sant’Ana, Paul Gepts, Leandro Simões Azeredo Gonçalves
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008986

Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans
Cited by: 23
Author(s): Kathryn Evans, Stefan Zdraljevic, Lewis Stevens, Kimberly D. Collins, Robyn E. Tanny, Erik C. Andersen
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1009580

Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos
Cited by: 10
Author(s): Longhua Guo, Joshua S. Bloom, Steve Sykes, Elaine Huang, Zain Kashif, Elise Pham, Katarina Ho, Ana Alcaraz, Xinshu Xiao, Sandra Duarte‐Vogel, Leonid Kruglyak
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2021.600040

A Stacking Ensemble Learning Framework for Genomic Prediction
Cited by: 26
Author(s): Mang Liang, Tianpeng Chang, Bingxing An, Xinghai Duan, Lili Du, Xiaoqiao Wang, Jianyin Miao, Lingyang Xu, Xue Gao, Lupei Zhang, Junya Li, Huijiang Gao
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41438-021-00462-w

Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population
Cited by: 23
Author(s): Waltram Ravelombola, Ainong Shi, Bao‐Lam Huynh
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes12040490

Genome-Wide Association Studies and Prediction of Tan Spot (Pyrenophora tritici-repentis) Infection in European Winter Wheat via Different Marker Platforms
Cited by: 13
Author(s): Quddoos H. Muqaddasi, Roop Kamal, Vilson Mirdita, Bernd Rodemann, Martin W. Ganal, Jochen C. Reif, Marion S. Röder
Software Mentions: 3
Published: over 3 years ago

10.1186/s12863-020-00871-1

Design of experiments for fine-mapping quantitative trait loci in livestock populations
Cited by: 5
Author(s): Dörte Wittenburg, Sarah Bonk, Michael Doschoris, Henry Reyer
Software Mentions: 3
Published: over 4 years ago

10.3390/genes10110841

Genomic Selection for Antioxidant Production in a Panel of Sorghum bicolor and S. bicolor × S. halepense Lines
Cited by: 13
Author(s): Ephrem Habyarimana, Marco Lopez‐Cruz
Software Mentions: 3
Published: about 5 years ago

10.1093/genetics/iyaa043

Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat (Avena sativaL.)
Cited by: 15
Author(s): Malachy T. Campbell, Haixiao Hu, Trevor H. Yeats, Melanie Caffe‐Treml, Lucı́a Gutiérrez, Kevin P. Smith, Mark E. Sorrells, Michael A. Gore, Jean Luc Jannink
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2019.01195

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection
Cited by: 17
Author(s): Sebastian Michel, Franziska Löschenberger, Jakob Hellinger, Verena Strasser, Christian Ametz, Bernadette Pachler, Ellen Sparry, Hermann Buerstmayr
Software Mentions: 3
Published: about 5 years ago

10.1111/pbi.13372

PANOMICS meets germplasm
Cited by: 69
Author(s): Wolfram Weckwerth, Arindam Ghatak, Anke Bellaire, Palak Chaturvedi, Rajeev K. Varshney
Software Mentions: 3
Published: over 4 years ago

10.1534/g3.119.400759

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum
Cited by: 22
Author(s): José Fortunato Ferreira Santos, Samuel B. Fernandes, Scott McCoy, Roberto Lozano, Patrick J. Brown, Andrew D. B. Leakey, Edward S. Buckler, Antônio Augusto Franco Garcia, Michael A. Gore
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2021.713667

Breeding With Major and Minor Genes: Genomic Selection for Quantitative Disease Resistance
Cited by: 18
Author(s): Lance F. Merrick, Adrienne B. Burke, Xianming Chen, Arron H. Carter
Software Mentions: 3
Published: over 3 years ago

10.1111/pbi.12888

Haplotype‐based genotyping‐by‐sequencing in oat genome research
Cited by: 82
Author(s): Wubishet A. Bekele, Charlene P. Wight, Shiaoman Chao, Catherine Howarth, Nicholas A. Tinker
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.118.200760

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar
Cited by: 96
Author(s): Renaud Rincent, Jean-Paul Charpentier, Patricia Faivre-Rampant, Etienne Paux, Jacques Le Gouis, Catherine Bastien, Vincent Segura
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0243666

Quantile regression in genomic selection for oligogenic traits in autogamous plants: A simulation study
Cited by: 4
Author(s): Gabriela França Oliveira, Ana Carolina Campana Nascimento, Moysés Nascimento, Isabela de Castro Sant’Anna, Juan Vicente Romero, Camila Ferreira Azevedo, Leonardo Lopes Bhering, Eveline Teixeira Caixeta Moura
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2021.709545

Multi-Trait Multi-Environment Genomic Prediction of Agronomic Traits in Advanced Breeding Lines of Winter Wheat
Cited by: 21
Author(s): Harsimardeep S. Gill, Jyotirmoy Halder, Jinfeng Zhang, Navreet K. Brar, S. Teerath, Colby Hall, Amy Bernardo, Paul St. Amand, Guihua Bai, Eric Olson, Shaukat Ali, Brent Turnipseed, Sunish K. Sehgal
Software Mentions: 3
Published: over 3 years ago

10.1534/g3.118.200917

Genomic Selection for Yield and Seed Composition Traits Within an Applied Soybean Breeding Program
Cited by: 51
Author(s): Benjamin B. Stewart-Brown, Qijian Song, Justin N. Vaughn, Zenglu Li
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3170-8

Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations
Cited by: 52
Author(s): Chunhui Li, Bo Sun, Yongxiang Li, Cheng Liu, Xun Wu, Dengfeng Zhang, Yunsu Shi, Yi Song, Edward S. Buckler, Zhiwu Zhang, Tianyu Wang, Yu Liu
Software Mentions: 3
Published: about 8 years ago

Projects: cran: rrBLUP

Papers Mentioning rrBLUP 263