Ecosyste.ms: Papers

10.1534/g3.119.400018

BGData - A Suite of R Packages for Genomic Analysis with Big Data
Cited by: 23
Author(s): Alexander Grueneberg, Gustavo de los Campos
Software Mentions: 16
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

10.1186/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

10.1371/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

10.3389/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

10.1534/g3.119.400126

An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction
Cited by: 38
Author(s): Osval A. Montesinos-L֯ópez, Abelardo Montesinos‐López, Francisco Javier Luna-Vázquez, Fernando H. Toledo, Paulino Pérez‐Rodríguez, Morten Lillemo, J. Crossa
Software Mentions: 8
Published: over 5 years ago

10.3390/genes11111270

Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes
Cited by: 23
Author(s): Jia Guo, Jahangir Khan, Sumit Pradhan, Dipendra Shahi, Naeem Khan, Muhsin Avci, Jordan C. McBreen, Stephen A. Harrison, Gina Brown-Guedira, J. Paul Murphy, J. W. Johnson, Maryati Mohamed, R. Esten Mason, Amir M. H. Ibrahim, Russel Sutton, Carl A. Griffey, Ali Babar
Software Mentions: 8
Published: about 4 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

10.3389/fgene.2021.710485

Evaluations of Genomic Prediction and Identification of New Loci for Resistance to Stripe Rust Disease in Wheat (Triticum aestivum L.)
Cited by: 7
Author(s): Vipin Tomar, G. S. Dhillon, Daljit Singh, Ravi P. Singh, Jesse Poland, Anis Ahmad Chaudhary, Pradeep Kumar Bhati, Arun Kumar Joshi, Uttam Kumar
Software Mentions: 7
Published: about 3 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

10.1186/s12863-017-0576-5

Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.)
Cited by: 14
Author(s): Qi Bin Kwong, Chee Keng Teh, Ai Ling Ong, Fook Tim Chew, Sean Mayes, Harikrishna Kulaveerasingam, Martti T. Tammi, Suat Hui Yeoh, David R. Appleton, Jennifer Ann Harikrishna
Software Mentions: 7
Published: about 7 years ago

10.1186/s12711-016-0219-8

Genome-wide prediction using Bayesian additive regression trees
Cited by: 35
Author(s): Patrik Waldmann
Software Mentions: 6
Published: over 8 years ago

10.1534/g3.118.200986

Genomic Selection with Allele Dosage in <i>Panicum maximum</i> Jacq.
Cited by: 34
Author(s): Letícia Aparecida de Castro Lara, M. F. Santos, Liana Jank, Lucimara Chiari, Mariane de Mendonça Vilela, Rodrigo R. Amadeu, José Fortunato Ferreira Santos, Guilherme da Silva Pereira, Zhao‐Bang Zeng, Antônio Augusto Franco Garcia
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-87296-7

Genomic prediction for growth using a low-density SNP panel in dromedary camels
Cited by: 9
Author(s): Morteza Bitaraf Sani, Javad Zare Harofte, Mohammad Hossein Banabazi, Saeid Esmaeilkhanian, Ali Naderi, Nader Salim, Abbas Teimoori, Ahmad Bitaraf, Mohammad Zadehrahmani, Pamela Anna Burger, V. Landi, Mohammad Silawi, Afsaneh Taghipour Sheshdeh, Mohammad Ali Faghihi
Software Mentions: 6
Published: over 3 years ago

10.1093/g3journal/jkab040

<i>EnvRtype</i>: a software to interplay enviromics and quantitative genomics in agriculture
Cited by: 44
Author(s): Germano Costa‐Neto, Giovanni Galli, Humberto Fanelli Carvalho, J. Crossa, Roberto Fritsche‐Neto
Software Mentions: 6
Published: almost 4 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

10.3835/plantgenome2017.03.0015

Prospects for Genomic Selection in Cassava Breeding
Cited by: 95
Author(s): Marnin D. Wolfe, Dunia Pino Del Carpio, Olumide Alabi, Lydia Ezenwaka, Ugochukwu N. Ikeogu, Siraj Ismail Kayondo, Roberto Lozano, Uche Godfrey Okeke, Alfred Ozimati, Williams Esuma, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 6
Published: about 7 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

10.1371/journal.pone.0234052

Can metabolic prediction be an alternative to genomic prediction in barley?
Cited by: 15
Author(s): Mathias Ruben Gemmer, Chris Richter, Yong Jiang, Thomas Schmutzer, Manish L. Raorane, Björn H. Junker, Klaus Pillen, Andreas Maurer
Software Mentions: 5
Published: over 4 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

10.1534/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

10.1186/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/g3.119.400968

Multi-trait Genomic Prediction Model Increased the Predictive Ability for Agronomic and Malting Quality Traits in Barley (<i>Hordeum vulgare</i> 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

10.1186/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

10.1038/s41598-020-63919-3

Increased Prediction Accuracy Using Combined Genomic Information and Physiological Traits in A Soft Wheat Panel Evaluated in Multi-Environments
Cited by: 12
Author(s): Jia Guo, Sumit Pradhan, Dipendra Shahi, Jahangir Khan, Jordan C. McBreen, Guihua Bai, J. Paul Murphy, Ali Babar
Software Mentions: 5
Published: over 4 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

10.1371/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.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.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

10.3389/fgene.2020.00513

Estimating Conformational Traits in Dairy Cattle With DeepAPS: A Two-Step Deep Learning Automated Phenotyping and Segmentation Approach
Cited by: 13
Author(s): Jessica Nye, Laura M. Zingaretti, Miguel Pérez‐Enciso
Software Mentions: 4
Published: over 4 years ago

10.1038/s41437-021-00412-1

A guide for kernel generalized regression methods for genomic-enabled prediction
Cited by: 12
Author(s): Abelardo Montesinos‐López, Osval A. Montesinos-L֯ópez, J. Cricelio Montesinos-López, Carlos Flores-Cortés, Roberto De Rosa, J. Crossa
Software Mentions: 4
Published: almost 4 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: over 6 years ago

10.3390/genes11080838

Insights into the Genetic Architecture of Bran Friability and Water Retention Capacity, Two Important Traits for Whole Grain End-Use Quality in Winter Wheat
Cited by: 3
Author(s): Sviatoslav Navrotskyi, Vikas Belamkar, P. S. Baenziger, Devin J. Rose
Software Mentions: 4
Published: over 4 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

10.1534/g3.120.401733

Maximum <i>a posteriori</i> Threshold Genomic Prediction Model for Ordinal Traits
Cited by: 3
Author(s): Abelardo Montesinos‐López, Humberto Gutiérrez Pulido, Osval A. Montesinos-L֯ópez, J. Crossa
Software Mentions: 4
Published: about 4 years ago

10.1534/g3.120.401244

Bayesian and Machine Learning Models for Genomic Prediction of Anterior Cruciate Ligament Rupture in the Canine Model
Cited by: 12
Author(s): Louise Baker, Mehdi Momen, K.C.K. Chan, Nathan Bollig, Fernando Brito Lopes, Guilherme J. M. Rosa, Rory J. Todhunter, Emily E. Binversie, Susannah J. Sample, Peter Muir
Software Mentions: 4
Published: over 4 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

10.1007/s00122-017-2944-y

Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing
Cited by: 77
Author(s): Elsa Sverrisdóttir, Stephen Byrne, Ea Høegh Riis Sundmark, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Kåre Lehmann Nielsen
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.119.400336

A Bayesian Genomic Multi-output Regressor Stacking Model for Predicting Multi-trait Multi-environment Plant Breeding Data
Cited by: 20
Author(s): Osval A. Montesinos-L֯ópez, Abelardo Montesinos‐López, J. Crossa, Jaime Cuevas, J. Cricelio Montesinos-López, Zitlalli Salas Gutiérrez, Morten Lillemo, Philomin Juliana, Ravi P. Singh
Software Mentions: 4
Published: about 5 years ago

10.3390/plants10030558

Comparison of Genomic Prediction Methods for Yellow, Stem, and Leaf Rust Resistance in Wheat Landraces from Afghanistan
Cited by: 11
Author(s): Muhammad Massub Tehseen, Zakaria Kehel, Carolina Sansaloni, Marta S. Lopes, Ahmed Amri, Ezgi Kurtulus, K. Nazari
Software Mentions: 4
Published: almost 4 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

10.1371/journal.pone.0240948

Predictions from algorithmic modeling result in better decisions than from data modeling for soybean iron deficiency chlorosis
Cited by: 2
Author(s): Zhanyou Xu, Andreomar Kurek, Steven B. Cannon, William D. Beavis
Software Mentions: 4
Published: over 3 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

10.1371/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

10.1534/g3.118.200908

OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices
Cited by: 3
Author(s): Zhi Xiong, Qingrun Zhang, Alexander Platt, Wenyuan Liao, Xinghua Shi, Gustavo de los Campos, Quan Long
Software Mentions: 4
Published: almost 6 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

10.3389/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

10.3389/fpls.2020.00025

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species
Cited by: 71
Author(s): Laura M. Zingaretti, Salvador A. Gezan, Luís Felipe Ventorim Ferrão, Luis F. Osorio, Amparo Monfort, Patricio Muñoz, Vance M. Whitaker, Miguel Pérez‐Enciso
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2020.580136

Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields
Cited by: 7
Author(s): Philomin Juliana, Ravi P. Singh, Hans‐Joachim Braun, Julio Huerta‐Espino, Leonardo Crespo‐Herrera, Thomas Payne, Jesse Poland, Sandesh Shrestha, Uttam Kumar, Arun Kumar Joshi, Muhammad Imtiaz, Mohammad Zillur Rahman, Fernando H. Toledo
Software Mentions: 4
Published: over 4 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: almost 6 years ago

10.3390/ani9110927

A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Bos grunniens)
Cited by: 3
Author(s): Donghai Fu, Xiaoming Ma, Jia Chen, Min Chen, Qinhui Lei, Zhiping Wen, Xiaoyun Wu, Jie Pei, Pengjia Bao, Xuezhi Ding, Xian Guo, Ping Yan, Chunnian Liang
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

10.34133/2021/9812910

Automatic Fruit Morphology Phenome and Genetic Analysis: An Application in the Octoploid Strawberry
Cited by: 12
Author(s): Laura M. Zingaretti, Amparo Monfort, Miguel Pérez‐Enciso
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0173810

Genome-wide association analysis in dogs implicates 99 loci as risk variants for anterior cruciate ligament rupture
Cited by: 36
Author(s): Louise Baker, Brian Kirkpatrick, Guilherme J. M. Rosa, Daniel Gianola, Bruno D. Valente, Julia P. Sumner, Wendy I. Baltzer, Zhengling Hao, Emily E. Binversie, Nicola J. Volstad, Alexander M Piazza, Susannah J. Sample, Peter Muir
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0179191

Leveraging genomic prediction to scan germplasm collection for crop improvement
Cited by: 28
Author(s): Leonardo de Azevedo Peixoto, Tara C. Moellers, Jiaoping Zhang, Aaron J. Lorenz, William D. Beavis, Asheesh K. Singh
Software Mentions: 3
Published: over 7 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

10.1371/journal.pone.0236853

Near-infrared spectroscopy outperforms genomics for predicting sugarcane feedstock quality traits
Cited by: 12
Author(s): Mateus Teles Vital Gonçalves, Gota Morota, Paulo Mafra de Almeida Costa, Pedro Marcus Pereira Vidigal, Márcio Henrique Pereira Barbosa, Luiz Alexandre Peternelli
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2020.01001

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress
Cited by: 45
Author(s): Beat Keller, Daniel Ariza-Suárez, Juan De la Hoz, Johan Aparicio, Ana Elisabeth Portilla-Benavides, Hector Fabio Buendia, Victor Mayor, Bruno Studer, Bodo Raatz
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2018.01118

The Value of Expanding the Training Population to Improve Genomic Selection Models in Tetraploid Potato
Cited by: 23
Author(s): Elsa Sverrisdóttir, Ea Høegh Riis Nielsen, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Glenn Bryan, Kåre Lehmann Nielsen
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2019.00670

Validation of Genotyping by Sequencing Using Transcriptomics for Diversity and Application of Genomic Selection in Tetraploid Potato
Cited by: 30
Author(s): Brittney M. Caruana, Luke W. Pembleton, Fiona Constable, Brendan Rodoni, Anthony T. Slater, Noel O. I. Cogan
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2021.664148

Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction
Cited by: 5
Author(s): Damiano Puglisi, Stefano Delbono, Andrea Visioni, Hakan Özkan, İbrahim Kara, Ana M. Casas, Ernesto Igartua, Giampiero Valè, Angela Roberta Lo Piero, L. Cattivelli, Alessandro Tondelli, Agostino Fricano
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2020.00042

Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat
Cited by: 24
Author(s): Jianting Chu, Yusheng Zhao, Sebastian Beier, Albert W. Schulthess, Nils Stein, Norman Philipp, Marion S. Röder, Jochen C. Reif
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.115.019745

Comparison of Genomic Selection Models to Predict Flowering Time and Spike Grain Number in Two Hexaploid Wheat Doubled Haploid Populations
Cited by: 43
Author(s): Saravanan Thavamanikumar, Rudy Dolferus, Bala R. Thumma
Software Mentions: 3
Published: about 9 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

10.3390/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

10.3390/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/s12711-016-0192-2

Genomic prediction of unordered categorical traits: an application to subpopulation assignment in German Warmblood horses
Cited by: 8
Author(s): Claas Heuer, C. Scheel, Jens Tetens, Christa Kühn, Georg Thaller
Software Mentions: 3
Published: almost 9 years ago

10.1093/genetics/iyaa043

Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat (<i>Avena sativa</i>L.)
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

10.1038/s41598-018-30154-w

Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai)
Cited by: 44
Author(s): Mai F. Minamikawa, Norio Takada, Shingo Terakami, Toshihiro Saito, Akio Onogi, Hiromi Kajiya‐Kanegae, Takeshi Hayashi, Takatsugu Yamamoto, Hiroyoshi Iwata
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-43031-x

Predicting Growth and Carcass Traits in Swine Using Microbiome Data and Machine Learning Algorithms
Cited by: 37
Author(s): Christian Maltecca, Deren Lu, Constantino Schillebeeckx, Nathan P. McNulty, Charles V. Schwab, Caleb M Shull, Francesco Tiezzi
Software Mentions: 3
Published: over 5 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

10.1007/s00122-018-3206-3

Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat
Cited by: 71
Author(s): Philomin Juliana, Osval A. Montesinos-L֯ópez, José Crossa, Suchismita Mondal, Lorena González Pérez, Jesse Poland, Julio Huerta Espino, Leonardo Crespo‐Herrera, Velu Govindan, Susanne Dreisigacker, Sandesh Shrestha, Paulino Pérez‐Rodríguez, Francisco Pinto, Ravi P. Singh
Software Mentions: 3
Published: about 6 years ago

10.1186/s12711-020-00561-7

Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine
Cited by: 13
Author(s): Piush Khanal, Christian Maltecca, Charles V. Schwab, Justin Fix, Matteo Bergamaschi, Francesco Tiezzi
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2021.703419

Reciprocal Recurrent Genomic Selection Is Impacted by Genotype-by-Environment Interactions
Cited by: 2
Author(s): Maximilian Rembe, Jochen C. Reif, Erhard Ebmeyer, Patrick Thorwarth, Viktor Korzun, Johannes Schacht, Philipp H. G. Boeven, Pierrick Varenne, Ebrahim Kazman, Norman Philipp, Sonja Kollers, Nina Pfeiffer, C. Friedrich H. Longin, Niklas Hartwig, Mario Gils, Yusheng Zhao
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-017-05100-x

Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits
Cited by: 97
Author(s): Mai F. Minamikawa, Kenichi Nonaka, Eli Kaminuma, Hiromi Kajiya‐Kanegae, Akio Onogi, Shingo Goto, Terutaka Yoshioka, Atsushi Imai, Hiroko Hamada, Takeshi Hayashi, Satomi Matsumoto, Yūichi Katayose, Atsushi Toyoda, Asao Fujiyama, Yasukazu Nakamura, Tokurou Shimizu, Hiroyoshi Iwata
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0222699

Functional models in genome-wide selection
Cited by: 3
Author(s): Ernandes Guedes Moura, Andrezza Kéllen Alves Pamplona, Márcio Balestre
Software Mentions: 2
Published: about 5 years ago

10.1007/s00122-021-03909-9

From gene banks to farmer’s fields: using genomic selection to identify donors for a breeding program in rice to close the yield gap on smallholder farms
Cited by: 6
Author(s): Reisaku Tanaka, Sarah Tojo Mandaharisoa, Mbolatantely Rakotondramanana, Harisoa Nicole Ranaivo, Juan Pariasca‐Tanaka, Hiromi Kajiya‐Kanegae, Hiroyoshi Iwata, Matthias Wissuwa
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0136594

Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding
Cited by: 80
Author(s): Cécile Grenier, Tuong-Vi Cao, Yolima Ospina, Constanza Quintero, Marc Châtel, Joe Tohmé, B. Courtois, Nourollah Ahmadi
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2017.01182

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding
Cited by: 22
Author(s): Yong‐Bi Fu, Mo-Hua Yang, Fangqin Zeng, Bill Biligetu
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2019.00394

High-Throughput Phenotyping Enabled Genetic Dissection of Crop Lodging in Wheat
Cited by: 98
Author(s): Daljit Singh, Xu Wang, Uttam Kumar, Liangliang Gao, Muhammad Noor, Muhammad Imtiaz, Ravi P. Singh, Jesse Poland
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2156-15-15

Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle
Cited by: 24
Author(s): Shinichiro Ogawa, Hideaki Matsuda, Yoshinori Taniguchi, Toshio Watanabe, Syoyo Nishimura, Yoshikazu Sugimoto, Hiroaki Iwaisaki
Software Mentions: 2
Published: almost 11 years ago

10.3389/fpls.2020.564183

Genomic Selection for Grain Yield in the CIMMYT Wheat Breeding Program—Status and Perspectives
Cited by: 25
Author(s): Philomin Juliana, Ravi P. Singh, Hans‐Joachim Braun, Julio Huerta‐Espino, Leonardo Crespo‐Herrera, Velu Govindan, Suchismita Mondal, Jesse Poland, Sandesh Shrestha
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2021.729328

Genomic Prediction and the Practical Breeding of 12 Quantitative-Inherited Traits in Cucumber (Cucumis sativus L.)
Cited by: 1
Author(s): Ce Liu, Huan Liu, Yike Han, Wang Xiao, Yuanyuan Ding, Huanwen Meng, Zhihui Cheng
Software Mentions: 2
Published: over 3 years ago

10.1534/g3.114.016097

Increased Prediction Accuracy in Wheat Breeding Trials Using a Marker × Environment Interaction Genomic Selection Model
Cited by: 229
Author(s): Marco Lopez‐Cruz, J. Crossa, David Bonnett, Susanne Dreisigacker, Jesse Poland, Jean‐Luc Jannink, Ravi P. Singh, Enrique Autrique, Gustavo de los Campos
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-020-72011-9

Influence of host genetics in shaping the rumen bacterial community in beef cattle
Cited by: 31
Author(s): Waseem Abbas, Jeremy Howard, Henry A. Paz, Kristin E Hales, John W. Wells, L. A. Kuehn, Galen E. Erickson, Matthew L Spangler, Samodha C. Fernando
Software Mentions: 2
Published: over 4 years ago

10.1534/g3.117.044263

Bayesian Networks Illustrate Genomic and Residual Trait Connections in Maize (<i>Zea mays</i> L.)
Cited by: 16
Author(s): Katrin Alexandra Töpner, Guilherme J. M. Rosa, Daniel Gianola, Chris‐Carolin Schön
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.117.300454

Genomic-Enabled Prediction Kernel Models with Random Intercepts for Multi-environment Trials
Cited by: 28
Author(s): Jaime Cuevas, Ítalo Stefanine Correia Granato, Roberto Fritsche‐Neto, Osval A. Montesinos-L֯ópez, Juan Burgueño, Massáine Bandeira e Sousa, J. Crossa
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.117.300199

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower
Cited by: 21
Author(s): Patrick Thorwarth, Eltohamy A. A. Yousef, Karl Schmid
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.117.300406

A Bayesian Genomic Regression Model with Skew Normal Random Errors
Cited by: 6
Author(s): Paulino Pérez‐Rodríguez, Rocío Acosta-Pech, Sergio Pérez-Elizalde, Ciro Velasco Cruz, Javier Suárez Espinosa, J. Crossa
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.118.200435

BGGE: A New Package for Genomic-Enabled Prediction Incorporating Genotype × Environment Interaction Models
Cited by: 40
Author(s): Ítalo Stefanine Correia Granato, Jaime Cuevas, Francisco Javier Luna-Vázquez, J. Crossa, Osval A. Montesinos-L֯ópez, Juan Burgueño, Roberto Fritsche‐Neto
Software Mentions: 2
Published: over 6 years ago

10.1111/ahg.12099

Effectiveness of Shrinkage and Variable Selection Methods for the Prediction of Complex Human Traits using Data from Distantly Related Individuals
Cited by: 14
Author(s): Swetlana Berger, Paulino Pérez‐Rodríguez, Yogasudha Veturi, Henner Simianer, Gustavo de los Campos
Software Mentions: 2
Published: almost 10 years ago

10.1534/g3.118.200613

Prediction of Subgenome Additive and Interaction Effects in Allohexaploid Wheat
Cited by: 9
Author(s): Nicholas Santantonio, Jean‐Luc Jannink, Mark E. Sorrells
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.118.200856

Hyperspectral Reflectance-Derived Relationship Matrices for Genomic Prediction of Grain Yield in Wheat
Cited by: 85
Author(s): Margaret Krause, Lorena González Pérez, José Crossa, Paulino Pérez‐Rodríguez, Osval A. Montesinos-L֯ópez, Ravi P. Singh, Susanne Dreisigacker, Jesse Poland, Jessica Rutkoski, Mark E. Sorrells, Michael A. Gore, Suchismita Mondal
Software Mentions: 2
Published: over 5 years ago

10.3390/plants9020275

Seed Weight as a Covariate in Association and Prediction Studies for Biomass Traits in Maize Seedlings
Cited by: 2
Author(s): Vlatko Galić, Maja Mazur, Andrija Brkić, Josip Brkić, Antun Jambrović, Zvonimir Zdunić, Domagoj Šimić
Software Mentions: 2
Published: almost 5 years ago

10.3390/plants9010099

Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx
Cited by: 19
Author(s): Paulina Ballesta, David R. Bush, Fabyano Fonseca e Silva, Freddy Mora
Software Mentions: 2
Published: almost 5 years ago

10.1534/g3.119.400498

Benchmarking Parametric and Machine Learning Models for Genomic Prediction of Complex Traits
Cited by: 88
Author(s): Christina B. Azodi, Emily Bolger, Andrew McCarren, Mark Roantree, Gustavo de los Campos, Shin-Han Shiu
Software Mentions: 2
Published: about 5 years ago

10.1534/g3.119.400880

Genomic Predictive Ability for Foliar Nutritive Traits in Perennial Ryegrass
Cited by: 17
Author(s): Sai Krishna Arojju, Mingshu Cao, M. Z. Z. Jahufer, Brent Barrett, Marty J. Faville
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13007-017-0212-4

Genomic Bayesian functional regression models with interactions for predicting wheat grain yield using hyper-spectral image data
Cited by: 36
Author(s): Abelardo Montesinos‐López, Osval A. Montesinos-L֯ópez, Jaime Cuevas, Walter A. Mata-López, Juan Burgueño, Sushismita Mondal, Julio Huerta, Ravi P. Singh, Enrique Autrique, Lorena González Pérez, José Crossa
Software Mentions: 2
Published: over 7 years ago