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For: Jarquín D, Crossa J, Lacaze X, Du Cheyron P, Daucourt J, Lorgeou J, Piraux F, Guerreiro L, Pérez P, Calus M, Burgueño J, de los Campos G. A reaction norm model for genomic selection using high-dimensional genomic and environmental data. Theor Appl Genet 2014;127:595-607. [PMID: 24337101 PMCID: PMC3931944 DOI: 10.1007/s00122-013-2243-1] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 11/20/2013] [Indexed: 05/18/2023]
Number Cited by Other Article(s)
1
Ribeiro PCO, Howard R, Jarquin D, Oliveira ICM, Chaves S, Carneiro PCS, Souza VF, Schaffert RE, Damasceno CMB, Parrella RAC, Dias KOG, Pastina MM. Prediction of biomass sorghum hybrids using environmental feature-enriched genomic combining ability models in tropical environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025;138:113. [PMID: 40343517 DOI: 10.1007/s00122-025-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/02/2025] [Indexed: 05/11/2025]
2
He K, Yu T, Gao S, Chen S, Li L, Zhang X, Huang C, Xu Y, Wang J, Prasanna BM, Hearne S, Li X, Li H. Leveraging Automated Machine Learning for Environmental Data-Driven Genetic Analysis and Genomic Prediction in Maize Hybrids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2412423. [PMID: 40047344 PMCID: PMC12061318 DOI: 10.1002/advs.202412423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 02/14/2025] [Indexed: 05/10/2025]
3
Wang J, Liu L, He K, Gebrewahid TW, Gao S, Tian Q, Li Z, Song Y, Guo Y, Li Y, Cui Q, Zhang L, Wang J, Huang C, Li L, Guo T, Li H. Accurate genomic prediction for grain yield and grain moisture content of maize hybrids using multi-environment data. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025;67:1379-1394. [PMID: 39960172 DOI: 10.1111/jipb.13857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 01/14/2025] [Indexed: 05/10/2025]
4
Lell M, Gogna A, Kloesgen V, Avenhaus U, Dörnte J, Eckhoff WM, Eschholz T, Gils M, Kirchhoff M, Koch M, Kollers S, Pfeiffer N, Rapp M, Wimmer V, Wolf M, Reif J, Zhao Y. Breaking down data silos across companies to train genome-wide predictions: A feasibility study in wheat. PLANT BIOTECHNOLOGY JOURNAL 2025. [PMID: 40253615 DOI: 10.1111/pbi.70095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 03/07/2025] [Accepted: 04/07/2025] [Indexed: 04/22/2025]
5
Xavier A, Runcie D, Habier D. Megavariate methods capture complex genotype-by-environment interactions. Genetics 2025;229:iyae179. [PMID: 39495661 PMCID: PMC12005252 DOI: 10.1093/genetics/iyae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 10/26/2024] [Indexed: 11/06/2024]  Open
6
Vitale P, Montesinos-López O, Gerard G, Velu G, Tadesse Z, Montesinos-López A, Dreisigacker S, Pacheco A, Toledo F, Saint Pierre C, Pérez-Rodríguez P, Gardner K, Crespo-Herrera L, Crossa J. Improving wheat grain yield genomic prediction accuracy using historical data. G3 (BETHESDA, MD.) 2025;15:jkaf038. [PMID: 40056458 PMCID: PMC12005153 DOI: 10.1093/g3journal/jkaf038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 02/08/2025] [Accepted: 02/12/2025] [Indexed: 03/10/2025]
7
Avagyan V, Boer MP, Solin J, van Dijk ADJ, Bustos-Korts D, van Rossum BJ, Ramakers JJC, van Eeuwijk F, Kruijer W. Penalized factorial regression as a flexible and computationally attractive reaction norm model for prediction in the presence of GxE. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025;138:88. [PMID: 40155554 PMCID: PMC11953130 DOI: 10.1007/s00122-025-04865-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 02/24/2025] [Indexed: 04/01/2025]
8
McBreen J, Babar MA, Jarquin D, Ampatzidis Y, Khan N, Kunwar S, Acharya JP, Adewale S, Brown‐Guedira G. Enhancing genomic-based forward prediction accuracy in wheat by integrating UAV-derived hyperspectral and environmental data with machine learning under heat-stressed environments. THE PLANT GENOME 2025;18:e20554. [PMID: 39779660 PMCID: PMC11711122 DOI: 10.1002/tpg2.20554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 12/10/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025]
9
Hudson O, Brawner J. Using genome-wide associations and host-by-pathogen predictions to identify allelic interactions that control disease resistance. THE PLANT GENOME 2025;18:e70006. [PMID: 39994874 PMCID: PMC11850958 DOI: 10.1002/tpg2.70006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 01/08/2025] [Accepted: 01/15/2025] [Indexed: 02/26/2025]
10
Mothukuri SR, Beyene Y, Gültas M, Burgueño J, Griebel S. Optimization of sparse phenotyping strategy in multi-environmental trials in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025;138:62. [PMID: 40016556 PMCID: PMC11868319 DOI: 10.1007/s00122-025-04825-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 01/15/2025] [Indexed: 03/01/2025]
11
Washburn JD, Varela JI, Xavier A, Chen Q, Ertl D, Gage JL, Holland JB, Lima DC, Romay MC, Lopez-Cruz M, de los Campos G, Barber W, Zimmer C, Trucillo Silva I, Rocha F, Rincent R, Ali B, Hu H, Runcie DE, Gusev K, Slabodkin A, Bax P, Aubert J, Gangloff H, Mary-Huard T, Vanrenterghem T, Quesada-Traver C, Yates S, Ariza-Suárez D, Ulrich A, Wyler M, Kick DR, Bellis ES, Causey JL, Soriano Chavez E, Wang Y, Piyush V, Fernando GD, Hu RK, Kumar R, Timon AJ, Venkatesh R, Segura Abá K, Chen H, Ranaweera T, Shiu SH, Wang P, Gordon MJ, Amos BK, Busato S, Perondi D, Gogna A, Psaroudakis D, Chen CPJ, Al-Mamun HA, Danilevicz MF, Upadhyaya SR, Edwards D, de Leon N. Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates. Genetics 2025;229:iyae195. [PMID: 39576009 PMCID: PMC12054733 DOI: 10.1093/genetics/iyae195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 11/13/2024] [Indexed: 11/27/2024]  Open
12
Tian Z, Nepomuceno AL, Song Q, Stupar RM, Liu B, Kong F, Ma J, Lee SH, Jackson SA. Soybean2035: A decadal vision for soybean functional genomics and breeding. MOLECULAR PLANT 2025;18:245-271. [PMID: 39772289 DOI: 10.1016/j.molp.2025.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/29/2024] [Accepted: 01/05/2025] [Indexed: 01/31/2025]
13
Crossa J, Montesinos-Lopez OA, Costa-Neto G, Vitale P, Martini JWR, Runcie D, Fritsche-Neto R, Montesinos-Lopez A, Pérez-Rodríguez P, Gerard G, Dreisigacker S, Crespo-Herrera L, Pierre CS, Lillemo M, Cuevas J, Bentley A, Ortiz R. Machine learning algorithms translate big data into predictive breeding accuracy. TRENDS IN PLANT SCIENCE 2025;30:167-184. [PMID: 39462718 DOI: 10.1016/j.tplants.2024.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 08/23/2024] [Accepted: 09/23/2024] [Indexed: 10/29/2024]
14
Jung M, Quesada-Traver C, Roth M, Aranzana MJ, Muranty H, Rymenants M, Guerra W, Holzknecht E, Pradas N, Lozano L, Didelot F, Laurens F, Yates S, Studer B, Broggini GAL, Patocchi A. Integrative multi-environmental genomic prediction in apple. HORTICULTURE RESEARCH 2025;12:uhae319. [PMID: 40041603 PMCID: PMC11879405 DOI: 10.1093/hr/uhae319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 11/07/2024] [Indexed: 03/06/2025]
15
Hu H, Rincent R, Runcie DE. MegaLMM improves genomic predictions in new environments using environmental covariates. Genetics 2025;229:1-41. [PMID: 39471330 PMCID: PMC11708919 DOI: 10.1093/genetics/iyae171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 09/19/2024] [Accepted: 09/25/2024] [Indexed: 11/01/2024]  Open
16
Resende RT, Xavier A, Silva PIT, Resende MPM, Jarquin D, Marcatti GE. GIS-based G × E modeling of maize hybrids through enviromic markers engineering. THE NEW PHYTOLOGIST 2025;245:102-116. [PMID: 39014516 PMCID: PMC11617650 DOI: 10.1111/nph.19951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/22/2024] [Indexed: 07/18/2024]
17
Nannuru VKR, Dieseth JA, Lillemo M, Meuwissen THE. Evaluating genomic selection and speed breeding for Fusarium head blight resistance in wheat using stochastic simulations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2025;45:14. [PMID: 39803632 PMCID: PMC11717775 DOI: 10.1007/s11032-024-01527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 12/15/2024] [Indexed: 01/16/2025]
18
de Verdal H, Segura V, Pot D, Salas N, Garin V, Rakotoson T, Raboin LM, VomBrocke K, Dusserre J, Castro Pacheco SA, Grenier C. Performance of phenomic selection in rice: Effects of population size and genotype-environment interactions on predictive ability. PLoS One 2024;19:e0309502. [PMID: 39715250 DOI: 10.1371/journal.pone.0309502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 12/03/2024] [Indexed: 12/25/2024]  Open
19
Shahi D, Guo J, Pradhan S, Avci M, Bai G, Khan J, Baik BK, Mergoum M, Babar MA. Genome-Wide Association Study and Genomic Prediction of Soft Wheat End-Use Quality Traits Under Post-Anthesis Heat-Stressed Conditions. BIOLOGY 2024;13:962. [PMID: 39765629 PMCID: PMC11727209 DOI: 10.3390/biology13120962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 11/15/2024] [Accepted: 11/17/2024] [Indexed: 01/15/2025]
20
Kimutai JJC, Makumbi D, Burgueño J, Pérez-Rodríguez P, Crossa J, Gowda M, Menkir A, Pacheco A, Ifie BE, Tongoona P, Danquah EY, Prasanna BM. Genomic prediction of the performance of tropical doubled haploid maize lines under artificial Striga hermonthica (Del.) Benth. infestation. G3 (BETHESDA, MD.) 2024;14:jkae186. [PMID: 39129203 PMCID: PMC11457060 DOI: 10.1093/g3journal/jkae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
21
Ndlovu N, Gowda M, Beyene Y, Das B, Mahabaleswara SL, Makumbi D, Ogugo V, Burgueno J, Crossa J, Spillane C, McKeown PC, Brychkova G, Prasanna BM. A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize. FRONTIERS IN PLANT SCIENCE 2024;15:1448961. [PMID: 39421144 PMCID: PMC11484028 DOI: 10.3389/fpls.2024.1448961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 09/05/2024] [Indexed: 10/19/2024]
22
Kusmec A, Yeh CT'E, Schnable PS. Data-driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates. THE NEW PHYTOLOGIST 2024;244:618-634. [PMID: 39183371 DOI: 10.1111/nph.19937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/20/2024] [Indexed: 08/27/2024]
23
Tibbs-Cortes LE, Guo T, Andorf CM, Li X, Yu J. Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize. Genome Res 2024;34:1253-1263. [PMID: 39271292 PMCID: PMC11444181 DOI: 10.1101/gr.279027.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024]
24
Washburn JD, Varela JI, Xavier A, Chen Q, Ertl D, Gage JL, Holland JB, Lima DC, Romay MC, Lopez-Cruz M, de los Campos G, Barber W, Zimmer C, Silva IT, Rocha F, Rincent R, Ali B, Hu H, Runcie DE, Gusev K, Slabodkin A, Bax P, Aubert J, Gangloff H, Mary-Huard T, Vanrenterghem T, Quesada-Traver C, Yates S, Ariza-Suárez D, Ulrich A, Wyler M, Kick DR, Bellis ES, Causey JL, Chavez ES, Wang Y, Piyush V, Fernando GD, Hu RK, Kumar R, Timon AJ, Venkatesh R, Abá KS, Chen H, Ranaweera T, Shiu SH, Wang P, Gordon MJ, Amos BK, Busato S, Perondi D, Gogna A, Psaroudakis D, Chen CPJ, Al-Mamun HA, Danilevicz MF, Upadhyaya SR, Edwards D, de Leon N. Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612969. [PMID: 39345633 PMCID: PMC11429743 DOI: 10.1101/2024.09.13.612969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
25
Bartholomé J, Ospina JO, Sandoval M, Espinosa N, Arcos J, Ospina Y, Frouin J, Beartschi C, Ghneim T, Grenier C. Genomic selection for tolerance to aluminum toxicity in a synthetic population of upland rice. PLoS One 2024;19:e0307009. [PMID: 39173048 PMCID: PMC11341055 DOI: 10.1371/journal.pone.0307009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/28/2024] [Indexed: 08/24/2024]  Open
26
Hudson O, Resende MFR, Messina C, Holland J, Brawner J. Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:196. [PMID: 39105819 PMCID: PMC11303470 DOI: 10.1007/s00122-024-04698-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 07/17/2024] [Indexed: 08/07/2024]
27
Fernandes IK, Vieira CC, Dias KOG, Fernandes SB. Using machine learning to combine genetic and environmental data for maize grain yield predictions across multi-environment trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:189. [PMID: 39044035 PMCID: PMC11266441 DOI: 10.1007/s00122-024-04687-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024]
28
Nascimento M, Nascimento ACC, Azevedo CF, de Oliveira ACB, Caixeta ET, Jarquin D. Enhancing genomic prediction with Stacking Ensemble Learning in Arabica Coffee. FRONTIERS IN PLANT SCIENCE 2024;15:1373318. [PMID: 39086911 PMCID: PMC11288849 DOI: 10.3389/fpls.2024.1373318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/12/2024] [Indexed: 08/02/2024]
29
Tadese D, Piepho HP, Hartung J. Accuracy of prediction from multi-environment trials for new locations using pedigree information and environmental covariates: the case of sorghum (Sorghum bicolor (L.) Moench) breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:181. [PMID: 38985188 PMCID: PMC11236881 DOI: 10.1007/s00122-024-04684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 06/25/2024] [Indexed: 07/11/2024]
30
Adak A, DeSalvio AJ, Arik MA, Murray SC. Field-based high-throughput phenotyping enhances phenomic and genomic predictions for grain yield and plant height across years in maize. G3 (BETHESDA, MD.) 2024;14:jkae092. [PMID: 38776257 PMCID: PMC11228873 DOI: 10.1093/g3journal/jkae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 04/24/2024] [Indexed: 05/24/2024]
31
Gaur A, Jindal Y, Singh V, Tiwari R, Juliana P, Kaushik D, Kumar KJY, Ahlawat OP, Singh G, Sheoran S. GWAS elucidated grain yield genetics in Indian spring wheat under diverse water conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:177. [PMID: 38972024 DOI: 10.1007/s00122-024-04680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
32
Ali B, Huguenin-Bizot B, Laurent M, Chaumont F, Maistriaux LC, Nicolas S, Duborjal H, Welcker C, Tardieu F, Mary-Huard T, Moreau L, Charcosset A, Runcie D, Rincent R. High-dimensional multi-omics measured in controlled conditions are useful for maize platform and field trait predictions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:175. [PMID: 38958724 DOI: 10.1007/s00122-024-04679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024]
33
Sadeh R, Ben-David R, Herrmann I, Peleg Z. Spectral-genomic chain-model approach enhances the wheat yield component prediction under the Mediterranean climate. PHYSIOLOGIA PLANTARUM 2024;176:e14480. [PMID: 39187437 DOI: 10.1111/ppl.14480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 08/28/2024]
34
Tiezzi F, Goda K, Morgante F. Using lifestyle information in polygenic modeling of blood pressure traits: a simple method to reduce bias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597631. [PMID: 38895222 PMCID: PMC11185601 DOI: 10.1101/2024.06.05.597631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
35
Carvalho HF, Rio S, García-Abadillo J, Isidro Y Sánchez J. Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators. PLANT METHODS 2024;20:85. [PMID: 38844940 PMCID: PMC11155189 DOI: 10.1186/s13007-024-01207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/08/2024] [Indexed: 06/10/2024]
36
Resende RT, Hickey L, Amaral CH, Peixoto LL, Marcatti GE, Xu Y. Satellite-enabled enviromics to enhance crop improvement. MOLECULAR PLANT 2024;17:848-866. [PMID: 38637991 DOI: 10.1016/j.molp.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
37
Montesinos-López OA, Crespo-Herrera L, Pierre CS, Cano-Paez B, Huerta-Prado GI, Mosqueda-González BA, Ramos-Pulido S, Gerard G, Alnowibet K, Fritsche-Neto R, Montesinos-López A, Crossa J. Feature engineering of environmental covariates improves plant genomic-enabled prediction. FRONTIERS IN PLANT SCIENCE 2024;15:1349569. [PMID: 38812738 PMCID: PMC11135473 DOI: 10.3389/fpls.2024.1349569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/11/2024] [Indexed: 05/31/2024]
38
Peixoto MA, Leach KA, Jarquin D, Flannery P, Zystro J, Tracy WF, Bhering L, Resende MFR. Utilizing genomic prediction to boost hybrid performance in a sweet corn breeding program. FRONTIERS IN PLANT SCIENCE 2024;15:1293307. [PMID: 38726298 PMCID: PMC11080654 DOI: 10.3389/fpls.2024.1293307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024]
39
Liu X, Wang M, Qin J, Liu Y, Wang S, Wu S, Zhang M, Zhong J, Wang J. GbyE: an integrated tool for genome widely association study and genome selection based on genetic by environmental interaction. BMC Genomics 2024;25:386. [PMID: 38641604 PMCID: PMC11027269 DOI: 10.1186/s12864-024-10310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/15/2024] [Indexed: 04/21/2024]  Open
40
Alemu A, Åstrand J, Montesinos-López OA, Isidro Y Sánchez J, Fernández-Gónzalez J, Tadesse W, Vetukuri RR, Carlsson AS, Ceplitis A, Crossa J, Ortiz R, Chawade A. Genomic selection in plant breeding: Key factors shaping two decades of progress. MOLECULAR PLANT 2024;17:552-578. [PMID: 38475993 DOI: 10.1016/j.molp.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/22/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
41
Crozier D, Winans ND, Hoffmann L, Patil NY, Klein PE, Klein RR, Rooney WL. Evaluating and Predicting the Performance of Sorghum Lines in an Elite by Exotic Backcross-Nested Association Mapping Population. PLANTS (BASEL, SWITZERLAND) 2024;13:879. [PMID: 38592905 PMCID: PMC10975396 DOI: 10.3390/plants13060879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/09/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
42
Araújo MS, Chaves SFS, Dias LAS, Ferreira FM, Pereira GR, Bezerra ARG, Alves RS, Heinemann AB, Breseghello F, Carneiro PCS, Krause MD, Costa-Neto G, Dias KOG. GIS-FA: an approach to integrating thematic maps, factor-analytic, and envirotyping for cultivar targeting. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:80. [PMID: 38472532 DOI: 10.1007/s00122-024-04579-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/06/2024] [Indexed: 03/14/2024]
43
Toda Y, Sasaki G, Ohmori Y, Yamasaki Y, Takahashi H, Takanashi H, Tsuda M, Kajiya-Kanegae H, Tsujimoto H, Kaga A, Hirai M, Nakazono M, Fujiwara T, Iwata H. Reaction norm for genomic prediction of plant growth: modeling drought stress response in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024;137:77. [PMID: 38460027 PMCID: PMC10924738 DOI: 10.1007/s00122-024-04565-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 03/11/2024]
44
Lopez-Cruz M, Pérez-Rodríguez P, de los Campos G. A fast algorithm to factorize high-dimensional tensor product matrices used in genetic models. G3 (BETHESDA, MD.) 2024;14:jkae001. [PMID: 38180089 PMCID: PMC11090460 DOI: 10.1093/g3journal/jkae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
45
Guo T, Wei J, Li X, Yu J. Environmental context of phenotypic plasticity in flowering time in sorghum and rice. JOURNAL OF EXPERIMENTAL BOTANY 2024;75:1004-1015. [PMID: 37819624 PMCID: PMC10837014 DOI: 10.1093/jxb/erad398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/17/2023] [Indexed: 10/13/2023]
46
Kang HI, Kim IS, Shim D, Kang KS, Cheon KS. Genomic selection for growth characteristics in Korean red pine (Pinus densiflora Seibold & Zucc.). FRONTIERS IN PLANT SCIENCE 2024;15:1285094. [PMID: 38322820 PMCID: PMC10844423 DOI: 10.3389/fpls.2024.1285094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024]
47
Barreto CAV, das Graças Dias KO, de Sousa IC, Azevedo CF, Nascimento ACC, Guimarães LJM, Guimarães CT, Pastina MM, Nascimento M. Genomic prediction in multi-environment trials in maize using statistical and machine learning methods. Sci Rep 2024;14:1062. [PMID: 38212638 PMCID: PMC10784464 DOI: 10.1038/s41598-024-51792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/09/2024] [Indexed: 01/13/2024]  Open
48
Lopez-Cruz M, Aguate FM, Washburn JD, de Leon N, Kaeppler SM, Lima DC, Tan R, Thompson A, De La Bretonne LW, de Los Campos G. Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America. Nat Commun 2023;14:6904. [PMID: 37903778 PMCID: PMC10616096 DOI: 10.1038/s41467-023-42687-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023]  Open
49
Lozano AC, Ding H, Abe N, Lipka AE. Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops. BMC Bioinformatics 2023;24:399. [PMID: 37884874 PMCID: PMC10604903 DOI: 10.1186/s12859-023-05519-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/03/2023] [Indexed: 10/28/2023]  Open
50
Bartholomé J, Frouin J, Brottier L, Cao TV, Boisnard A, Ahmadi N, Courtois B. Genomic selection for salinity tolerance in japonica rice. PLoS One 2023;18:e0291833. [PMID: 37756295 PMCID: PMC10530037 DOI: 10.1371/journal.pone.0291833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]  Open
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