Multimodal deep learning methods enhance genomic prediction of wheat breeding
文献类型: 外文期刊
第一作者: Montesinos-Lopez, Abelardo
作者: Montesinos-Lopez, Abelardo;Rivera, Carolina;Pinto, Francisco;Pinera, Francisco;Gonzalez, David;Reynolds, Mathew;Crossa, Jose;Perez-Rodriguez, Paulino;Crossa, Jose;Li, H.;Li, H.;Montesinos-Lopez, Osval A.
作者机构:
关键词: conventional genomic prediction method; novel deep learning method; genomic prediction accuracy (GP accuracy)
期刊名称:G3-GENES GENOMES GENETICS ( 影响因子:2.6; 五年影响因子:3.0 )
ISSN: 2160-1836
年卷期: 2023 年 13 卷 5 期
页码:
收录情况: SCI
摘要: While several statistical machine learning methods have been developed and studied for assessing the genomic prediction (GP) accuracy of unobserved phenotypes in plant breeding research, few methods have linked genomics and phenomics (imaging). Deep learning (DL) neural networks have been developed to increase the GP accuracy of unobserved phenotypes while simultaneously accounting for the complexity of genotype-environment interaction (GE); however, unlike conventional GP models, DL has not been investigated for when genomics is linked with phenomics. In this study we used 2 wheat data sets (DS1 and DS2) to compare a novel DL method with conventional GP models. Models fitted for DS1 were GBLUP, gradient boosting machine (GBM), support vector regression (SVR) and the DL method. Results indicated that for 1 year, DL provided better GP accuracy than results obtained by the other models. However, GP accuracy obtained for other years indicated that the GBLUP model was slightly superior to the DL. DS2 is comprised only of genomic data from wheat lines tested for 3 years, 2 environments (drought and irrigated) and 2-4 traits. DS2 results showed that when predicting the irrigated environment with the drought environment, DL had higher accuracy than the GBLUP model in all analyzed traits and years. When predicting drought environment with information on the irrigated environment, the DL model and GBLUP model had similar accuracy. The DL method used in this study is novel and presents a strong degree of generalization as several modules can potentially be incorporated and concatenated to produce an output for a multi-input data structure.
分类号:
- 相关文献
作者其他论文 更多>>
-
Deep learning methods improve genomic prediction of wheat breeding
作者:Montesinos-Lopez, Abelardo;Ramos-Pulido, Sofia;Crespo-Herrera, Leonardo;Dreisigacker, Susanna;Gerard, Guillermo;Vitale, Paolo;Saint Pierre, Carolina;Govindan, Velu;Tarekegn, Zerihun Tadesse;Crossa, Jose;Flores, Moises Chavira;Perez-Rodriguez, Paulino;Crossa, Jose;Lillemo, Morten;Li, Huihui;Montesinos-Lopez, Osval A.
关键词:GBLUP model; genomic prediction; multi-modal deep learning model; machine learning methods; relationship matrices
-
Wheat genetic resources have avoided disease pandemics, improved food security, and reduced environmental footprints: A review of historical impacts and future opportunities
作者:King, Julie;Grewal, Surbhi;King, Ian P.;Dreisigacker, Susanne;Reynolds, Matthew;Bandyopadhyay, Anindya;Braun, Hans-Joachim;Crespo-Herrera, Leonardo;Crossa, Jose;Govindan, Velu;Huerta, Julio;Ibba, Maria Itria;Saint Pierre, Carolina;Singh, Pawan K.;Singh, Ravi P.;Achary, V. Mohan Murali;Bhavani, Sridhar;Blasch, Gerald;Gerard, Guillermo;He, Xinyao;Hearne, Sarah;Hodson, David;Jalal Kamali, Mohammad Reza;Karwat, Hannes;Kommerell, Victor Maurice;Pixley, Kevin;Rivera-Amado, Carolina;Sansaloni, Carolina;Schulthess, Urs;Tiwari, Thakur Prasad;Crossa, Jose;Perez-Rodriguez, Paulino;Huerta, Julio;Robles-Zazueta, Carlos A.;Singh, Ravi P.;Lan, Caixia;Cheng, Shifeng;Dempewolf, Hannes;Kishii, Masahiro;Subbarao, Guntar;Flavell, Richard B.;Griffiths, Simon;Nicholson, Paul;Uauy, Cristobal;Hawkesford, Malcolm;Shewry, Peter;Howell, Phil;Kilian, Benjamin;Sharma, Shivali;Lagudah, Evans;Rebetzke, Greg;Montesinos-Lopez, Osval A.;Pinto, Francisco;Schulthess, Urs;Trethowan, Richard
关键词:climate resilience; input use efficiency; less fungicide dependence; rust epidemics; widening crop gene pools
-
New wheat breeding paradigms for a warming climate
作者:Xiong, Wei;Wang, Daowen;Chen, Feng;Xiong, Wei;Reynolds, Matthew P.;Montes, Carlo;Crossa, Jose;Snapp, Sieglinde;Li, Huihui;He, Zhonghu;Akin, Beyhan;Mesut, Keser;Ozdemir, Fatih;Li, Huihui;He, Zhonghu
关键词:
-
Low-depth Raw Reads of Nanopore Sequencing Enables Rapid and Accurate Bacterial Identification
作者:Gao, W.;Hong, W.;Wu, Y.;Liu, Y.;Fan, X.;Wang, H.;Wang, M.;Yang, B.;Wang, T.;Li, H.;Liu, S.;Li, J.
关键词:assembly; reads; Nanopore sequencing; Illumina sequencing; bacterial identification
-
Global consortium for the classification of fungi and fungus-like taxa
作者:Hyde, K. D.;Dai, D. Q.;Du, T. Y.;Li, Q.;Liu, X. F.;Tibpromma, S.;Wijayawardene, N. N.;Hyde, K. D.;Absalan, S.;Afshari, N.;Amuhenage, T. B.;Apurillo, C. C. S.;Armand, A.;Asghari, R.;Bera, I;Bhunjun, C. S.;Boonmee, S.;Bundhun, D.;Chaharmiri-Dokhaharani, S.;Chen, C.;Chethana, K. W. T.;Du, T. Y.;Gajanayake, A. J.;Gentekaki, E.;Gomdola, D.;Gomes de Farias, A. R.;Gunarathne, A.;He, S.;Huanraluek, N.;Hurdeal, V. G.;Jayawardena, R. S.;Karimi, O.;Khyaju, S.;Lestari, A. S.;Li, C. J. Y.;Li, H.;Li, L.;Li, Y. X.;Liao, C. F.;Linn, M. M.;Lu, L.;Luangharn, T.;Luo, L.;Ma, J.;Madagammana, A. D.;Mapook, A.;Marasinghe, D. S.;Meng, Q. F.;Mukhopadyay, S.;Noorabadi, M. T.;Norphanphoun, C.;Pem, D.;Perera, R. H.;Phonemany, M.;Phukhamsakda, C.;Phutthacharoen, K.;Rathnayaka, A. R.;Samarakoon, B. C.;Seifollahi, E.;Su, H. L.;Sun, Y. R.;Sysouphanthong, P.;Tan, T. H.;Tang, X.;Tavakol, N. M.;Thiyagaraja, V;Thongklang, N.;Walker, A.;Wannasawang, N.;Wijesinghe, S. N.;Wu, N.;Xiong, Y. R.;Xu, R. F.;Xu, R. J.;Yang, H. D.;Yang, J.;Yang, Y. H.;Yasanthika, E.;Yu, F. M.;Zeng, M.;Zhang, F.;Zhang, J. Y.;Zin, H. H.;Hyde, K. D.;Amuhenage, T. B.;Apurillo, C. C. S.;Armand, A.;Asghari, R.;Bhunjun, C. S.;Boonmee, S.;Bundhun, D.;Chen, C.;Chethana, K. W. T.;Gajanayake, A. J.;Gentekaki, E.;Gomdola, D.;Gunarathne, A.;He, S.;Hurdeal, V. G.;Jayawardena, R. S.;Karimi, O.;Khyaju, S.;Lestari, A. S.;Li, C. J. Y.;Li, H.;Li, L.;Li, Y. X.;Liao, C. F.;Linn, M. M.;Liu, X. F.;Luo, L.;Ma, J.;Madagammana, A. D.;Meng, Q. F.;Mukhopadyay, S.;Pem, D.;Phonemany, M.;Phutthacharoen, K.;Samarakoon, B. C.;Su, H. L.;Sun, Y. R.;Tang, X.;Thongklang, N.;Walker, A.;Wu, N.;Xiong, Y. R.;Xu, R. F.;Xu, R. J.;Yang, H. D.;Yang, Y. H.;Yasanthika, E.;Yu, F. M.;Zeng, M.;Zhang, F.;Zhang, J. Y.;Zin, H. H.;Abdel-Wahab, M. A.;Abdollahzadeh, J.;Abeywickrama, P. D.;Yan, J. Y.;Zhang, W.;Absalan, S.;Afshari, N.;de Silva, N., I;Lumyong, S.;Promputtha, I;Tennakoon, D. S.;Ainsworth, A. M.;Kirk, P. M.;Liimatainen, K.;Akulov, O. Y.;Aleoshin, V. V.;Mikhailov, K., V;Aleoshin, V. V.;Mikhailov, K., V;Al-Sadi, A. M.;Thamodini, G. K.;Alvarado, P.;Alves, A.;Amalfi, M.;De Kesel, A.;Ertz, D.;Haelewaters, D.;Amalfi, M.;Ertz, D.;Amira, Y.;Anderson, J. L.;Antonin, V;Aouali, S.;Aptroot, A.;Apurillo, C. C. S.;Araujo, J. P. M.;Ariyawansa, H. A.;Arumugam, E.;Gunaseelan, S.;Kaliyaperumal, M.;Kezo, K.;Murugadoss, R.;Assis, D. M. A.;Barbosa, R. N.;da Silva, D. K. A.;da Silva, G. A.;da Silva, R. M. F.;da Silva Santos, A. C.;de Oliveira, N. T.;Diniz, A. G.;Gibertoni, T. B.;Machado, A. R.;Malosso, E.;Meiras-Ottoni, A.;Melo, R. F. R.;Mendes-Alvarenga, R. L.;Santiago, A. L. C. M. A.;Souza-Motta, C. M.;Tiago, P., V;Vieira, L. C.;Atienza, V;Garrido-Benavent, I;Avasthi, S.;Azevedo, E.;Caeiro, M. F.;Azevedo, E.;Caeiro, M. F.;Bahkali, A. H.;Bhat, D. J.;Jones, E. B. G.;Bakhshi, M.;Zare, R.;Banihashemi, Z.;Bao, D. F.;Luo, Z. L.;Shen, H. W.;Baral, H. O.;Barata, M.;Barata, M.;Barbosa, F. R.;Barreto, R. W.;Thines, M.;Thines, M.;Thines, M.;Belamesiatseva, D. B.;Shabashova, T. G.;Bennett Reuel, M.;dela Cruz, T. E. E.;Bennett Reuel, M.;Bezerra, J. D. P.;Bezerra, J. D. P.;Bezerra, J. L.;Bhat, D. J.;Bianchinotti, M., V;Blaszkowski, J.;Boekhout, T.;Tedersoo, L.;Bonito, G.;Boonyuen, N.;Luangsa-ard, J. J.;Bregant, C.;Linaldeddu, B. T.;Buchanan, P.;Johnston, P. R.;McKenzie, E. H. C.;Burgaud, G.;Jany, J. L.;Burgess, T.;Buyck, B.;Cabarroi-Hernandez, M.;Castro-Jauregui, O.;Cortes-Perez, A.;Guzman-Davalos, L.;Ramirez-Cruz, V;Caceres, M. E. S.;Zhang, J. F.;Cai, L.;Raza, M.;Wei, X. L.;Cai, M. F.;Calabon, M. S.;Calaca, F. J. S.;Calaca, F. J. S.;Callalli, M.;Callalli, M.;Callalli, M.;Camara, M. P. S.;Cano-Lira, J. F.;Cantillo, T.;Cao, B.;He, M. Q.;Liu, F.;Liu, S. L.;Wang, K.;Zhao, R. L.;Zhou, L. W.;Carlavilla, J. R.;Carvalho, A.;Castaneda-Ruiz, R. F.;Castlebury, L.;Catania, M. D., V;Cavalcanti, L. H.;Cazabonne, J.;Cazabonne, J.;Cedeno-Sanchez, M. L.;Chaiwan, N.;Chakraborty, N.;Chaverri, P.;Chaverri, P.;Cheewangkoon, R.;Samarakoon, M. C.;Thiyagaraja, V;Chen, C. Y.;Chen, K. H.;Chen, Q.;Chen, W. H.;Chen, Y. P.;Dissanayake, A. J.;Li, W. L.;Liu, J. K.;Maharachchikumbura, S. S. N.;Tian, Q.;Tian, W. H.;Wu, N.;Yu, X. D.;Yu, Y. X.;Zhang, S. N.;Coleine, C.;Li, C. J. Y.;Selbmann, L.;Conde, T. O.;Corazon-Guivin, M. A.;Corazon-Guivin, M. A.;Costa-Rezende, D. H.;Courtecuisse, R.;Crouch, J. A.;Crous, P. W.;Groenewald, J. Z.;Groenewald, M.;Herandez-Restrepo, M.;Houbraken, J.;Sandoval-Denis, M.;Cui, B. K.;Dai, Y. C.;He, S. H.;Li, Y.;Liu, S.;Liu, Z. B.;Song, C. G.;Sun, Y. F.;Wang, C. G.;Xu, T. M.;Yuan, Y.;Zhang, Q. Y.;Zhang, Y.;Zhao, H.;Zhou, M.;Cui, Y. Y.;Ge, Z-W;He, S.;Li, Y. C.;Luo, L.;Su, H. L.;Wang, X. Y.;Worthy, F. R.;Xu, R. F.;Xu, R. J.;Cui, Y. Y.;Li, Y. C.;Wang, X. Y.;Worthy, F. R.;Wu, G.;da Silva, I. R.;Anderson, J. L.;Fernandes, I;Fryar, S. C.;Damm, U.;Darmostuk, V;Flakus, A.;Janik, P.;Rodriguez-Flakus, P.;Ronikier, A.;Zoha, Daroodi;Das, K.;Das, K.;Davoodian, N.;Davydov, E. A.;Dayarathne, M. C.;Decock, C.;Blondelle, A.;de Groot, M. D.;De Lange, R.;Haelewaters, D.;Santamaria, B.;Schoutteten, N.;Sulistyo, B.;Van Caenegem, W.;de Groot, M. D.;Zamora, J. C.;Karakehian, J. M.;Delgado, G.;Denchev, C. M.;Denchev, T. T.;de Silva, N., I;Tennakoon, D. S.;de Souza, F. A.;Dentinger, B.;Devadatha, B.;Devadatha, B.;Dianese, J. C.;Dima, B.;Dissanayake, L. S.;Dogan, H. H.;Chen, C.;Doilom, M.;Dong, W.;Dong, Z. Y.;Li, H.;Li, Y. X.;Liao, C. F.;Luo, M.;Manawasinghe, I. S.;Xiong, Y. R.;Xu, B.;Yang, Y. H.;Zhang, Y. X.;Dolatabadi, S.;Ma, J.;Nanayakkara, C. M.;Dos Santos, L. A.;Alves-Silva, G.;Drechsler-Santos, E. R.;Dubey, M. K.;Dutta, A. K.;Egidi, E.;Elliott, T. F.;Elshahed, M. S.;Youssef, N. H.;Erdogdu, M.;Etayo, J.;Evans, H. C.;Fan, X. L.;Fan, Y. G.;Fedosova, A. G.;Zhurbenko, M. P.;Fell, J.;Fernandes, I;Fernandes, I;Firmino, A. L.;Fiuza, P. O.;Xu, R.;Fragoso de Souza, C. A.;Frisvad, J. C.;Fryar, S. C.;Gabaldon, T.;Torruella, G.;Gabaldon, T.;Torruella, G.;Gabaldon, T.;Gabaldon, T.;Gannibal, P. B.;Gannibal, P. B.;Garcia, D.;Gene, D. J.;Garcia, D.;Gene, D. J.;Garcia-Sandoval, S. R.;Garcia-Sandoval, S. R.;Senanayake, I. C.;Garzoli, L.;Gautam, A. K.;Wu, H. X.;Ghobad-Nejhad, M.;Giachini, A. J.;Goes-Neto, A.;Galindo, L. J.;Gorjon, S. P.;Goto, B. T.;Granados-Montero, M. M.;Granados-Montero, M. M.;Griffith, G. W.;Grossart, H. P.;Grossart, H. P.;Gueidan, C.;Baschien, C.;Yurkov, A.;Gusmao, L. F. P.;Gutierrez, A. C.;Chen, J.;Haelewaters, D.;Haelewaters, D.;Halling, R.;Halling, R.;Han, Y. F.;Hapuarachchi, K. K.;Zhao, C. L.;Harder, C. B.;Harrington, T. C.;Hattori, T.;Wu, W. P.;Healy, R.;Heredia, G.;Hodge, K. T.;Iturriaga, T.;Holgado-Rojas, M.;Holgado-Rojas, M.;Holgado-Rojas, M.;Hongsanan, S.;Hongsanan, S.;Horak, E.;Horak, E.;Hosoya, T.;Takamatsu, S.;Huang, S. K.;Hur, J. S.;Hustad, V. P.;Iotti, M.;Leonardi, M.;Rossi, W.;Jafar, E.;Xu, R.;Jayalal, R. G. U.;Jayasiri, S. C.;Jayawardena, R. S.;Jeewon, R.;Jeewon, R.;Jin, J.;Zafari, D.;Jones, E. B. G.;Zhang, H.;Justo, A.;Kaishian, P.;Kakishima, M.;Piepenbring, M.;Kang, G. P.;Tan, T. H.;Kang, G. P.;Tan, T. H.;Kang, J. C.;Karpov, S. A.;Karunarathna, S. C.;Kaufmann, M.;Kemler, M.;Kirchmair, M.;Neuhauser, S.;Peintner, U.;Zucconi, L.;Kitaura, M. J.;Klawonn, I;Kolarik, M.;Kong, A.;Kuhar, F.;Kukwa, M.;Kumar, S.;Kusan, I;Matocec, N.;Mesic, A.;Posta, A.;Tkalcec, Z.;Lado, C.;Larsson, K. H.;Larsson, K. H.;Latha, K. P. D.;Leontyev, D. L.;Leontyev, D. L.;Lestari, A. S.;Li, D. W.;Li, H. Y.;Li, L.;Lu, Y. Z.;Ma, J.;Zhang, J. Y.;Li, Q. R.;Wurzbacher, C.;Xiao, Y. P.;Lee, H. B.;Wijayawardene, N. N.;Lim, Y. W.;Lim, Y. W.;Lin, C. G.;Linde, C. C.;Liu, N. G.;Liu, N. G.;Liu, X. Y.;Liu, X. Z.;Wisitrassameewong, K.;Lumbsch, H. T.;Lumyong, S.;Lumyong, S.;White, J. F.;Zeng, N. K.;Madrid, H.;Magurno, F.;Magyar, D.;Mahadevan, N.;Mahadevan, N.;Maharachchikumbura, S. S. N.;Maimaiti, Y.;Raza, M.;Manamgoda, D. S.;Udayanga, D.;Wartchow, F.;Mardones, M.;Cedeno-Sanchez, M. L.;Marin-Felix, Y.;Stadler, M.;Cedeno-Sanchez, M. L.;Marin-Felix, Y.;Stadler, M.;Marquez, R.;Masigol, H.;May, T. W.;Yuan, H. S.;Mendieta, S.;Meng, Q. F.;Menkis, A.;Menolli, N., Jr.;Nascimento, C. C.;Silva-Filho, A. G. S.;Meza Calvo, J. G.;Miller, S. L.;Moncada, B.;Moncada, B.;Moncalvo, J. M.;Moncalvo, J. M.;Monteiro, J. S.;Monteiro, J. S.;Monteiro, M.;Mora-Montes, H. M.;Moreau, P. A.;Mueller, G. M.;Nagy, L. G.;Najafiniya, M.;Nascimento, C. C.;Nei, Y.;Neves, M. A.;Niego, A. G. T.;Nilsson, R. H.;Niskanen, T.;Niveiro, N.;Noordeloos, M. E.;Noordeloos, M. E.;Nunez Otano, N. B.;O'Donnell, R. P.;Oehl, F.;Olariaga, I;Orlando, O. P.;Pang, K. L.;Pang, K. L.;Papp, V;Pawlowska, J.;Pereira, O. L.;Perera, R. H.;Perera, R. H.;Perez-Moreno, J.;Perez-Ortega, S.;Peter, G.;Phillips, A. J. L.;Jeronimo, G. H.;Jesus, A. L.;Pires-Zottarelli, C. L. A.;Poinar, G.;Prieto, M.;Quandt, C. A.;Radek, R.;Rahnama, K.;Raj, K. N. A.;Rajeshkumar, K. C.;Sruthi, O. P.;Rama, T.;Rama, T.;Rambold, G.;Rasconi, S.;Ren, G. C.;Ren, G. C.;Robledo, G. L.;Flakus, A.;Rodriguez-Flakus, P.;Ryberg, M.;Ryvarden, L. R.;Salvador-Montoya, C. A.;Samant, B.;Sanchez-Castro, I;Sanchez-Garcia, M.;Sarma, V. V.;Savchenko, A.;Savchenko, K.;Saxena, R. K.;Scholler, M.;Selbmann, L.;Selcuk, F.;Senanayake, I. C.;Shen, Y. M.;Simmons, D. R.;Singh, R.;Sir, E. B.;Yu, Q.;Stemler, J.;Stemler, J.;Stemler, J.;Stemler, J.;Stephenson, S. L.;Strassert, J. F. H.;Su, L.;Su, L.;Suetrong, S.;Norphanphoun, C.;Sun, Y. R.;Wang, Y.;Zeng, X. Y.;Svantesson, S.;Svantesson, S.;Takamatsu, S.;Tanaka, K.;Tang, A. M. C.;Tang, X.;Wei, D. P.;Tanney, J. B.;Taylor, J. E.;Taylor, P. W. J.;Tedersoo, L.;Zhang, F.;Zhang, J. F.;Thiyagaraja, V;Wanasinghe, D. N.;Tibell, L.;Tibell, S.;Tomsovsky, M.;Toome-Heller, M.;Yakovchenko, L.;Yang, H. D.;Yang, Z. L.;Yu, F. M.;Zeng, M.;Zhao, Q.;Tsurykau, A.;Tsurykau, A.;Untereiner, W. A.;Uzunov, B. A.;Valle, L. G.;Van den Wyngaert, S.;Van Vooren, N.;Velez, P.;Verma, R. K.;Vieira, W. A. S.;Vizzini, A.;Walker, A. K.;Yapa, N.;Joshi, Y.;Wang, S. X.;Wijesundara, D. S. A.;Xu, L. J.;Yu, Z. F.
关键词:classification; nomenclature; scientific criticism; taxonomy
-
Ethephon Stimulation on Trunk Leads to Leaf Physiological Changes in Rubber Tree Seedlings
作者:Li, H.;Chen, H.;Kang, X.;Liu, C.;Huang, J.
关键词:Hevea brasiliensis Muell; Arg; Enzymes activity; Photosynthesis; Starch; Sucrose
-
DNNGP, a deep neural network-based method for genomic prediction using multi-omics data in plants
作者:Wang, Kelin;Rasheed, Awais;Li, Huihui;Wang, Kelin;Abid, Muhammad Ali;Li, Huihui;Rasheed, Awais;Crossa, Jose;Hearne, Sarah
关键词:deep learning; genomic selection; multi-omics data; prediction method