Article
Biotechnology & Applied Microbiology
Martijn F. L. Derks, Christian Gross, Marcos S. Lopes, Marcel J. T. Reinders, Mirte Bosse, Arne B. Gjuvsland, Dick de Ridder, Hendrik-Jan Megens, Martien A. M. Groenen
Summary: The genotype-phenotype link is complex and important in life sciences. Pigs are a valuable model for studying causal variations and molecular pathways underlying important phenotypes, and a new approach has been proposed in this study to accelerate the discovery of novel causal variants and molecular mechanisms affecting these phenotypes.
Article
Genetics & Heredity
David Gonzalez-Dieguez, Andres Legarra, Alain Charcosset, Laurence Moreau, Christina Lehermeier, Simon Teyssedre, Zulma G. Vitezica
Summary: This study revisited the theory of hybrid genetic evaluation models in a genomic context and found that GCA accounts for most variation in hybrids, while variances due to dominance and epistasis have similar magnitudes. Different models based on defining effects showed similar predictive abilities for hybrids.
Article
Plant Sciences
Germano Costa-Neto, Jose Crossa, Roberto Fritsche-Neto
Summary: Quantitative genetics explains that phenotypic variation is a result of the interaction between genetic and environmental factors. Predictive breeding based on this theory has led to the development of an enviromic assembly approach, which combines ecophysiology knowledge to enhance whole-genome predictions for plant breeding. This approach aims to more accurately represent the putative phenotypic variation observed across diverse growing conditions and has shown better performance than traditional genetic predictions, especially with smaller training sets.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Osval A. Montesinos-Lopez, Leonardo Crespo-Herrera, Carolina Saint Pierre, Alison R. Bentley, Roberto de la Rosa-santamaria, Jose Alejandro Ascencio-Laguna, Afolabi Agbona, Guillermo S. Gerard, Abelardo Montesinos-Lopez, Jose Crossa
Summary: This study investigates the integration of environmental information with genotypic information in genomic selection (GS) and proposes the use of feature selection methods for this purpose. Results show that the optimal incorporation of environmental covariates using feature selection significantly improves prediction accuracy in most cases, providing empirical evidence for the use of feature selection in GS to enhance prediction power.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Abelardo Montesinos-Lopez, Daniel E. Runcie, Maria Itria Ibba, Paulino Perez-Rodriguez, Osval A. Montesinos-Lopez, Leonardo A. Crespo, Alison R. Bentley, Jose Crossa
Summary: Implementing genomic-based prediction models in genomic selection involves understanding how to evaluate prediction accuracy from different models and methods using multi-trait data. This study compared prediction accuracy using six large multi-trait wheat datasets and found that a corrected Pearson's correlation method was more accurate than the traditional method. For grain yield, using a multi-trait model yielded higher prediction performance compared to a single-trait model, with the benefits increasing as genetic correlations between traits strengthen.
G3-GENES GENOMES GENETICS
(2021)
Article
Plant Sciences
Abdulqader Jighly, Matthew Hayden, Hans Daetwyler
Summary: The new 3GS model significantly improves prediction accuracy for deviated environments with low to negative correlations to other environments, predicts new genotypes in unobserved environments with high accuracy, and has linearly increasing computational complexity with the number of environments and population size, making it much faster than standard models for large data sets.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Genetics & Heredity
Marnin D. Wolfe, Ariel W. Chan, Peter Kulakow, Ismail Rabbi, Jean-Luc Jannink
Summary: The study introduced genomic mate selection criteria suitable for organisms of arbitrary homozygosity level, successfully predicting the genetic distribution of cassava families. Breeders can now use predictions to select future parents and develop varieties.
Article
Genetics & Heredity
Morgane Roth, Aurelien Beugnot, Tristan Mary-Huard, Laurence Moreau, Alain Charcosset, Julie B. Fievet
Summary: This study aimed to test methodological developments for modeling inbreeding and nonadditive effects, and found that inbreeding has a strong impact on plant traits and prediction models that include inbreeding and nonadditive parameters can improve prediction accuracy.
Article
Genetics & Heredity
Xabi Cazenave, Bernard Petit, Marc Lateur, Hilde Nybom, Jiri Sedlak, Stefano Tartarini, Francois Laurens, Charles-Eric Durel, Helene Muranty
Summary: In this study, the potential of combining genetic resources and elite material to construct a large training set with high genetic diversity for genomic selection in apple breeding was investigated. The study compared the predictive ability of different models within-population, across-population, and when combining both populations. The results showed that combining the two populations into a unique training set could slightly increase the predictive ability for some traits. The study also found that using an optimization algorithm to choose genotypes in the training set led to higher predictive abilities.
G3-GENES GENOMES GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Zipeng Zhang, Shaolei Shi, Qin Zhang, Gert P. Aamand, Mogens S. Lund, Guosheng Su, Xiangdong Ding
Summary: The size of the reference population is critical in improving the accuracy of genomic prediction. Combining reference populations from different breeding organizations has proven to be effective. Combining the Chinese and Nordic Holstein reference populations substantially improves genomic prediction accuracy for traits with high or moderate genetic correlations, but does not improve accuracy for traits with low genetic correlations in either population.
Article
Biochemistry & Molecular Biology
Marion Sinclair-Waters, Nikolai Piavchenko, Annukka Ruokolainen, Tutku Aykanat, Jaakko Erkinaro, Craig R. Primmer
Summary: Efforts to understand the genetic basis of phenotypic variation in molecular ecology are increasing. In Atlantic salmon, a study utilizing natural recombination between two candidate genes, vgll3 and akap11, found strong association between vgll3 single nucleotide polymorphisms (SNPs) and early maturation, while little or no association was found with akap11 SNPs. This suggests vgll3 as the primary candidate gene influencing early maturation.
Article
Genetics & Heredity
Susanne Dreisigacker, Paulino Perez-Rodriguez, Leonardo Crespo-Herrera, Alison R. Bentley, Jose Crossa
Summary: This study demonstrates the potential of rapid-cycle recurrent genomic selection (RCRGS) to increase grain yield in wheat, achieving a consistent genetic gain of 12.3% over 3 cycles of recombination.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Nicolay Leme da Cunha, Haoran Xue, Stephen Wright, Spencer C. H. Barrett
Summary: This study compares the genetic diversity of two related water hyacinth species, E. crassipes and E. azurea, and finds that the highly clonal E. crassipes exhibits lower clonal diversity and weaker genetic structure compared to the moderately clonal E. azurea.
Article
Plant Sciences
Bo Sun, Rui Guo, Zhi Liu, Xiaolei Shi, Qing Yang, Jiayao Shi, Mengchen Zhang, Chunyan Yang, Shugang Zhao, Jie Zhang, Jianhan He, Jiaoping Zhang, Jianhui Su, Qijian Song, Long Yan
Summary: In this study, genomic selection (GS) was used to predict protein and oil content in soybean. The prediction accuracy of oil content was found to be higher than that of protein content. The accuracy of prediction increased with the size of the training population and was improved when the training population had similar phenotype or close genetic relationships with the prediction population. The highest prediction accuracy for both protein and oil content was achieved when approximately 3,000 markers with -log(10)(P) greater than 1 were included.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Rachael M. Giglio, Tonie E. Rocke, Jorge E. Osorio, Emily K. Latch
Summary: Utah prairie dogs are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Genetic diversity is lower in low-elevation sites compared to high-elevation sites, with population divergence high among sites following an isolation-by-distance model. Genetic drift plays a substantial role in population divergence, despite environmental associations with outlier loci.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Agronomy
H. Chiango, N. Jafarikouhini, D. Pradhan, A. Figueiredo, J. Silva, T. R. Sinclair, J. Holland
Summary: This study tested maize genotypes released for production in southern Africa and identified four genotypes with specific soil water-conservation traits that show promise for increased yield under water-limited conditions. These genotypes are genetic resources for further research to improve maize drought resilience.
JOURNAL OF CROP IMPROVEMENT
(2022)
Article
Agronomy
Teclemariam Weldekidan, Heather Manching, Nicole Choquette, Natalia de Leon, Sherry Flint-Garcia, James Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, Major M. Goodman, Randall J. Wisser
Summary: Tropical strains of maize typically flower late in temperate environments, limiting diversification and improvement efforts in those regions. A parallel selection experiment spanning 28 degrees of latitude across the United States was conducted to investigate early flowering time adaptation. The resulting maize population offers a novel resource for breeders and researchers studying adaptation.
JOURNAL OF PLANT REGISTRATIONS
(2022)
Article
Agronomy
You Zhang, Ben Ovenden, Yao He, Wenwei Ye, Xianjun Wu, William James Peacock, Elizabeth S. Dennis
Summary: Hybrid vigour (heterosis) is an important breeding strategy in crop improvement programs, but its molecular mechanisms are not yet well understood. This study found that hybrid vigour in hybrids derived from certain rice varieties was approximately 40% greater than in the better parents at the early seedling stage. In addition, stable high-yielding lines were developed from these hybrids through selfing and recurrent selection. The importance of photosynthesis in early seedling development and its role in hybrid vigour were demonstrated.
Article
Plant Sciences
Nicole E. Choquette, James B. Holland, Teclemariam Weldekidan, Justine Drouault, Natalia de Leon, Sherry Flint-Garcia, Nick Lauter, Seth C. Murray, Wenwei Xu, Randall J. Wisser
Summary: Through experimental evolution in maize, this study investigated the response to selection and the possibility of moving plant germplasm across different geographical zones. The results showed that the flowering time of maize has plasticity, and different selection methods and photoperiods had significant effects on the selection outcomes. This study demonstrated the potential of phenotypic selection in rapidly shifting the phenology and plasticity of crops, and highlighted the importance of selecting crops to local conditions for climate change adaptation.
Review
Biochemistry & Molecular Biology
Andrew F. Bowerman, Caitlin S. Byrt, Stuart John Roy, Spencer M. Whitney, Jenny C. Mortimer, Rachel A. Ankeny, Matthew Gilliham, Dabing Zhang, Anthony A. Millar, Greg J. Rebetzke, Barry J. Pogson
Summary: This article reviews the impact of climate change on farming systems and discusses the traits and technologies needed to develop climate-resilient crops. It emphasizes the importance of public engagement and highlights the challenges of feeding a growing population under harsh and unpredictable climate conditions. It also emphasizes the need to prepare for floods, droughts, frosts, and heat waves, and advocates for modifying current practices and innovative breeding methods.
Review
Agronomy
Peter Langridge, Michael Alaux, Nuno Felipe Almeida, Karim Ammar, Michael Baum, Faouzi Bekkaoui, Alison R. Bentley, Brian L. Beres, Bettina Berger, Hans-Joachim Braun, Gina Brown-Guedira, Christopher James Burt, Mario Jose Caccamo, Luigi Cattivelli, Gilles Charmet, Peter Civan, Sylvie Cloutier, Jean-Pierre Cohan, Pierre J. Devaux, Fiona M. Doohan, M. Fernanda Dreccer, Moha Ferrahi, Silvia E. German, Stephen B. Goodwin, Simon Griffiths, Carlos Guzman, Hirokazu Handa, Malcolm John Hawkesford, Zhonghu He, Eric Huttner, Tatsuya M. Ikeda, Benjamin Kilian, Ian Philip King, Julie King, John A. Kirkegaard, Jacob Lage, Jacques Le Gouis, Suchismita Mondal, Ewen Mullins, Frank Ordon, Jose Ivan Ortiz-Monasterio, Hakan Ozkan, Irfan Ozturk, Silvia A. Pereyra, Curtis J. Pozniak, Hadi Quesneville, Martin C. Quincke, Greg John Rebetzke, Jochen Christoph Reif, Teresa Saavedra-Bravo, Ulrich Schurr, Shivali Sharma, Sanjay Kumar Singh, Ravi P. Singh, John W. Snape, Wuletaw Tadesse, Hisashi Tsujimoto, Roberto Tuberosa, Tim G. Willis, Xueyong Zhang
Summary: Wheat plays a crucial role in global food security by providing carbohydrates and protein, but faces threats from climate change and rising resource costs. The international wheat research community is working to find solutions to ensure global wheat production can meet demand.
Article
Green & Sustainable Science & Technology
Shilai Zhang, Guangfu Huang, Yujiao Zhang, Xiutao Lv, Kejiang Wan, Jian Liang, Yupeng Feng, Jinrong Dao, Shukang Wu, Lin Zhang, Xu Yang, Xiaoping Lian, Liyu Huang, Lin Shao, Jing Zhang, Shiwen Qin, Dayun Tao, Timothy E. Crews, Erik J. Sacks, Jun Lyu, Len J. Wade, Fengyi Hu
Summary: The successful breeding and cultivation of perennial rice provides an opportunity for sustainable development, increasing crop productivity, farmer livelihoods, and soil health while reducing resource use. Planting perennial rice not only improves crop yields but also accumulates organic carbon and nitrogen in the soil, thus improving soil quality. Farmers prefer cultivating perennial rice as it saves labor and input costs.
NATURE SUSTAINABILITY
(2023)
Article
Agronomy
J. Bancic, B. Ovenden, G. Gorjanc, D. J. Tolhurst
Summary: This paper develops a single-stage genomic selection approach that incorporates information on multiple traits and multiple environments within a partially separable factor analytic framework, providing breeders with an informative framework to utilize genotype by environment by trait interaction for efficient selection.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Multidisciplinary Sciences
Alice Feurtey, Cecile Lorrain, Megan C. McDonald, Andrew Milgate, Peter S. Solomon, Rachael Warren, Guido Puccetti, Gabriel Scalliet, Stefano F. F. Torriani, Lilian Gout, Thierry C. Marcel, Frederic Suffert, Julien Alassimone, Anna Lipzen, Yuko Yoshinaga, Christopher Daum, Kerrie Barry, Igor V. Grigoriev, Stephen B. Goodwin, Anne Genissel, Michael F. Seidl, Eva H. Stukenbrock, Marc-Henri Lebrun, Gert H. J. Kema, Bruce A. McDonald, Daniel Croll
Summary: Human activity affects the evolution of many species. Global trade of agricultural goods contributes to the spread of pathogens and alters their genetic makeup. Understanding how pathogens adapt and cope with new climates is crucial for predicting their impact on crop diseases.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
B. E. Stummer, B. M. Flohr, G. J. Rebetzke, R. Meiklejohn, A. Ware, B. Haskins, R. Whitworth, T. McBeath
Summary: Long coleoptile (LC) - wheat genotypes, sown deeper than current practice, enable earlier deep sowing into subsurface soil moisture. The LC genotype shows promise to broaden sowing windows and remove reliance on the shifting seasonal break for crop establishment. Investigation is needed to identify suitable environments for potential establishment benefits in the highly variable soils of the southern Australian wheatbelt.
ENVIRONMENTAL RESEARCH COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Dayane Cristina Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Bridget A. McFarland, Shawn Kaeppler, David Ertl, Maria Cinta Romay, Joseph L. Gage, James Holland, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint-Garcia, Candice N. Hirsch, Elizabeth Hood, David C. Hooker, Joseph E. Knoll, Judith M. Kolkman, Sanzhen Liu, John McKay, Richard Minyo, Danilo E. Moreta, Seth C. Murray, Rebecca Nelson, James C. Schnable, Rajandeep S. Sekhon, Maninder P. Singh, Peter Thomison, Addie Thompson, Mitchell Tuinstra, Jason Wallace, Jacob D. Washburn, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu, Natalia de Leon
Summary: This report presents the release of the 2018-2019 Maize G X E project datasets, which evaluate maize hybrids and inbred lines across different environments. The datasets include phenotypic, genotypic, environmental, and metadata information. Collaborators collected and verified the data before its release.
Article
Genetics & Heredity
Nicole E. Choquette, Teclemariam Weldekidan, Jason Brewer, Scott B. Davis, Randall J. Wisser, James B. Holland
Summary: Tropical maize can contribute to temperate breeding programs, but its adaptation to temperate environments requires extensive phenotypic selection. This study investigated the use of genomic selection in an off-season nursery to accelerate the incorporation of tropical diversity in temperate breeding pools. Prediction models were trained using flowering time data from diverse populations. The results showed that genomic selection in a single off-season generation can significantly increase genetic gains for flowering time in comparison to direct selection in summer seasons.
G3-GENES GENOMES GENETICS
(2023)
Article
Biology
Dayane Cristina Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Alden Perkins, Dylan L. Schoemaker, Martin Costa, Kathryn J. Michel, Shawn Kaeppler, David Ertl, Maria Cinta Romay, Joseph L. Gage, James Holland, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint-Garcia, Michael A. Gore, Candice N. Hirsch, Joseph E. Knoll, John Mckay, Richard Minyo, Seth C. Murray, James Schnable, Rajandeep S. Sekhon, Maninder P. Singh, Erin E. Sparks, Peter Thomison, Addie Thompson, Mitchell Tuinstra, Jason Wallace, Jacob D. Washburn, Teclemariam Weldekidan, Wenwei Xu, Natalia de Leon
Summary: The Maize GxE project aims to understand genotype by environment interactions and improve resource allocation efficiency and genotype predictability and stability through the collected information.
BMC RESEARCH NOTES
(2023)
Editorial Material
Biology
Dayane Cristina Lima, Jacob D. Washburn, Jose Ignacio Varela, Qiuyue Chen, Joseph L. Gage, Maria Cinta Romay, James Holland, David Ertl, Marco Lopez-Cruz, Fernando M. Aguate, Gustavo de los Campos, Shawn Kaeppler, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint-Garcia, Michael A. Gore, Candice N. Hirsch, Joseph E. Knoll, John McKay, Richard Minyo, Seth C. Murray, Osler A. Ortez, James C. Schnable, Rajandeep S. Sekhon, Maninder P. Singh, Erin E. Sparks, Addie Thompson, Mitchell Tuinstra, Jason Wallace, Teclemariam Weldekidan, Wenwei Xu, Natalia de Leon
Summary: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022, as well as soil, weather, environmental covariates data, and metadata information for all environments.
BMC RESEARCH NOTES
(2023)
Article
Agriculture, Multidisciplinary
J. De Faveri, A. P. Verbyla, G. Rebetzke
Summary: This study proposes an efficient and accurate approach for modeling genotype response over time and across environments, while considering non-genetic sources of variation such as spatial and temporal correlation. The approach provides robust genotype predictions, facilitates genotype selection and investigation of genotype by environment interaction (G x E) in different measurement times and trials.
CROP & PASTURE SCIENCE
(2023)