1
|
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]
Abstract
KEY MESSAGE We propose an "enviromics" prediction model for recommending cultivars based on thematic maps aimed at decision-makers. Parsimonious methods that capture genotype-by-environment interaction (GEI) in multi-environment trials (MET) are important in breeding programs. Understanding the causes and factors of GEI allows the utilization of genotype adaptations in the target population of environments through environmental features and factor-analytic (FA) models. Here, we present a novel predictive breeding approach called GIS-FA, which integrates geographic information systems (GIS) techniques, FA models, partial least squares (PLS) regression, and enviromics to predict phenotypic performance in untested environments. The GIS-FA approach enables: (i) the prediction of the phenotypic performance of tested genotypes in untested environments, (ii) the selection of the best-ranking genotypes based on their overall performance and stability using the FA selection tools, and (iii) the creation of thematic maps showing overall or pairwise performance and stability for decision-making. We exemplify the usage of the GIS-FA approach using two datasets of rice [Oryza sativa (L.)] and soybean [Glycine max (L.) Merr.] in MET spread over tropical areas. In summary, our novel predictive method allows the identification of new breeding scenarios by pinpointing groups of environments where genotypes demonstrate superior predicted performance. It also facilitates and optimizes cultivar recommendations by utilizing thematic maps.
Collapse
Affiliation(s)
- Maurício S Araújo
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Saulo F S Chaves
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Luiz A S Dias
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Filipe M Ferreira
- Department of Crop Science - College of Agricultural Sciences, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Guilherme R Pereira
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Rodrigo S Alves
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Alexandre B Heinemann
- Brazilian Agricultural Research Corporation (Embrapa Rice and Beans), Santo Antônio de Goiás, Goiás, Brazil
| | - Flávio Breseghello
- Brazilian Agricultural Research Corporation (Embrapa Rice and Beans), Santo Antônio de Goiás, Goiás, Brazil
| | - Pedro C S Carneiro
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | | | | | - Kaio O G Dias
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
| |
Collapse
|
2
|
Bakare MA, Kayondo SI, Aghogho CI, Wolfe MD, Parkes EY, Kulakow P, Egesi C, Jannink JL, Rabbi IY. Parsimonious genotype by environment interaction covariance models for cassava ( Manihot esculenta). FRONTIERS IN PLANT SCIENCE 2022; 13:978248. [PMID: 36212387 PMCID: PMC9532941 DOI: 10.3389/fpls.2022.978248] [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: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
The assessment of cassava clones across multiple environments is often carried out at the uniform yield trial, a late evaluation stage, before variety release. This is to assess the differential response of the varieties across the testing environments, a phenomenon referred to as genotype-by-environment interaction (GEI). This phenomenon is considered a critical challenge confronted by plant breeders in developing crop varieties. This study used the data from variety trials established as randomized complete block design (RCBD) in three replicates across 11 locations in different agro-ecological zones in Nigeria over four cropping seasons (2016-2017, 2017-2018, 2018-2019, and 2019-2020). We evaluated a total of 96 varieties, including five checks, across 48 trials. We exploited the intricate pattern of GEI by fitting variance-covariance structure models on fresh root yield. The goodness-of-fit statistics revealed that the factor analytic model of order 3 (FA3) is the most parsimonious model based on Akaike Information Criterion (AIC). The three-factor loadings from the FA3 model explained, on average across the 27 environments, 53.5% [FA (1)], 14.0% [FA (2)], and 11.5% [FA (3)] of the genetic effect, and altogether accounted for 79.0% of total genetic variability. The association of factor loadings with weather covariates using partial least squares regression (PLSR) revealed that minimum temperature, precipitation and relative humidity are weather conditions influencing the genotypic response across the testing environments in the southern region and maximum temperature, wind speed, and temperature range for those in the northern region of Nigeria. We conclude that the FA3 model identified the common latent factors to dissect and account for complex interaction in multi-environment field trials, and the PLSR is an effective approach for describing GEI variability in the context of multi-environment trials where external environmental covariables are included in modeling.
Collapse
Affiliation(s)
- Moshood A. Bakare
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Cynthia I. Aghogho
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Marnin D. Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- Department of Crop, Soil and Environmental Sciences, College of Agriculture, Auburn University, Auburn, AL, United States
| | | | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Umuahia, Nigeria
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | | |
Collapse
|
3
|
Coast O, Posch BC, Rognoni BG, Bramley H, Gaju O, Mackenzie J, Pickles C, Kelly AM, Lu M, Ruan YL, Trethowan R, Atkin OK. Wheat photosystem II heat tolerance: evidence for genotype-by-environment interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1368-1382. [PMID: 35781899 DOI: 10.1111/tpj.15894] [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: 03/07/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
High temperature stress inhibits photosynthesis and threatens wheat production. One measure of photosynthetic heat tolerance is Tcrit - the critical temperature at which incipient damage to photosystem II (PSII) occurs. This trait could be improved in wheat by exploiting genetic variation and genotype-by-environment interactions (GEI). Flag leaf Tcrit of 54 wheat genotypes was evaluated in 12 thermal environments over 3 years in Australia, and analysed using linear mixed models to assess GEI effects. Nine of the 12 environments had significant genetic effects and highly variable broad-sense heritability (H2 ranged from 0.15 to 0.75). Tcrit GEI was variable, with 55.6% of the genetic variance across environments accounted for by the factor analytic model. Mean daily growth temperature in the month preceding anthesis was the most influential environmental driver of Tcrit GEI, suggesting biochemical, physiological and structural adjustments to temperature requiring different durations to manifest. These changes help protect or repair PSII upon exposure to heat stress, and may improve carbon assimilation under high temperature. To support breeding efforts to improve wheat performance under high temperature, we identified genotypes superior to commercial cultivars commonly grown by farmers, and demonstrated potential for developing genotypes with greater photosynthetic heat tolerance.
Collapse
Affiliation(s)
- Onoriode Coast
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
- School of Environmental and Rural Sciences, Faculty of Science Agriculture Business and Law, University of New England, Armidale, NSW, 2351, Australia
| | - Bradley C Posch
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bethany G Rognoni
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
| | - Oorbessy Gaju
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Lincoln Institute of Agri-Food Technology, University of Lincoln, Riseholme Park, Lincoln, Lincolnshire, LN2 2LG, UK
| | - John Mackenzie
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Claire Pickles
- Birchip Cropping Group, 73 Cumming Avenue, Birchip, VIC, 3483, Australia
| | - Alison M Kelly
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD, 4350, Australia
| | - Meiqin Lu
- Australian Grain Technologies, 12656 Newell Highway, Narrabri, NSW, 2390, Australia
| | - Yong-Ling Ruan
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Owen K Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| |
Collapse
|
4
|
Lozano-Jaramillo M, Komen H, Wientjes YCJ, Mulder HA, Bastiaansen JWM. Optimizing design to estimate genetic correlations between environments with common environmental effects. J Anim Sci 2020; 98:5722360. [PMID: 32017843 PMCID: PMC7039408 DOI: 10.1093/jas/skaa034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/10/2020] [Indexed: 11/23/2022] Open
Abstract
Breeding programs for different species aim to improve performance by testing members of full-sib (FS) and half-sib (HS) families in different environments. When genotypes respond differently to changes in the environment, this is defined as genotype by environment (G × E) interaction. The presence of common environmental effects within families generates covariance between siblings, and these effects should be taken into account when estimating a genetic correlation. Therefore, an optimal design should be established to accurately estimate the genetic correlation between environments in the presence of common environmental effects. We used stochastic simulation to find the optimal population structure using a combination of FS and HS groups with different levels of common environmental effects. Results show that in a population with a constant population size of 2,000 individuals per environment, ignoring common environmental effects when they are present in the population will lead to an upward bias in the estimated genetic correlation of on average 0.3 when the true genetic correlation is 0.5. When no common environmental effects are present in the population, the lowest standard error (SE) of the estimated genetic correlation was observed with a mating ratio of one dam per sire, and 10 offspring per sire per environment. When common environmental effects are present in the population and are included in the model, the lowest SE is obtained with mating ratios of at least 5 dams per sire and with a minimum number of 10 offspring per sire per environment. We recommend that studies that aim to estimate the magnitude of G × E in pigs, chicken, and fish should acknowledge the potential presence of common environmental effects and adjust the mating ratio accordingly.
Collapse
Affiliation(s)
- Maria Lozano-Jaramillo
- Animal Breeding and Genomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Hans Komen
- Animal Breeding and Genomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Yvonne C J Wientjes
- Animal Breeding and Genomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Han A Mulder
- Animal Breeding and Genomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - John W M Bastiaansen
- Animal Breeding and Genomics Group, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
5
|
Rahman MM, Siddique A, Rahman MA, Rahman SM, Asaduzzaman M, Khanom M, Khatun MM, Hasan MM. The interactive effects of paternal size and offspring feeding strategy on offspring fitness of an Indian major carp
Labeo rohita
(Hamilton, 1822). AQUACULTURE RESEARCH 2020; 51:2421-2431. [DOI: 10.1111/are.14586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/18/2020] [Indexed: 09/27/2023]
Affiliation(s)
- Md. Moshiur Rahman
- Tokyo University of Marine Science and Technology Tokyo Japan
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
| | - Asif Siddique
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
| | - Md. Ashikur Rahman
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
| | - Sheikh Mustafizur Rahman
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
- Fish Resources Research Center King Faisal University Hofuf Al‐Ahsa Kingdom of Saudi Arabia
| | - Md. Asaduzzaman
- Department of Marine Bioresource Science Chittagong Veterinary and Animal Sciences University Chittagong Bangladesh
| | - Momotaz Khanom
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
| | - Mst. Muslima Khatun
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
| | - Md. Mehedi Hasan
- Fisheries & Marine Resource Technology Discipline Khulna University Khulna Bangladesh
- Sydney School of Veterinary Science Faculty of Science The University of Sydney Camden NSW Australia
| |
Collapse
|
6
|
Bartolomé E, Menéndez-Buxadera A, Molina A, Valera M. Plasticity effect of rider-horse interaction on genetic evaluations for Show Jumping discipline in sport horses. J Anim Breed Genet 2018; 135:138-148. [PMID: 29363192 DOI: 10.1111/jbg.12315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022]
Abstract
To obtain a sport horse that excels in the highest levels of competition, breeders must take into account certain genetic and environmental factors that could influence the sport horse's performance, such as the rider-horse interaction (RHI). The main aim of this study was to describe this interaction in a genetic model by modelling it in relation to the horse's age. A total of 31,129 sport results from Spanish Sport Horses were used from a total of 1,101 animals evaluated, and these were grouped in three age levels and had been ridden by 606 different riders. Only riders who had ridden more than one horse (and vice-versa) were considered for the analyses. Five linear models with different random effects were analysed according to the covariates, the homogeneity/heterogeneity of the RHI and the relevant residual random effects. The model of best fit was then selected for the genetic evaluation of the animal. In general, models including the RHI effect (M2, M4 and M5) fitted better than the other models, and the best fit was obtained for M4 (with heterogeneous residual variance). The genetic variance increased constantly with age, whereas heritability showed a response on three intervals. This study revealed the varied evolution of the RHI with age, showing the different "plastic abilities" of this relationship.
Collapse
Affiliation(s)
- E Bartolomé
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| | | | - A Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - M Valera
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| |
Collapse
|
7
|
Sae-Lim P, Kause A, Mulder HA, Olesen I. BREEDING AND GENETICS SYMPOSIUM: Climate change and selective breeding in aquaculture. J Anim Sci 2017; 95:1801-1812. [PMID: 28464113 DOI: 10.2527/jas.2016.1066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aquaculture is the fastest growing food production sector and it contributes significantly to global food security. Based on Food and Agriculture Organization (FAO) of the United Nations, aquaculture production must increase significantly to meet the future global demand for aquatic foods in 2050. According to Intergovernmental Panel on Climate Change (IPCC) and FAO, climate change may result in global warming, sea level rise, changes of ocean productivity, freshwater shortage, and more frequent extreme climate events. Consequently, climate change may affect aquaculture to various extents depending on climatic zones, geographical areas, rearing systems, and species farmed. There are 2 major challenges for aquaculture caused by climate change. First, the current fish, adapted to the prevailing environmental conditions, may be suboptimal under future conditions. Fish species are often poikilothermic and, therefore, may be particularly vulnerable to temperature changes. This will make low sensitivity to temperature more important for fish than for livestock and other terrestrial species. Second, climate change may facilitate outbreaks of existing and new pathogens or parasites. To cope with the challenges above, 3 major adaptive strategies are identified. First, general 'robustness' will become a key trait in aquaculture, whereby fish will be less vulnerable to current and new diseases while at the same time thriving in a wider range of temperatures. Second, aquaculture activities, such as input power, transport, and feed production contribute to greenhouse gas emissions. Selection for feed efficiency as well as defining a breeding goal that minimizes greenhouse gas emissions will reduce impacts of aquaculture on climate change. Finally, the limited adoption of breeding programs in aquaculture is a major concern. This implies inefficient use of resources for feed, water, and land. Consequently, the carbon footprint per kg fish produced is greater than when fish from breeding programs would be more heavily used. Aquaculture should use genetically improved and robust organisms not suffering from inbreeding depression. This will require using fish from well-managed selective breeding programs with proper inbreeding control and breeding goals. Policymakers and breeding organizations should provide incentives to boost selective breeding programs in aquaculture for more robust fish tolerating climatic change.
Collapse
|
8
|
Sae-Lim P, Mulder H, Gjerde B, Koskinen H, Lillehammer M, Kause A. Genetics of Growth Reaction Norms in Farmed Rainbow Trout. PLoS One 2015; 10:e0135133. [PMID: 26267268 PMCID: PMC4534094 DOI: 10.1371/journal.pone.0135133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/18/2015] [Indexed: 11/19/2022] Open
Abstract
Rainbow trout is farmed globally under diverse uncontrollable environments. Fish with low macroenvironmental sensitivity (ES) of growth is important to thrive and grow under these uncontrollable environments. The ES may evolve as a correlated response to selection for growth in one environment when the genetic correlation between ES and growth is nonzero. The aims of this study were to quantify additive genetic variance for ES of body weight (BW), defined as the slope of reaction norm across breeding environment (BE) and production environment (PE), and to estimate the genetic correlation (rg(int, sl)) between BW and ES. To estimate heritable variance of ES, the coheritability of ES was derived using selection index theory. The BW records from 43,040 rainbow trout performing either in freshwater or seawater were analysed using a reaction norm model. High additive genetic variance for ES (9584) was observed, inferring that genetic changes in ES can be expected. The coheritability for ES was either -0.06 (intercept at PE) or -0.08 (intercept at BE), suggesting that BW observation in either PE or BE results in low accuracy of selection for ES. Yet, the rg(int, sl) was negative (-0.41 to -0.33) indicating that selection for BW in one environment is expected to result in more sensitive fish. To avoid an increase of ES while selecting for BW, it is possible to have equal genetic gain in BW in both environments so that ES is maintained stable.
Collapse
Affiliation(s)
- Panya Sae-Lim
- Aquaculture and Genetics, Nofima, Osloveien 1, Ås, Norway
- * E-mail:
| | - Han Mulder
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Bjarne Gjerde
- Aquaculture and Genetics, Nofima, Osloveien 1, Ås, Norway
| | - Heikki Koskinen
- Aquaculture Unit, Natural Resources Institute Finland, Tervo, Finland
| | | | - Antti Kause
- Biometrical Genetics, Natural Resources Institute Finland, Jokioinen, Finland
| |
Collapse
|
9
|
Genotype by Environment Interaction for Growth in Atlantic Cod (Gadus morhua L.) in Four Farms of Norway. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3020412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|