Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

Yin, Xinyou; Struik, P.C.

doi:10.1111/j.1469-8137.2008.02424.x

Cited by 84 publications

(65 citation statements)

References 84 publications

(121 reference statements)

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“…Models can be applied at various levels from the genome to the crop (Yin and Struik 2008) and further up to the agro-ecosystems level. For this study, we used simulated 90-year climate datasets and a crop growth model with temperature, solar radiation, CO 2 concentration, rainfall, and reference evapotranspiration as input data: LINTUL-Potato (Spitters 1990;Kooman and Haverkort 1994).…”

Section: Introductionmentioning

confidence: 99%

Climate Change and Potato Production in Contrasting South African Agro-ecosystems 1. Effects on Land and Water Use Efficiencies

et al. 2013

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Explorations of the impact of climate change on potential potato yields were obtained by downscaling the projections of six different coupled climate models to high spatial resolution over southern Africa. The simulations of daily maximum and minimum temperatures, precipitation, wind speed, and solar radiation were used as input to run the crop growth model LINTUL-Potato. Pixels representative for potato growing areas were selected for four globally occurring agro-ecosystems: rainy and dry winter and summer crops. The simulated inter-annual variability is much greater for rainfall than for temperature. Reference evapotranspiration and radiation are projected to hardly decline over the 90-year period, whilst temperatures are projected to rise significantly by about 1.9°C. From literature, it was found that radiation use efficiency of potato increased with elevated CO 2 concentrations by almost 0.002 gMJ −1 ppm −1 . This ratio was used to calculate the CO 2 effect on yields between 1960 and 2050, when CO 2 concentration increases from 315 to 550 ppm. Within this range, evapotranspiration by the potato crop was reduced by about 13% according to literature. Simulated yield increase was strongest in the Mediterraneantype winter crop (+37%) and least under Mediterranean summer (+12%) and relatively warm winter conditions (+14%) closer to the equator. Water use efficiency also increased most in the cool rainy Mediterranean winter (+45%) and least so in the winter crop closer to the equator (+14%). It is concluded from the simulations that for all four agro-ecosystems possible negative effects of rising temperatures and reduced availability of water for potato are more than compensated for by the positive effect of increased CO 2 levels on water use efficiency and crop productivity.

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Section: Introductionmentioning

confidence: 99%

Climate Change and Potato Production in Contrasting South African Agro-ecosystems 1. Effects on Land and Water Use Efficiencies

et al. 2013

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“…For the next 'Green Revolution' to happen, we have to deal with many genes so that they work in concert. Alterations made at the genome level, though substantial, could have little effect on the crop-level phenotypes (Sinclair et al, 2004;Yin and Struik, 2008). Systems biology should not be the privilege of only those working on molecular, sub-cellular or cellular levels.…”

Section: Final Remarksmentioning

confidence: 99%

Modelling Gene-Trait-Crop Relationships: Past Experiences and Future Prospects

Yin¹,

Struik²

2012

Acta Hortic.

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Classical crop models have long been established to understand crop responses to environmental factors, by integrating quantitative functional relationships for various physiological processes. In view of the potential added value of robust crop modelling to classical quantitative genetics, model-input parameters or traits are increasingly considered to represent 'genetic coefficients'. A number of case studies, in which the effects of quantitative trait loci or genes have been incorporated into existing ecophysiological models to replace model-input traits, have shown promise of using models in analyzing genotype-phenotype relationships of more complex crop traits. Studies of functional genomics will increasingly enable the elucidation of the molecular genetic basis of these modelinput traits. To fulfil the great expectations from this integrated modelling, crop models should be upgraded based on understandings at lower organizational levels. The recently proposed 'crop systems biology', which combines modern genomics, traditional physiology and biochemistry, and advanced modelling, is believed ultimately to realize the expected roles of in silico modelling in narrowing genotypephenotype gaps. We will summarise recent research activities and express our opinions on perspectives for modelling genotype-by-environment interactions at crop level.

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“…Xu and Crouch 2008;Backes and Østergard 2008; Table 1, weakness). Although the efficiency of MAS largely depends on exact initial phenotyping, an even more effective way to bridge the gap and to deal with the interaction between genotype, environment and management (cultivation practices) is the opportunity given by integrating genetics, agronomy and crop physiology (Yin and Struik 2008;Struik and Yin 2009). Their approach, including QTL-based ecophysiological modeling, could also provide the tools to breed for complex trait, such as nutrient-use efficiency, in a more efficient way and making use of markers.…”

Section: Selection At Gene or Phenotypic Levelmentioning

confidence: 99%

The role of molecular markers and marker assisted selection in breeding for organic agriculture

et al. 2010

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Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder's perspectives and perspectives seen from the organic sector's standpoint. Clear strengths were identified, e.g. better knowledge about gene pool of breeding material, more efficient introgression of new resistance genes from wild relatives and testing pyramided genes. There were also common concerns among breeders aiming at breeding for organic and/ or conventional agriculture, such as the increasing competition and cost investments to get access to marker technology, and the need for bridging the gap between phenotyping and genotyping especially with complex and quantitative inherited traits such as nutrient-efficiency. A major conclusion of the authors is that more interaction and mutual understanding between organic and molecular oriented breeders is necessary and can benefit both research communities.

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Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

Cited by 84 publications

References 84 publications

Climate Change and Potato Production in Contrasting South African Agro-ecosystems 1. Effects on Land and Water Use Efficiencies

Climate Change and Potato Production in Contrasting South African Agro-ecosystems 1. Effects on Land and Water Use Efficiencies

Modelling Gene-Trait-Crop Relationships: Past Experiences and Future Prospects

The role of molecular markers and marker assisted selection in breeding for organic agriculture

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