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Phon Green - One of the best experts on this subject based on the ideXlab platform.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    Nature Protocols, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    'Speed Breeding' (SB) shortens the Breeding cycle and accelerates Crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral Crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several Crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    Nature Protocols, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    We acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) strategic programmes Designing Future Wheat (BB/P016855/1), Molecules from Nature (BB/P012523/1), Understanding and Exploiting Plant and Microbial Metabolism (BB/J004561/1), Food and Health (BB/J004545/1) and Food Innovation and Health (BB/R012512/1), and also support from the Gatsby Charitable Foundation. Development of the benchtop cabinet was supported by an OpenPlant Fund grant from the joint Engineering and Physical Sciences Research Council and BBSRC-funded OpenPlant Synthetic Biology Research Centre grant BB/L014130/1. S.G. was supported by a Monsanto Beachell-Borlaug International Scholarship and the 2Blades Foundation, A.Sarkar by the BBSRC Detox Grasspea project (BB/L011719/1) and the John Innes Foundation, A.W. by an Australian Post-graduate Award and the Grains Research and Development Corporation (GRDC) Industry Top-up Scholarship (project code GRS11008), M.M.-S. by CONACYT-I2T2 Nuevo Leon (grant code 266954/399852), and L.T.H. by an Australian Research Council Early Career Discovery Research Award (project code DE170101296). We acknowledge M. Grantham and D. Napier from Heliospectra for their help in the choice of LED lights; L. Hernan and C. Ramirez from Newcastle University for their support and advice in the design of the benchtop cabinet; C. Moreau from the John Innes Centre and J. Ghosh from the University of Bedfordshire for help with the pea and grass pea experiments, respectively; and the JIC and UQ horticulture services for plant husbandry and their support in scaling up SB in glasshouses.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    bioRxiv, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in Crop Breeding. One way this can be achieved is through 9speed Breeding9 (SB), which shortens the Breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plant9s daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral Crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several Crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

José Luis Araus - One of the best experts on this subject based on the ideXlab platform.

  • field high throughput phenotyping the new Crop Breeding frontier
    Trends in Plant Science, 2014
    Co-Authors: José Luis Araus, Jill E Cairns
    Abstract:

    Constraints in field phenotyping capability limit our ability to dissect the genetics of quantitative traits, particularly those related to yield and stress tolerance (e.g., yield potential as well as increased drought, heat tolerance, and nutrient efficiency, etc.). The development of effective field-based high-throughput phenotyping platforms (HTPPs) remains a bottleneck for future Breeding advances. However, progress in sensors, aeronautics, and high-performance computing are paving the way. Here, we review recent advances in field HTPPs, which should combine at an affordable cost, high capacity for data recording, scoring and processing, and non-invasive remote sensing methods, together with automated environmental data collection. Laboratory analyses of key plant parts may complement direct phenotyping under field conditions. Improvements in user-friendly data management together with a more powerful interpretation of results should increase the use of field HTPPs, therefore increasing the efficiency of Crop genetic improvement to meet the needs of future generations.

  • high throughput phenotyping and genomic selection the frontiers of Crop Breeding converge
    Journal of Integrative Plant Biology, 2012
    Co-Authors: Llorenc Cabrerabosquet, Jarislav Von Zitzewitz, Maria Dolors Serret, José Crossa, José Luis Araus
    Abstract:

    Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the Crop Breeding community from both the public and private sectors world-wide. Both approaches promise to revolutionize the prediction of complex traits, including growth, yield and adaptation to stress. Whereas high-throughput phenotyping may help to improve understanding of Crop physiology, most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and comparable to genomic selection. Despite the fact that the two methodological approaches represent the extremes of what is understood as the Breeding process (phenotype versus genome), they both consider the targeted traits (e.g. grain yield, growth, phenology, plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e. physiological) putatively related to the target trait. Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology. This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as Crop growth and yield.

Sreya Ghosh - One of the best experts on this subject based on the ideXlab platform.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    Nature Protocols, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    'Speed Breeding' (SB) shortens the Breeding cycle and accelerates Crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral Crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several Crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    Nature Protocols, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    We acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) strategic programmes Designing Future Wheat (BB/P016855/1), Molecules from Nature (BB/P012523/1), Understanding and Exploiting Plant and Microbial Metabolism (BB/J004561/1), Food and Health (BB/J004545/1) and Food Innovation and Health (BB/R012512/1), and also support from the Gatsby Charitable Foundation. Development of the benchtop cabinet was supported by an OpenPlant Fund grant from the joint Engineering and Physical Sciences Research Council and BBSRC-funded OpenPlant Synthetic Biology Research Centre grant BB/L014130/1. S.G. was supported by a Monsanto Beachell-Borlaug International Scholarship and the 2Blades Foundation, A.Sarkar by the BBSRC Detox Grasspea project (BB/L011719/1) and the John Innes Foundation, A.W. by an Australian Post-graduate Award and the Grains Research and Development Corporation (GRDC) Industry Top-up Scholarship (project code GRS11008), M.M.-S. by CONACYT-I2T2 Nuevo Leon (grant code 266954/399852), and L.T.H. by an Australian Research Council Early Career Discovery Research Award (project code DE170101296). We acknowledge M. Grantham and D. Napier from Heliospectra for their help in the choice of LED lights; L. Hernan and C. Ramirez from Newcastle University for their support and advice in the design of the benchtop cabinet; C. Moreau from the John Innes Centre and J. Ghosh from the University of Bedfordshire for help with the pea and grass pea experiments, respectively; and the JIC and UQ horticulture services for plant husbandry and their support in scaling up SB in glasshouses.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    bioRxiv, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in Crop Breeding. One way this can be achieved is through 9speed Breeding9 (SB), which shortens the Breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plant9s daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral Crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several Crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

Markus Schilhabel - One of the best experts on this subject based on the ideXlab platform.

Ricardo H Ramirezgonzalez - One of the best experts on this subject based on the ideXlab platform.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    Nature Protocols, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    'Speed Breeding' (SB) shortens the Breeding cycle and accelerates Crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral Crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several Crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    Nature Protocols, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    We acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) strategic programmes Designing Future Wheat (BB/P016855/1), Molecules from Nature (BB/P012523/1), Understanding and Exploiting Plant and Microbial Metabolism (BB/J004561/1), Food and Health (BB/J004545/1) and Food Innovation and Health (BB/R012512/1), and also support from the Gatsby Charitable Foundation. Development of the benchtop cabinet was supported by an OpenPlant Fund grant from the joint Engineering and Physical Sciences Research Council and BBSRC-funded OpenPlant Synthetic Biology Research Centre grant BB/L014130/1. S.G. was supported by a Monsanto Beachell-Borlaug International Scholarship and the 2Blades Foundation, A.Sarkar by the BBSRC Detox Grasspea project (BB/L011719/1) and the John Innes Foundation, A.W. by an Australian Post-graduate Award and the Grains Research and Development Corporation (GRDC) Industry Top-up Scholarship (project code GRS11008), M.M.-S. by CONACYT-I2T2 Nuevo Leon (grant code 266954/399852), and L.T.H. by an Australian Research Council Early Career Discovery Research Award (project code DE170101296). We acknowledge M. Grantham and D. Napier from Heliospectra for their help in the choice of LED lights; L. Hernan and C. Ramirez from Newcastle University for their support and advice in the design of the benchtop cabinet; C. Moreau from the John Innes Centre and J. Ghosh from the University of Bedfordshire for help with the pea and grass pea experiments, respectively; and the JIC and UQ horticulture services for plant husbandry and their support in scaling up SB in glasshouses.

  • speed Breeding in growth chambers and glasshouses for Crop Breeding and model plant research
    bioRxiv, 2018
    Co-Authors: Sreya Ghosh, Amy Watson, Oscar E Gonzaleznavarro, Ricardo H Ramirezgonzalez, Luis Yanes, Marcela Mendozasuarez, James Simmonds, Rachel Wells, Tracey Rayner, Phon Green
    Abstract:

    To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in Crop Breeding. One way this can be achieved is through 9speed Breeding9 (SB), which shortens the Breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plant9s daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral Crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several Crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

  • polymarker a fast polyploid primer design pipeline
    Bioinformatics, 2015
    Co-Authors: Ricardo H Ramirezgonzalez, Cristobal Uauy, Mario Caccamo
    Abstract:

    Summary: The design of genetic markers is of particular relevance in Crop Breeding programs. Despite many economically important Crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specific. PolyMarker is a pipeline that selects candidate primers for a specified genome using local alignments and standard primer design tools (e.g. primer3) to test the viability of the primers. A command line tool and a web interface are available to the community. Availability PolyMarker is available as a ruby BioGem: bio-polyploid-tools.