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Tag: phenotyping

A researcher collects field data at CIMMYT’s experiment station in Ciudad Obregón, Mexico. (Photo: Alfonso Cortés/CIMMYT)

New publications: Breeders can benefit much more from phenotyping tools

Written by Emma Orchardson on . Posted in Publications.

In crop research fields, it is now a common sight to see drones or other high-tech sensing tools collecting high-resolution data on a wide range of traits — from simple measurement of canopy temperature to complex 3D reconstruction of photosynthetic canopies.

This technological approach to collecting precise plant trait information, known as phenotyping, is becoming ubiquitous, but according to experts at the International Maize and Wheat Improvement Center (CIMMYT) and other research institutions, breeders can profit much more from these tools, when used judiciously.

In a new article in the journal Plant Science, CIMMYT researchers outline the different ways in which phenotyping can assist breeding — from large-scale screening to detailed physiological characterization of key traits — and why this methodology is crucial for crop improvement.

“While having been the subject of debate in the past, extra investment for phenotyping is becoming more accepted to capitalize on recent developments in crop genomics and prediction models,” explain the authors.

Their review considers different contexts for phenotyping, including breeding, exploration of genetic resources, parent building and translations research to deliver other new breeding resources, and how these different categories of phenotyping apply to each. Some of the same tools and rules of thumb apply equally well to phenotyping for genetic analysis of complex traits and gene discovery.

The authors make the case for breeders to invest in phenotyping, particularly in light of the imperative to breed crops for warmer and harsher climates. However, wide scale adoption of sophisticated phenotyping methods will only occur if new techniques add efficiency and effectiveness.

In this sense, “breeder-friendly” phenotyping should complement existing breeding approaches by cost-effectively increasing throughput during segregant selection and adding new sources of validated complex traits to crossing blocks. With this in mind, stringent criteria need to be applied before new traits or phenotyping protocols are incorporated into mainstream breeding pipelines.

Read the full article in Plant Science:
Breeder friendly phenotyping.

A researcher flies a UAV to collect field data at CIMMYT’s experiment station in Ciudad Obregón, Mexico. (Photo: Alfonso Cortés/CIMMYT)
A researcher flies a UAV to collect field data at CIMMYT’s experiment station in Ciudad Obregón, Mexico. (Photo: Alfonso Cortés/CIMMYT)

See more recent publications from CIMMYT researchers:

  1. Genome-wide association study to identify genomic regions influencing spontaneous fertility in maize haploids. 2019. Chaikam, V., Gowda, M., Nair, S.K., Melchinger, A.E., Prasanna, B.M. In: Euphytica v. 215, no. 8, art. 138.
  2. Adapting irrigated and rainfed wheat to climate change in semi-arid environments: management, breeding options and land use change. 2019. Hernandez-Ochoa, I.M., Pequeno, D.N.L., Reynolds, M.P., Md Ali Babar, Sonder, K., Molero, A., Hoogenboom, G., Robertson, R., Gerber, S., Rowland, D.L., Fraisse, C.W., Asseng, S. In: European Journal of Agronomy.
  3. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. 2019. Gardiner, L.J., Brabbs, T., Akhunova, A., Jordan, K., Budak, H., Richmond, T., Sukhwinder-Singh, Catchpole, L., Akhunov, E., Hall, A.J.W. In: GigaScience v. 8, no. 4, art. giz018.
  4. Rethinking technological change in smallholder agriculture. 2019. Glover, D., Sumberg, J., Ton, G., Andersson, J.A., Badstue, L.B. In: Outlook on Agriculture v. 48, no. 3, p. 169-180.
  5. Food security and agriculture in the Western Highlands of Guatemala. 2019. Lopez-Ridaura, S., Barba‐Escoto, L., Reyna, C., Hellin, J. J., Gerard, B., Wijk, M.T. van. In: Food Security v. 11, no. 4, p. 817-833.
  6. Agronomic, economic, and environmental performance of nitrogen rates and source in Bangladesh’s coastal rice agroecosystems. 2019. Shah-Al Emran, Krupnik, T.J., Kumar, V., Ali, M.Y., Pittelkow, C. M. In: Field Crops Research v. 241, art. 107567.
  7. Highlights of special issue on “Wheat Genetics and Breeding”. 2019. He Zhonghu, Zhendong Zhao, Cheng Shun-He In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 207-209.
  8. Progress in breeding for resistance to Ug99 and other races of the stem rust fungus in CIMMYT wheat germplasm. 2019. Bhavani, S., Hodson, D.P., Huerta-Espino, J., Randhawa, M.S., Singh, R.P. In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 210-224.
  9. China-CIMMYT collaboration enhances wheat improvement in China. 2019. He Zhonghu, Xianchun Xia, Yong Zhang, Zhang Yan, Yonggui Xiao, Xinmin Chen, Li Simin, Yuanfeng Hao, Rasheed, A, Zhiyong Xin, Zhuang Qiaosheng, Ennian Yang, Zheru Fan, Yan Jun, Singh, R.P., Braun, H.J. In: Frontiers of Agricultural Science and Engineering v. 6. No. 3, p. 233-239.
  10. International Winter Wheat Improvement Program: history, activities, impact and future. 2019. Morgounov, A.I., Ozdemir, F., Keser, M., Akin, B., Payne, T.S., Braun, H.J. In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 240-250.
  11. Genetic improvement of wheat grain quality at CIMMYT. 2019. Guzman, C., Ammar, K., Velu, G., Singh, R.P. In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 265-272.
  12. Comments on special issue on “Wheat Genetics and Breeding”. 2019. He Zhonghu, Liu Xu In: Frontiers of Agricultural Science and Engineering, v. 6. No. 3, p. 309.
  13. Spectral reflectance indices as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait associations. 2019. Caiyun Liu, Pinto Espinosa, F., Cossani, C.M., Sukumaran, S., Reynolds, M.P. In: Frontiers of Agricultural Science and Engineering, v. 6, no. 3, p. 296-308.
  14. Beetle and maize yield response to plant residue application and manual weeding under two tillage systems in northern Zimbabwe. 2019. Mashavakure, N., Mashingaidze, A.B., Musundire, R., Gandiwa, E., Thierfelder, C., Muposhi, V.K. In: Applied Soil Ecology v. 144, p. 139-146.
  15. Optimizing dry-matter partitioning for increased spike growth, grain number and harvest index in spring wheat. 2019. Rivera Amado, A.C., Trujillo, E., Molero, G., Reynolds, M.P., Sylvester Bradley, R., Foulkes, M.J. In: Field Crops Research v. 240, p. 154-167.
  16. Small businesses, potentially large impacts: the role of fertilizer traders as agricultural extension agents in Bangladesh. 2019. Mottaleb, K.A., Rahut, D.B., Erenstein, O. In: Journal of Agribusiness in Developing and Emerging Economies v. 9, no. 2, p. 109-124.
  17. Heterogeneous seed access and information exposure: implications for the adoption of drought-tolerant maize varieties in Uganda. 2019. Simtowe, F.P., Marenya, P. P., Amondo, E., Regasa, M.W., Rahut, D.B., Erenstein, O. In: Agricultural and Food Economics v. 7. No. 1, art. 15.
  18. Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. 2019. Krause, M., Gonzalez-Perez, L., Crossa, J., Perez-Rodriguez, P., Montesinos-Lopez, O.A., Singh, R.P., Dreisigacker, S., Poland, J.A., Rutkoski, J., Sorrells, M.E., Gore, M.A., Mondal, S. In: G3: Genes, Genomes, Genetics v.9, no. 4, p. 1231-1247.
  19. Unravelling the complex genetics of karnal bunt (Tilletia indica) resistance in common wheat (Triticum aestivum) by genetic linkage and genome-wide association analyses. 2019. Emebiri, L.C., Sukhwinder-Singh, Tan, M.K., Singh, P.K., Fuentes Dávila, G., Ogbonnaya, F.C. In: G3: Genes, Genomes, Genetics v. 9, no. 5, p. 1437-1447.
  20. Healthy foods as proxy for functional foods: consumers’ awareness, perception, and demand for natural functional foods in Pakistan. 2019. Ali, A., Rahut, D.B. In: International Journal of Food Science v. 2019, art. 6390650.
  21. Northern Himalayan region of Pakistan with cold and wet climate favors a high prevalence of wheat powdery mildew. 2019. Khan, M.R., Imtiaz, M., Farhatullah, Ahmad, S., Sajid Ali.In: Sarhad Journal of Agriculture v. 35, no. 1, p. 187-193.
  22. Resistance to insect pests in wheat—rye and Aegilops speltoides Tausch translocation and substitution lines. 2019. Crespo-Herrera, L.A., Singh, R.P., Sabraoui, A., Moustapha El Bouhssini In: Euphytica v. 215, no. 7, art.123.
  23. Productivity and production risk effects of adopting drought-tolerant maize varieties in Zambia. 2019. Amondo, E., Simtowe, F.P., Rahut, D.B., Erenstein, O. In: International Journal of Climate Change Strategies and Management v. 11, no. 4, p. 570-591.
  24. Review: new sensors and data-driven approaches—A path to next generation phenomics. 2019. Roitsch, T., Cabrera-Bosquet, L., Fournier, A., Ghamkhar, K., Jiménez-Berni, J., Pinto Espinosa, F., Ober, E.S. In: Plant Science v. 282 p. 2-10.
  25. Accountability mechanisms in international climate change financing. 2019. Basak, R., van der Werf, E. In: International Environmental Agreements: Politics, Law and Economics v. 19, no. 3, p. 297-313.
  26. Enhancing the rate of genetic gain in public-sector plant breeding programs: lessons from the breeder’s equation. 2019. Cobb, J.N., Juma, R.U., Biswas, P.S., Arbelaez, J.D., Rutkoski, J., Atlin, G.N., Hagen, T., Quinn, M., Eng Hwa Ng. In: Theoretical and Applied Genetics v. 132, no. 3, p. 627-645.
Remote sensing specialist Francisco Pinto operates a UAV at CIMMYT's research station in Ciudad Obregón, in Mexico's Sonora state.

Breeder friendly phenotyping

Written by Marcia MacNeil on . Posted in Infographics.

In crop research fields, drones and other high-tech sensing tools are now a common sight. They collect high-resolution data on a wide range of traits — from simple measurement of canopy temperature to complex 3D reconstruction of photosynthetic canopies.

This technological approach to collecting precise plant trait information, known as phenotyping, is becoming ubiquitous. According to experts at the International Maize and Wheat Improvement Center (CIMMYT) and other research institutions, breeders can profit much more from these tools, when used judiciously.

Examples of different classes and applications of breeder friendly phenotyping. (Image: M. Reynolds et al.)
Examples of different classes and applications of breeder friendly phenotyping. (Image: M. Reynolds et al.)

In a new article in the journal Plant Science, CIMMYT Wheat Physiologist Matthew Reynolds and colleagues explain the different ways that phenotyping can assist breeding — from simple to use, “handy” approaches for large scale screening, to detailed physiological characterization of key traits to identify new parental sources — and why this methodology is crucial for crop improvement. The authors make the case for breeders to invest in phenotyping, particularly in light of the imperative to breed crops for warmer and harsher climates.

Read the full article: 
Breeder friendly phenotyping.

This article was originally published on WHEAT.

Cover photo: Remote sensing specialist Francisco Pinto operates a UAV at CIMMYT’s research station in Ciudad Obregón, in Mexico’s Sonora state.

A researcher uses a vertical probe to measure moisture at different soil depths. (Photo: CIMMYT)

New manual provides quantitative approach to drought stress phenotyping

Written by Carolyn Cowan on . Posted in News.

A researcher uses a vertical probe to measure moisture at different soil depths. (Photo: CIMMYT)
A researcher uses a vertical probe to measure moisture at different soil depths. (Photo: CIMMYT)

Since 1900, more than two billion people have been affected by drought worldwide, according to the Food and Agriculture Organization of the United Nations (FAO). Drought affects crops by limiting the amount of water available for optimal growth and development, thereby lowering productivity. It is one of the major abiotic stresses responsible for variability in crop yield, driving significant economic, environmental and social impacts.

A new technical manual, “Management of drought stress in field phenotyping,” provides a quantitative approach to drought stress phenotyping in crops. Phenotyping is a procedure vital to the success of crop breeding programs that involves physical assessment of plants for desired traits.

The manual provides guidance for crop breeders, crop physiologists, agronomists, students and field technicians who are working on improving crop tolerance to drought stress. It will help ensure drought screening trials yield accurate and precise data for use by breeding programs.

A sprinkler system irrigates a drought phenotyping trial field in Hyderabad, India. (Photo: CIMMYT)
A sprinkler system irrigates a drought phenotyping trial field in Hyderabad, India. (Photo: CIMMYT)

Based on decades of CIMMYT’s research and experience, the manual covers aspects related to field site selection, effects of weather, crop management, maintaining uniform stress in trials, and duration of stress. It focuses on an approach that standardizes the required intensity, timing and uniformity of imposed drought stress during field trials.

Such a rigorous and accurate approach to drought screening allows for precision phenotyping. Careful management of imposed drought stress also allows the full variability in a population’s genotype to be expressed and identified during phenotyping, which means the full potential of the drought tolerance trait can be harnessed.

Variability among maize genotypes for agronomic and yield traits under managed drought stress. (Photo: CIMMYT)
Variability among maize genotypes for agronomic and yield traits under managed drought stress. (Photo: CIMMYT)

“Crop breeding programs using conventional or molecular breeding approaches to develop crops with drought tolerance rely heavily on high-quality phenotypic data generated from drought screening trials,” said author and CIMMYT scientist P.H. Zaidi. “By following the guidance in this manual, users can maximize their quality standards.”

The International Maize and Wheat Improvement Center (CIMMYT) has been a pioneer in developing and deploying protocols for drought stress phenotyping, selection strategy and breeding for drought tolerance. CIMMYT’s research on drought stress in maize began in the 1970s and has since remained a top priority for the organization. Drought-tolerant maize is now one of CIMMYT’s flagship products and is a key component of CIMMYT’s portfolio of products aimed to cope with the effects of climate change in the tropics.

Read the manual:
Pervez H. Zaidi, 2019. Management of drought stress in field phenotyping. CIMMYT, Mexico.

The information presented in the manual is based on the work on quantitative management of drought stress phenotyping under field conditions that received strong and consistent support from several donor agencies, especially Germany’s Federal Ministry for Economic Cooperation and Development (BMZ), Germany’s GIZ and the CGIAR Research Program on Maize (MAIZE). The manual itself was funded by the CGIAR Excellence in Breeding (EiB) platform.