After my last post, it is natural to wonder why I chose France in the first place. These two are my main reasons: firstly, the project that I am working on is well-aligned with my background and is the cutting-edge research in my field. Secondly, I am interested in exploring another European culture that is not rooted from the same culture as the Dutch one.
My project is about phenomic selection, which perhaps does not really ring a bell when one first encounter this term. Essentially, it refers to a technique to predict how individuals will perform based on their absorbance on the near-infrared spectra. A model is trained with individuals who have been measured on the field and also analysed under the infrared spectra. This model acts as a function that relates both information. Suppose we can effectively define this relationship, we will be able to predict the traits of new individuals using only their spectra data. Cool, isn’t it?
Well, prediction methods have been widely adopted in modern breeding as they save a significant amount of time and money. Imagine being a traditional breeder who has to evaluate a thousand candidate varieties and manage a thousand plots to be able to assess their performance. This field-based evaluation, or in fancier words called phenotyping, also limits the scale of evaluated genotypes to a smaller number, which may lead to losing potential superior candidates.
In the early 2000s, genomic selection was popularized after a renowned paper from Meuwissen et al1. The idea was to use genomic data (read: DNA sequences) to predict the genetic values of new individuals. However, obtaining genomic data is still expensive enough that genomic selection has not been a routine practice in small breeding companies or in low-income countries. Moreover, many orphan crops that are not as widely traded as wheat or maize are still lagging in genotyping. Therefore, Rincent et al. (2018)2 proposed phenomic selection which uses near-infrared measurement as an alternative to genomic data, which was found to be comparably accurate and cheaper in cost. Even in a pessimistic scenario where it is not as accurate as genomic selection, having this low-cost method allows breeders to evaluate more individuals and therefore gain a higher genetic gain. For some crops such as major cereal crops, breeders even have routinely collected the spectra to measure quality traits, so unlike genomic selection, the phenomic one will bring no extra cost.
My project itself will focus on adapting phenomic selection for a hybrid breeding program. Hybrid breeding is more complicated than other programs as we would like to generate hybrids that outperform both parents. Many factors are involved in optimizing the selection itself such as mating design or how many hybrids per parental line should be created (because, of course, it is impossible to evaluate each combination of father and mother lines). In relation to phenomic selection, this means that we like to know whether we can predict the hybrid performance using the spectra measured on their parents. That sounds ambitious, right? Therefore this project has an element of quantitative genetics, maize breeding, and statistics in my project which somehow builds a thread between my bachelor study and master’s. I should also mention the fact that I am doing this internship in the biggest lab of quantitative geneticists in the whole of France.
That was a lengthy story about my project, but I believe it’s important for you to know. As for the second reason, I am interested in French culture. In sociology, it’s commonly understood that the primary components of culture are symbols, language, norms, values, and artefacts. My focus is on French values, as reflected in their motto: “Liberty, Equality, and Fraternity”. I am interested in experiencing how those values are reflected in their work and daily life. Specifically, I want to observe their communication styles, whether they are direct or read between the lines, their manners and politeness levels, how formal they are, how important hierarchy is in organizations, and more. I am also excited to experience other cultural aspects, such as food and nature. Trying French cuisine is a must for me, as it is globally renowned for being among the best. Some dishes, like snails or escargot, may seem strange, but I’m eager to try them. In fact, I’ve tried them and it was not as strange as how people put it. Additionally, I’m looking forward to seeing the diverse landscapes of France, from forests to seas to mountains.
Remember why you started, remember where you’re headed, think of how great it will be to get there, and keep going
Ralph Marston
- Meuwissen, T. H., Hayes, B. J., & Goddard, M. (2001). Prediction of total genetic value using genome-wide dense marker maps. genetics, 157(4), 1819-1829. ↩︎
- Rincent, R., Charpentier, J. P., Faivre-Rampant, P., Paux, E., Le Gouis, J., Bastien, C., & Segura, V. (2018). Phenomic selection is a low-cost and high-throughput method based on indirect predictions: proof of concept on wheat and poplar. G3: Genes, Genomes, Genetics, 8(12), 3961-3972. ↩︎
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