M2/ENGINEERING INTERNSHIP: GENETIC DIVERSITY OF CORN

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

Context

The search for relevant sources of genetic diversity and their introduction into breeding programs is a major challenge for maintaining the long-term efficiency of breeding programs and enabling the adaptation of selection criteria to new challenges related to climate change and evolving farming practices. Various sources of diversity can be considered to enrich an elite program (see typology by Sanchez et al., 2023). Simulation studies (Allier et al. 2020; Sanchez et al., 2023) carried out by GQE-Le Moulon, have shown that the success of an introduction program depends on the performance gap between elite genotypes and diversity donors and on the ability to identify the most interesting donors to complement the elite material. Different approaches can be considered when selecting donors, based on their agronomic performance or on criteria based on genomic predictions that take into account complementarity with elite material across the genome (Sanchez et al., 2023).

In the case of cross-pollinated species such as maize, breeding schemes aim to produce hybrid varieties obtained by crossing two unrelated lines. This process requires managing complementarity between complementary gene pools (known as heterotic groups) to prevent inbreeding of intergroup hybrids. The existence of these heterotic groups, largely shaped by one century of modern hybrid breeding, limits gene flow between groups and the possibilities for introducing ancient genetic resources (from ancient population varieties, grown before the advent of hybrids) or sources of diversity created from commercial hybrids. The hybrid variety protection system in the United States (“Patent Variety Protection” or “pvp”) prevents hybrids from being used in breeding. Once the protection expires after 20 years, the parental lines of the hybrids become accessible (known as “ex-PVP” lines) and constitute a source of potential diversity, albeit an old one, but one that corresponds to lines that have been commercially successful. The UPOV protection system, used in France in particular, is based on the protection of hybrids whose parental lines are not accessible, but allows breeders to use hybrid varieties currently on the market as a source of diversity in their breeding programs (“breeder’s exception”). These two protection systems therefore raise interesting questions in terms of accessibility to genetic diversity. The choice between these two sources of diversity illustrates the trade-off between (i) the age of the material, which favors more recent commercial hybrids, and (ii) its positioning in well-established heterotic groups in the US and Europe, which favors ex-PVP lines that generally belong to a clearly identified group.

Objectives

The objectives of the internship are (i) to evaluate genetic progress and the evolution of divergence between heterotic groups over time in an elite program (ii) to evaluate the relative value of different sources of diversity (recent ex-PVP, lines derived from commercial hybrids, lines derived from traditional populations) and (ii) to identify the most relevant donors to enrich the diversity of two complementary heterotic groups by considering different criteria. The internship is based on the analysis of a panel of lines, evaluated for their hybrid performance, dedicated to the detection of donors providing chromosomal fragments superior to those already present in the elite pools currently under selection.

Plant material:

A panel of 400 lines was assembled in consultation between MAS Seeds, INRAE, and Agri Obtentions (INRAE subsidiary in charge of variety obtentions). It includes lines of different origins (public lines and MAS Seeds lines) corresponding to different selection periods and covering both protection systems (USA versus UPOV).

This panel was crossed with two MAS Seeds testers belonging to two complementary heterotic groups. The resulting hybrids (800) were evaluated jointly by MAS Seeds and INRAE in a total of three trials between 2024 and 2025. In addition, the student will have access to data from a factorial evaluation conducted on a multi-trial network by MAS Seeds.

All material has been genotyped and approximately 20K SNPs will be available for this study. 

Analyses:

During the internship, the student will:

-Analyze genotyping data to study diversity in the panel and position the diversity present in MAS Seeds material in relation to potential donors of diversity and estimate genetic distance matrices that will be used for genomic prediction. These data will also be used to estimate a coefficient of inbreeding for hybrids. 

-Process raw phenotypic data from various trials in order to correct for any field heterogeneity, estimate variance components (G, GxE, etc.), and decompose hybrid performance into AGC and ASC.

-Estimate the evolution of the elite genetic level over time (long series ranging from historical lines to more recent MAS Seeds lines), which will enable us to answer the following questions: how quickly does the performance gap between donors and elite material evolve depending on the number of selection cycles between them? How has specific combination ability developed over time? This work will be carried out taking into account the covariate of inbreeding estimated on the basis of molecular markers (see Larièpe et al., 2017; Roth et al., 2022).

-Compare plant variety protection systems by studying material from the two protection systems, USA and UPOV. 

-Calibrate genomic prediction models to evaluate the ability of such models to detect donors of interest.

-Visualize the value of haplotypes (highlighted using a method to be determined) along the genome for suitability for combination with each of the two groups.

-The work as a whole will enable the recommendation of haplotypes from donors to be introgressed into the two elite populations of MAS Seeds.

Bibliography:

Allier, A., Teyssèdre, S., Lehermeier, C., Claustres B., Maltese S., Melkior, Moreau L., Charcosset A. (2019) Assessment of breeding programs sustainability: application of phenotypic and genomic indicators to a North European grain maize program. Theor Appl Genet 132, 1321–1334. https://doi.org/10.1007/s00122-019-03280

Larièpe A., L. Moreau, J. Laborde, C. Bauland, S. Mezmouk, et al., 2016 General and specific combining abilities in a maize (Zea mays L.) test-cross hybrid panel: relative importance of population structure and genetic divergence between parents. Theor. Appl. Genet. https://doi.org/10.1007/s00122-016-2822-z

Roth M., Beugnot A., Mry-Huard T., Moreau l., Charcosset A, Fievet J., 2022 Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts, Genetics 220  https://doi.org/10.1093/genetics/iyac018

Sanchez D., Ben Sadoun S, Mary-Huard T, Allier A., Moreau L, Charcosset A. (2023) Improving the use of plant genetic resources to sustain breeding programs’ efficiency. PNAS Vol. 120  No. 14 e2205780119.  https://doi.org/10.1073/pnas.2205780119

Training and skills

Skills and abilities:

The intern must be highly motivated in quantitative genetics, data analysis, and statistics, and have knowledge of R software.

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

I send my CV and my motivation letter