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Scientists generate farmer-preferred haplotype-resolved cassava reference genome
February 26, 2024

IITA–CGIAR PhD student Michael Landi, with the support of IITA scientists Livia Stavolone, Trushar Shah, and Andreas Gisel and in collaboration with the Swedish University of Agricultural Sciences in Uppsala, Sweden, the University of Fribourg in Switzerland, and the Italian Research Council in Bari, Italy, generated a haplotype-resolved diploid assembly of the cassava cultivar TMEB117, a farmer-preferred cassava cultivar, using PacBio HiFi reads. The high-quality genome assembly was published in December 2023 and is a part of the EpiCass and CassavaNet4Dev projects, both funded by the Swedish Research Council.

This plot displays repeat and gene densities for the two haplotypes visualized in 1 Mbp sliding windows. The tracks from the outer to inner show (i) Repeat density for hap1 genome, (ii) Gene density for hap1 genome, (iii) Repeat density for hap2 genome, and (iv) Gene density for hap2 genome.
This plot displays repeat and gene densities for the two haplotypes visualized in 1 Mbp sliding windows. The tracks from the outer to inner show (i) Repeat density for hap1 genome, (ii) Gene density for hap1 genome, (iii) Repeat density for hap2 genome, and (iv) Gene density for hap2 genome.

TMEB117 (also called TME117 or isunikankiyan) is a Nigerian cassava landrace highly susceptible to African cassava mosaic virus (ACMV). This genotype served as a reference for ACMV studies, and this high-resolution genome will pave the way for the ongoing investigations in epigenetics and small RNA expression analysis to learn more about the mechanisms of ACMV resistance in cassava and the large variability in storage root yield between plants of the same genotype in the same field. The outcome of these studies will give insight into the molecular mechanisms and create data and knowledge to support future breeding programs.

Chromosome by chromosome comparison of TME117 haplotype 1 genome (blue line) with the official Cassava reference genome sequence version 8 (orange line). Sequence inversions are visualized in orange connections between the two genomes, and in grey, the similar regions and the empty regions are inserts or deletions.
Chromosome by chromosome comparison of TME117 haplotype 1 genome (blue line) with the official Cassava reference genome sequence version 8 (orange line). Sequence inversions are visualized in orange connections between the two genomes, and in grey, the similar regions and the empty regions are inserts or deletions.

Despite the use of various sequencing technologies over time, there are unresolved gaps in the genome. The reference genome AM560-2, derived from a Colombian cassava line MCol505, has undergone steady improvement over a decade and has had five major releases, with the current version being AM560-2 version 8. While this reference genome benefits the cassava community, it lacks haplotypic separation and does not capture the genetic diversity in African cassava cultivars grown by smallholder farmers due to its homozygous nature.

Recently, attempts have been made to assemble genomes of African cassava lines such as TME3, 60444, TME7, and TME204, using a combination of Illumina short reads, PacBio long reads, bio-nano optical mapping, and chromatin conformation capture (Hi-C) sequence technologies. Only the last two attempts produced high-quality and haplotype-resolved reference genomes of African cassava genotypes.

Contributed by Andreas Gisel

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Olaosebikan, Olamide

Olamide Deborah Nwanze is a Senior Research Associate specializing in gender mainstreaming research to inform participatory and inclusive breeding, variety development, and seed systems policies regarding root, tuber, and banana (RTB) crops in the International Institute of Tropical Agriculture Headquarters, Ibadan, Nigeria. She is a PhD candidate at the University of Ibadan and holds an MSc and B. Agric in Agricultural Extension and Rural Development. Olamide is a fellow of the African Women in Agricultural Research and Development – Gender Responsive Agricultural Systems Policy (AWARD-GRASP) and the Gender Responsive Researchers Equipped for Agricultural Transformation (GREAT). She seeks to apply her gender-mainstreaming learnings, gender-responsive research, and policy development, and review expertise to facilitate women, youth, children, and vulnerable social group’s access to and adoption of agricultural Innovations that guarantee food, nutrition, income, and livelihood security in Africa. Her current roles include mentoring research fellows, development of guides and training manuals, implementation and adaptation of gender frameworks and tools, value chain actors’ engagement as citizen science partners, policy review and redesign, data management, and analysis. Her current research explores mixed methods and participatory and interdisciplinary approaches to capture and highlight gender dynamics, needs, preferences, and challenges stakeholders face within the agricultural livelihood value chain to prioritize gender-inclusive strategies in breeding programs, policy design, and implementation.

At IITA, she contributes to the implementation of the CGIAR Accelerated Breeding Initiative and Genetic Innovation Programs; participatory and gender research within the NextGen Cassava, HarvestPlus, RTBFoods, and Tricot-ClimMob 1000Farms Projects; and gender knowledge communication via the G-LENS webinar series, video documentary, policy briefs, publications, and blogs.

 

Recent publications

de Sousa, K., van Etten, J., Manners, R. Bello, A., Teeken, B., Olaosebikan, O., et al. 2024. The tricot approach: an agile framework for decentralized on-farm testing supported by citizen science. A retrospective. Agron. Sustain. Dev. 44, 8. https://doi.org/10.1007/s13593-023-00937-1

Madu, T., Onwuka, S., Nwafor, S., Onyemauwa, N., Ejechi, M., Ofoeze, M., Ukeje, B., Eluagu, C., Olaosebikan, O., Okoye, B., 2024. Gender-Inclusive Consumer Studies Improve Cassava Breeding in Nigeria in: Frontiers in Sociology, volume 9, number: 1224504, doi: 10.3389/fsoc.2024.1224504

Olaosebikan, O.; Bello, A.; Utoblo, O.; Okoye, B.; Olutegbe, N.; Garner, E.; Teeken, B.; Bryan, E.; Forsythe, L.; Cole, S.; Madu, T. 2023.  Stressors and Resilience within the Cassava Value Chain in Nigeria: Preferred Cassava Variety Traits and Response Strategies of Men and Women to Inform Breeding. Sustainability 15, 7837. https://doi.org/10.3390/su15107837

Okoye, B., Ofoeze, M., Ejechi, M., Onwuka, S., Nwafor, S., Onyemauwa, N., Ukeje, B., Eluagu, C., Obidiegwu, J.*, Olaosebikan, O., Madu, T.* 2023. Prioritizing preferred traits in the yam value chain in Nigeria: a gender situation analysis in: Frontiers in Sociology, volume 8, number: 1232626, pages 1 – 9, ISSN 2297-7775, 2023. https://www.frontiersin.org/articles/10.3389/fsoc.2023.1232626/full

Olaosebikan, O., Bello, A. A., de Sousa, K., Ndjouenkeu, R., Adesokan, M., Alamu, E. O., Agbona, A., van Etten, J., Kegah, F. N.*, Dufour, D., Bouniol, A., Teeken, B. 2023. Consumer acceptability of cassava gari-eba food products across cultural and environmental settings using the triadic comparison of technologies approach (tricot) in: Journal of the Science of Food and Agriculture,

Teeken, B., Olaosebikan, O., Bello, A. A., Madu, T.*, Cole, S. M. 2023. Qualitative assessment on the positionality and preferences of dyads in relation to cassava-related activities: working with tricot trial citizen scientists https://hdl.handle.net/10568/138326 Type: Manual

Bouniol, A., Ceballos, H., Bello, A. A., Teeken, B., Olaosebikan, O., Owoade, D., Agbona, A., Fotso Kuate, A., Madu, T.*, Okoye, B.*, Ofoeze, M.*, Nwafor, S.*, Onyemauwa, N.*, Adinsi, L.*, Forsythe, L., Dufour, D. 2023. Varietal impact on women’s labour, workload and related drudgery in processing root, tuber and banana crops: focus on cassava in sub-Saharan Africa in: Journal of the Science of Food and Agriculture, pages 1 – 25, ISSN 0022-5142,

Bello, A. A., Agbona, A., Olaosebikan, O., Edughaen, G., Dufour, D., Bouniol, A., Iluebbey, P., Ndjouenkeu, R.*, Rabbi, I. Y., Teeken, B. 2023. Genetic and environmental effects on processing productivity and food product yield: drudgery of women’s work in: Journal of the Science of Food and Agriculture, pages 1 – 32, ISSN 0022-5142, 5

Cavicchioli, M., Zimbiti, T., Teeken, B., Nwanze, D.O., Liani, M., Parkes, E. & Bello, A. 2023. IITA-Gender Responsive Breeding Training Report. Genetic Resources Center, IITA-HQ, Ibadan, 21-23 September, 2022. Ibadan, Nigeria: IITA, (34 p.).https://hdl.handle.net/10568/131368

Agbona, A. Peteti P., Teeken B., Olaosebikan O. Bello, A. A., Parkes, E., Rabbi, I. Y., Mueller, L., Egesi, C., Kulakow, P. 2022. Data Management in Multi-disciplinary African RTB Crop Breeding Programs. In: Williamson, H.F., Leonelli, S. (eds) Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development. Springer, Cham. https://doi.org/10.1007/978-3-031-13276-6_5

Lora Forsythe, Pricilla Marimo, Sarah Mayanja, Olamide D. Olaosebikan, Esme Stuart, Bela Teeken, Benjamin Okoye, Tessy Madu, (2021). Cross-product Gender Analysis of RTBfoods Step 2 Gendered Food Mapping on RTB Products. Understanding the Drivers of Trait Preferences and the Development of Multi-user RTB Product Profiles, WP1. London, UK: RTBfoods Field Scientific Report, 30 p.

Teeken, B., Garner, E., Agbona, A., Balogun, I., Olaosebikan, O., Bello, A., Madu, T., Okoye, B., Egesi, C., Kulakow, P. and Tufan, H.A. 2021. Beyond “Women’s Traits”: Exploring How Gender, Social Difference, and Household Characteristics Influence Trait Preferences. Frontiers Sustainable Food Systems 5:740926. https://doi.org/10.3389/fsufs.2021.740926

Teeken, B., Agbona, A., Bello, A., Olaosebikan, O., Alamu, E., Adesokan, M., Awoyale, W., Madu, T., Okoye, B., Chijioke, U., Owoade, D., Okoro, M., Bouniol, A., Dufour, D., Hershey, C., Rabbi, I., Maziya‐Dixon, B., Egesi, C., Tufan, H. and Kulakow, P. (020. Understanding cassava varietal preferences through pairwise ranking of gari‐eba and fufu prepared by local farmer–processors. Int J Food Sci Technol. https://doi.org/10.1111/ijfs.14862

Bela Teeken, Olamide Olaosebikan, Ireti Balogun, Benjamin Okoye, Tessy Madu, Steven Cole, Abolore Bello, Elizabeth Parkes. (2020). Piloting the G+ customer and product profile tools for gender-responsive cassava breeding in Nigeria. Nigeria: International Institute of Tropical Agriculture (IITA). https://hdl.handle.net/20.500.11766/13000