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ARS Home » Pacific West Area » Kimberly, Idaho » Northwest Irrigation and Soils Research » Research » Publications at this Location » Publication #427629
Research Project: Decipher Molecular Mechanisms for Genetic Variations in Agronomically Important Traits to Improve Sugar Beet Disease Resistance and Yield

Location: Northwest Irrigation and Soils Research

Title: Unlocking genetic diversity in Colombian cassava landraces for accelerated breeding

Author
item ZHAO, KEHAN - University Of California, Davis
item Long, Evan
item SANCHEZ, FRANCISCO - International Center For Tropical Agriculture (CIAT)
item MONIER, ERWAN - University Of California, Davis
item CHAVARRIAGA, PAUL - International Center For Tropical Agriculture (CIAT)
item MONROE, GREY - University Of California, Davis

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2025
Publication Date: 1/19/2026
Citation: Zhao, K., Long, E.M., Sanchez, F., Monier, E., Chavarriaga, P., Monroe, G. 2026. Unlocking genetic diversity in Colombian cassava landraces for accelerated breeding. New Phytologist. 250(3):1905-1917. https://doi.org/10.1111/nph.70918.
DOI: https://doi.org/10.1111/nph.70918

Interpretive Summary: This study examines 387 newly sequenced cassava landrace (prebreeding) varieties from diverse Colombian climates. These landraces, originating near the Amazon basin, showcase significant genetic diversity, unlike the bottlenecked breeding lines from Asia and Africa. The genetic variation aligns with geographic and climatic origins, potentially serving a wealth of adaptive traits that can improve modern crop varieties. This study examines the genetic diversity, giving special attention to high impact Loss-of-Function mutations that may explain local adaptation. Understanding the causal mutations that may define local environmental adaptation can accelerate breeding efforts to expand growing regions of crops and help develop cassava varieties adapted to specific regions of the world.

Technical Abstract: Cassava (Manihot esculenta Crantz) is a staple food for hundreds of millions across the global south. In this study, we investigated genomic diversity among over 1000 cassava genotypes, with a particular focus on the addition of 387 newly sequenced landrace varieties originating from diverse climates across Colombia. As cassava was domesticated in or near the Amazon basin, these landraces represent untapped genetic diversity that could be used to help improve modern varieties. As theory predicts, we found that landraces retain high genetic diversity, observing variation lacking in breeding lines from Asia and Africa, where introductions likely caused population bottlenecks. Genetic differentiation in landraces reflects both space and climate of origin, suggesting the combined effects of demography and selection. To identify alleles with the potential to inform targets for gene editing, we assessed the diversity of loss-of-function (LoF) mutations across these landraces. We found evidence that deleterious LoF alleles were purged by inbreeding. Notably, genes retaining LoF alleles despite inbreeding were significantly enriched for functions related to the biosynthesis of coumarins and the regulation of plant immunity, suggesting selection on postharvest quality and disease resistance. We further identified specific loci associated with climates of origin, motivating future experiments using targeted knockouts to test hypotheses about the adaptive value of specific LoF alleles. This work supports longstanding hypotheses about landraces as a reservoir of genetic diversity and establishes the foundation to leverage this variation in cassava to discover alleles for accelerated breeding via gene editing.