Association mapping and molecular marker development for cassava brown streak disease resistance
7 affiliations
- 1International Center for Tropical Agriculture (CIAT)
- 2Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
- 3International Institute for Tropical Agriculture (IITA)
- 4Department of Plant Sciences, University of California
- 5Tanzania Agricultural Research Institute (TARI)
- 6State Key Laboratory of Genome and Multi-omics Technologies, BGI Research
- 7International Center for Tropical Agriculture (CIAT) Asia Office
Abstract
Introduction: Cassava brown streak disease (CBSD) – caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) – severely threatens cassava production and food security in sub-Saharan Africa. Breeding for resistance is the most sustainable control strategy, but it requires reliable resistance sources and a clear understanding of the underlying genetic mechanisms.
Methods: In this study, we utilized resistance introduced from Latin American cassava germplasm and mapped the genetic basis of CBSD resistance relevant to African environments. Whole-genome sequencing (WGS) was applied to a segregating population consisting of 426 F1 progeny derived from crosses with CBSD-resistant lines and genome-wide association studies (GWAS) conducted to dissect the genetic basis of resistance.
Results and discussion: A major QTL on chromosome 11 was consistently and significantly associated with CBSD resistance across multiple GWAS models tested and marker types (SNPs and indels), explaining up to 34.89% of the phenotypic variation. Three Kompetitive Allele Specific PCR (KASP) markers were developed and validated from the associated SNPs. All three markers successfully differentiated between known resistant and susceptible parental lines and the mapping population, and one remained significantly associated with resistance in a broader validation population. Interestingly, the same resistance region was previously reported in genetic mapping of East African germplasm, highlighting the central role of this locus across diverse genetic backgrounds. Developing these markers targeting the major chromosome 11 QTL provides a practical molecular tool to accelerate marker-assisted selection and facilitate the development of resistant cassava varieties, ultimately enhancing food security and supporting farmer livelihoods in regions affected by CBSD in Africa.
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BibTeX
@article{sanchezsarria2026association,
title = {{Association mapping and molecular marker development for cassava brown streak disease resistance}},
author = {Camilo E. Sánchez-Sarria and Samar Sheat and Stephan Winter and Edward Kanju and Xiaofei Zhang and Nelson Morante and Carmen A. Bolaños and Luz A. Gómez-Martínez and Adriana Bohorquez-Chaux and Edda Mushi and Emmanuel Mrema and Kasele Salum and Ting Yang and Tong Wei and Jonathan Newby and Winnie Gimode},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1977387},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1977387/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Association mapping and molecular marker development for cassava brown streak disease resistance
AU - Camilo E. Sánchez-Sarria
AU - Samar Sheat
AU - Stephan Winter
AU - Edward Kanju
AU - Xiaofei Zhang
AU - Nelson Morante
AU - Carmen A. Bolaños
AU - Luz A. Gómez-Martínez
AU - Adriana Bohorquez-Chaux
AU - Edda Mushi
AU - Emmanuel Mrema
AU - Kasele Salum
AU - Ting Yang
AU - Tong Wei
AU - Jonathan Newby
AU - Winnie Gimode
PY - 2026
DA - 2026/10/16
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1977387
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1977387/full
AB - Introduction: Cassava brown streak disease (CBSD) – caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) – severely threatens cassava production and food security in sub-Saharan Africa. Breeding for resistance is the most sustainable control strategy, but it requires reliable resistance sources and a clear understanding of the underlying genetic mechanisms. Methods: In this study, we utilized resistance introduced from Latin American cassava germplasm and mapped the genetic basis of CBSD resistance relevant to African environments. Whole-genome sequencing (WGS) was applied to a segregating population consisting of 426 F1 progeny derived from crosses with CBSD-resistant lines and genome-wide association studies (GWAS) conducted to dissect the genetic basis of resistance. Results and discussion: A major QTL on chromosome 11 was consistently and significantly associated with CBSD resistance across multiple GWAS models tested and marker types (SNPs and indels), explaining up to 34.89% of the phenotypic variation. Three Kompetitive Allele Specific PCR (KASP) markers were developed and validated from the associated SNPs. All three markers successfully differentiated between known resistant and susceptible parental lines and the mapping population, and one remained significantly associated with resistance in a broader validation population. Interestingly, the same resistance region was previously reported in genetic mapping of East African germplasm, highlighting the central role of this locus across diverse genetic backgrounds. Developing these markers targeting the major chromosome 11 QTL provides a practical molecular tool to accelerate marker-assisted selection and facilitate the development of resistant cassava varieties, ultimately enhancing food security and supporting farmer livelihoods in regions affected by CBSD in Africa.
SN - 1664-462X
ER -