Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America

• Published in: Scientific reports 2024-10, Vol.14 (1), p.23141-13, Article 23141
• Main Authors: Ospina, Jessica A., Lopez-Alvarez, Diana, Gimode, Winnie, Wenzl, Peter, Carvajal-Yepes, Monica
• Format: Article
• Language: English
• Subjects: 631/208; 631/337; 631/449; 631/61; Association analysis; Cassava; Cassava brown streak disease (CBSD); Chromosomes; Crop diversification; Crops; Disease; Disease resistance; Disease Resistance - genetics; Ex-situ conservation; Gene frequency; Gene polymorphism; Genetic analysis; Genetic diversity; Genetic resources; Genetic variance; Genetics; Genome, Plant; Genome-wide association studies; Genome-Wide Association Study; Genome-wide association study (GWAS); Genomes; Genomic analysis; Genotype; Genotypes; Germplasm; Humanities and Social Sciences; Immune response; Manihot - genetics; Manihot - parasitology; Manihot - virology; Manihot esculenta; Molecular breeding; multidisciplinary; New varieties; Plant breeding; Plant Diseases - genetics; Plant Diseases - virology; Polymorphism, Single Nucleotide; Potyviridae; Raw materials; Science; Science (multidisciplinary); Single-nucleotide polymorphism; South America; Transcription activation
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-74161-6

Cassava ( Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world’s largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.