Solarte Certuche, D. C. | Search bioRxiv

bioRxiv2026

Uncovering genomic regions controlling root quality traits in Cassava (Manihot esculenta Crantz) using different GWAS models

Cassava is a major staple crop in tropical regions, and improving its root nutritional quality, particularly carotenoid and dry matter content (DMC), remains a central breeding goal. To elucidate the genetic basis of these traits by locating genomic regions associated with them, we analyzed 3,043 cassava clones from the Brazilian Agricultural Research Corporation (Embrapa) breeding program, phenotyped across 188 multi-environment trials conducted from 2011 to 2022 in Brazil. All clones were genotyped using Genotyping-by-Sequencing (27,045 Single Nucleotide Polymorphism - SNPs) and Diversity Arrays Technology - DArTseq (25,923 SNPs). Trait values were estimated using a two-stage mixed model to obtain deregressed BLUPs (Best Linear Unbiased Predictions), and genome-wide association analyses were performed using both the Mixed Linear Model (MLM) and Multi-Locus Mixed Model (MLMM). We detected six significant SNPs consistently associated with carotenoid content and DMC after Bonferroni correction. These SNPs mapped to six candidate genes involved in pathways relevant to root physiology, including Abscisic Acid ABA-related signaling, hydrolase activity affecting carotenoid conversion, fatty-acid biosynthesis within plastids, cell-wall remodeling, and glycolytic energy metabolism. The loci jointly explained 75.56 % of the phenotypic variance for carotenoids and 76.23 % for DMC, with individual SNP effects ranging from [~]17 % to [~]42 % PVE (Proportion of Variance Explained). Broad-sense heritability was H2 = 0.78 for carotenoids and H{superscript 2} = 0.34 for DMC, confirming substantial genetic control and suitability for molecular breeding. Haplotype analyses revealed four superior haplotypes for carotenoids and one key haplotype for DMC, each showing significantly higher trait values compared with other allelic combinations. These haplotypes represent promising targets for marker-assisted selection and genomic selection, with direct applicability for accelerating genetic gain in elite breeding populations. The results provide actionable genomic resources for breeding programs aiming to develop biofortified and high-root quality cultivars and establish a foundation for future multi-omics and functional validation studies.

genetics↗

bioRxiv2026

Unraveling candidate genomic regions responsible for delayed post-harvest deterioration in Cassava (Manihot esculenta Crantz)

Post-harvest physiological deterioration (PPD) represents a significant challenge of cassava production and commercialization. This multifaceted biological process involves a series of mechanisms, including enzymatic stress responses, alterations in gene expression, protein synthesis, accumulation of secondary metabolites, and ultimately, programmed cell death. These changes render the storage roots unpalatable and unmarketable. Therefore, unraveling the genetic architecture of PPD and exploring the interactions of associated genes during its early and late stages is essential for the crop production. We used modern genetic resources to unravel the genetic basis of PPD, based on a genome-wide association study (GWAS), utilizing a combination of different models, including BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway), SUPER (Settlement of MLM Under Progressively Exclusive Relationship), and MLMM (Multi-locus mixed models). The phenotyping dataset spanned five years and included evaluations from 42 different trials, evaluating the Embrapa (Brazilian Agricultural Research Corporation) germplasm along with a population derivative from a genomic selection cycle. We utilized a genotype dataset comprising 26,000 high-quality SNPs (single nucleotide polymorphisms). Our findings indicated four significant genetic variants located on chromosomes 2, 5, and 13, which together explain 35.83 % of the phenotypic variation. These variants are associated with genes that are closely linked to the pathways activated during the early and late symptoms of PPD. The identification of these three key genes provides valuable insights into the genetic architecture of PPD and lays a strong foundation for molecular breeding, supporting the efforts to identify cassava genotypes with enhanced PPD tolerance, the identified genomic regions may be incorporated into genomic selection models, thereby enhancing marker-assisted selection (MAS) and improving breeding strategies for long shelf life and high-quality agronomic cassava cultivars for the cassava community.

genetics↗