Multi-parental population linkage-based analysis reveals QTL for quality traits in cassava

The quality of cassava roots is a major goal for cassava cultivation and breeding all over the world. Understanding the genetic architecture of quality traits in cassava is a valuable tool for root improvement that favors consumer preference and industrial applications. Thus, quality traits such as dry matter content (DMC), hydrogen cyanide content (HCN), and water absorption (WAB) are critical in cassava improvement programs. Multi-parental populations leveraging both parental genetic diversity and genetic linkage are expected to increase quantitative trait loci (QTL) detection power and usefulness. Hence, this study aimed to identify QTL for quality traits in cassava using linkage-based analysis for multiparental populations. Derived from seven parents, five populations comprising 218 cassava clones were genotyped using whole genome sequencing and evaluated for DMC, HCN, WAB_20, and WAB_30 (WAB after 20 and 30 minutes, respectively) by CIAT, in Cali, Colombia. Linkage maps were constructed for the individual populations, followed by consensus map integration using the mappoly2 package. QTL analysis associating quality traits and the resulting haplotype probabilities derived from the consensus map was performed using the stagegenMPP v. 1.0.2 package. Our results showed a significant (p < 0.001) and strong (r > 0.6) correlation among DMC, WAB_20, and WAB_30, while heritability values ​​ranged between 0.32 (HCN) and 0.67 (DMC). A 2,810-cM consensus map made up of 4,625 SNPs revealed four QTLs, one on Chr01, Chr03, Chr08, and Chr09 each. A major QTL, on Chr01_34582819, was found to be associated with DMC (R ² = 59.8%, LOD = 6.83), WAB_20 (R ² = 50.6%, LOD = 4.70), and WAB_30 (R ² = 39.1%, LOD = 4.31). Parental contributions to quality traits revealed COL1910, COL1505, and COL2246 contributed positively to DMC, WAB_20, and WAB_30, while VEN25, SM3759-36, and COL2246 contributed negatively to HCN. This major QTL (Chr01_34582819) can assist in the simultaneous selection or improvement of DMC, WAB_20, and WAB_30. While QTL-associated markers would be valuable assets for marker-assisted and genomic selection, parents or progenies identified in this study with haplotypes of interest can serve as breeding lines for cassava quality traits in improvement programs.