Integrated map construction and QTL mapping in a tetraploid potato multi-parental population

Unraveling the genetic architecture of potato tuber traits can guide selection and enhance breeding effectiveness. However, this task is challenging due to the complex nature of these traits and the potato’s polyploidy. Fortunately, the development of high-throughput and cost-effective single nucleotide polymorphism (SNP) marker panels, coupled with polyploid-specialized software, have provided efficient ways for discovering quantitative trait loci (QTL) based on genetic linkage-based studies. This study aimed to construct an integrated genetic linkage map from interconnected potato families to identify QTLs linked to tuber shape and skin color traits. These traits are crucial selection targets for meeting the demands of both fresh and processing markets. A multi-parental population was created at EMBRAPA by crossing five females and three males, resulting in seven full-sib families with 36 to 59 individuals per family, totaling 335 individuals. These populations were used to construct an integrated genetic linkage map spanning 1,480.82cM with 2,264 SNPs using the mappoly software package (v. 0.3.3). We identified putative QTL using the diaQTL software package (v 1.10) and estimated additive effects of parental haplotype by regressing phenotypes on the haplotype probabilities. Our analysis revealed a significant QTL on chromosomes 2 and 4, explaining 9% and 14% of the phenotypic variance in tuber shape, respectively. In addition, we detected several QTLs for skin color on chromosomes 1, 2, 9, and 10, with the proportion of explained variation ranging from 3 to 5%. Some of the QTLs identified in our study have been validated by previous research, while others have been newly discovered. We selected six and five clones who inherited desirable alleles based on the effects of particular haplotypes for respective tuber shape and skin color traits. These discoveries improve our understanding of the genetic basis of potato tuber traits, identify significant SNPs for marker-assisted selection, and facilitate the early selection of offspring with increased frequencies of alleles associated with the desired tuber traits, thereby enabling their cultivation in the next breeding cycle. The integrated genetic map derived from the multi-parental population encompasses a large genetic background and enhances the ability to detect QTLs across different genomic regions.