Mid-density SNP panel allows for parentage confirmation and identification of loci associated to flesh and skin color in sweetpotato

Ipomoea batatas (L.) Lam., known as sweetpotato, is a hexaploid (2n=6x=90) root crop of global importance for food security. Recent advances in genotyping technologies, particularly Diversity Arrays Target Genotyping (DArTag), have enabled routine molecular characterization in this species. More specifically, parentage analysis aims to confirm the identity of parents, track crosses, and construct reliable pedigrees, whereas genome-wide association studies (GWAS) are used to link single-nucleotide polymorphisms (SNP) to phenotypes. Here, we performed a parentage analysis to correctly identify families, and GWAS for flesh and skin colour using DArTag-derived SNPs. Two F₁ populations were obtained by the Sweetpotato Genetic Improvement Program of the Universidade Federal de Lavras (UFLA). A common parent “Ligeirinha” (cream fleshed) was crossed with “Irene” (orange fleshed, rich in β-carotene) and “UFLA R-1440” (purple fleshed, rich in anthocyanin), resulting in 109 and 228 individuals, respectively. Out of 3120 SNPs, 2380 were kept after filtering. A dendrogram derived from the genome relationship matrix (AGHmatrix R package), and a principal component analysis (pcaMethods R package) have shown the existence of putative mislabeled individuals across families. Maximum likelihood-based parentage analysis (PolyGene software) was run based on 300 SNPs from random selection of 20 independent SNPs (r² < 0.2) per chromosome. Parents were correct for most individuals: 218 individuals were effectively derived from “Ligeirinha” and “UFLA R-1440” crossing, and 106 individuals from “Ligeirinha” and “Irene” (confidence > 95%). The remaining individuals were linked to additional three different parents from the UFLA germplasm bank population, indicating contamination. The corrected “Ligeirinha” × “UFLA R-1440” biparental population revealed association (GWASpoly R package) in chromosomes 11 and 12 for flesh colour; and in chromosomes 7, 12 and 14 for skin colour. The SNPs in chromosome 12 coincide with the anthocyanin-related MYB gene clusters in I. trifida and I. triloba reference genomes. This study shed light to future marker-assisted selection applications and identification of genes related to traits of interest. Promisingly, correct pedigree will facilitate further linkage-based map and quantitative trait loci studies.