Does pedigree tell the whole story? Comparing pedigree-based and genomic relationships in tropical wheat

Pedigree information describes the expected relationship among genotypes, whereas molecular markers provide a direct representation of the realized genomic relationship. This study compared pedigree-based and genomic relationships in tropical wheat germplasm from the Wheat Breeding Program of the Federal University of Viçosa. A total of 342 cultivars, breeding lines, and progenies were genotyped with the Wheat 3.9K DArTag panel. After quality control, 335 genotypes and 2,382 SNP/INDEL markers were retained. The additive relationship matrix based on pedigree (A) and the genomic relationship matrix proposed by VanRaden (G) were compared using Pearson and Spearman correlations and the Mantel test. The matrices showed a significant positive association, with Pearson and Spearman correlations of 0.571 and 0.540, respectively, and a significant Mantel test (p = 0.0001). Matrix A presented a discrete distribution concentrated near zero and at expected relationship classes, whereas matrix G showed a continuous distribution from negative to positive values. Therefore, pedigree captured an important part of the genetic structure, but genomic information revealed variation not represented by genealogical records. The joint use of A and G provides complementary information for germplasm organization, redundancy identification, and parental selection.