Verifying the Mandarin Breeding: Lessons from Parentage Analysis of Citrus Varieties

Eliminating the genotyping error is essential for minimizing false correlation on linkage analysis, but the difficulties of estimating it on various combinations of varieties will give ambiguities on pedigree analysis or genome wide association study (GWAS). The higher polymorphism frequencies among citrus varieties due to wide genetic variations within them often hinder applying these markers on different crosses that could harbor an unforeseen polymorphic site within primer binding site. These unforeseen polymorphisms result to give combination dependent aberrant segregation (CASE) because of their false genotypes. Validating the probability of CASE for each DNA marker is a high priority, but the evaluation is often difficult to achieve due to the constraints of preparing parent-child materials for every combination of the varieties.In this study, we evaluated SSR markers for their segregation by more than 90 trio sets selected from our breeding program. The passed SSR markers showed no discrepancy on most of the trios examined, and remained trios were wrong combination of their parents. Based on these studies, we confirmed the parent of Clementine, and the parentage of these hybrids. Then, we identified the parent of Satsuma mandarin, and estimated the birth of it. Accordingly, we could understand an offspring of Satsuma mandarin or Clementine as an offspring of their grandparents. These observations enable us to understand the genetic background of mandarin hybrid obtained by our breeding program as a hybrid of their distant progenitors, and it would also contribute improving the estimation accuracy of GWAS analysis.