Species-specific plastid SSR markers reveal evidence of cultivar misassignments in Brazilian pecan orchards

Abstract Pecan is an important perennial species introduced in southern Brazil more than 80 years ago with cultivars originating from the USA. The expansion of planted areas in Brazil is limited due to poor performance of some cultivars in regions climatically different from the original distribution area of the species. The development of cultivars adapted to the Brazilian edaphoclimatic conditions is, therefore, needed. As the correct identification of registered cultivars is essential for the development of pecan breeding programs, this study aimed at using a novel set of plastid SSR markers for identifying possible misassignments in Pecan cultivars from southern Brazilian orchards. Twenty-four plants of eight commercial cultivars and three plants from open-pollinated origin were genotyped using ten plastid SSR markers. These markers were developed from the plastid genome of the pecan cultivar Imperial. The plastid markers, which have maternal inheritance in pecan, clearly represented the parental relationship among cultivars Shawnee, Jackson, Success, and Barton. The low genetic differentiation between cultivars Shawnee and Jackson reflected the close relationship of half-sibs since both have cultivar Schley as maternal parent. The samples of cultivar Barton formed a single clade in the UPGMA cluster analysis. On the other hand, there was no consistent grouping of plants identified as Imperial, Melhorada, Mahan, Jackson, Shawnee, Success, as well as those from open-pollinated origin. Thus, samples named Barton have the same genetic patterns, while some samples named Imperial, Melhorada, Mahan, Jackson, Shawnee, Success are likely misassigned. The plastid microsatellite markers used in this study are relevant tools for advancing breeding programs of pecan, through the selection of genotypes, characterization of genetic diversity and identification of genitors.