ARS | Publication request: Plastid microsatellite markers in Carya

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 11, 2009
Publication Date: April 1, 2010
Citation: Grauke, L.J., Mendoza-Herrera, M., Binzel, M. 2010. Plastid microsatellite markers in Carya. Acta Horticulturae. 859:237-246.

Interpretive Summary: Plants have DNA that comes in small organelles called plastids. Some plants, like pines, receive the plastid DNA from their male parent in pollen. Some plants receive it from their female parent in the egg. Special molecular markers have been reported that show differences in the plastid DNA. Sometimes, these differences can be used to study the relationships of species in the same genus, or different geographic populations of the same species. We studied 8 plastid markers in the Carya genus, which includes pecan and hickories, and found 3 markers that showed important differences. The plastid DNA in pecans and hickories comes from the mother tree. Species of Carya from Asia were easy to separate from the species in the U.S. and Mexico. The U.S. Carya species share common patterns in their plastid DNA, so it is hard to tell species apart. This is because they have been interbreeding for a long time. The plastid markers were more variable in Mexican pecan populations than they were in pecans collected in the northern U.S. This is probably because the northern pecans are not as old as the Mexican pecans. The plastid markers from Mexican pecans are sometimes different, even in populations that are fairly close together. This may be because the land keeps the trees separated, and people have not mixed the trees together. We do not see the same differences if we use DNA markers from the nucleus of the plant cell, which comes from both the female and male parent. The plastid markers will be useful tools to help us understand how pecans and hickories have moved across large distances over time. Being able to see differences between trees using these markers will help us design tests to see how much the differences matter in things like disease resistance. Having these markers should help us do a better job recognizing differences so we can protect important trees and learn to use them better.

Technical Abstract: PCR primers capable of amplifying polymorphic regions of the plastid genome in Carya have broad applications for characterizing the genus and for conservation and improvement of pecan. We evaluated 8 "universal" plastid primers and qualified 3 as polymorphic and informative. Pecans of known lineage and geographic origin, representatives of other Carya species and interspecific hybrids were profiled. In an analysis of 169 Carya accessions, 21 alleles were observed among the three loci, and combined to form 16 unique plastid microsatellite (cpSSR) haplotypes. Single base pair differences were consistently detectable using the capillary system. Accurate scoring is facilitated using FlexiBinV2. Open pollinated seedlings of a common maternal parent were indistinguishable from each other and the seed parent. Sympatric species of the genus share common plastid haplotypes, while Asian species and the Mexican endemic Carya palmeri have unique profiles. Of the 151 pecans profiled, the 11 haplotypes observed were found to vary in relation to latitude of origin: Mexican pecan populations were the most diverse with 9 haplotypes, 5 of which were found only in Mexico. Northern US pecan populations were characterized by two haplotypes found in members of Section Carya and in Mexico. Plastid markers have been used to maximize diversity in the establishment of seed stock trials for disease resistance.