Inter- and intraspecific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiata D. Don

Abstract

DNA sequence analysis of chloroplast genomes has revealed many short nucleotide repeats analogous to nuclear microsatellites, or simple sequence repeats (SSRs). We designed PCR primers flanking five of these regions identified in the chloroplast sequence from Pinus thunbergii and tested them for amplification in Pinus radiata, P. elliotii, P. taeda, P. strobus, Pseudotsuga menziesii, Cupressus macrocarpa, four New Zealand native conifer species (Podocarpus totara, Podocarpus hallii, Podocarpus nivalis, Agathis australis), and four angiosperms (Vitex lucens, Nestegis cunninghamii, Actinidia chinensis, and Arabidopsis thaliana). A PCR product in the expected size range was amplified from all species and interspecific polymorphism was detected at all five loci. Intraspecific polymorphism was detected in P. radiata with four of the five primer pairs. One of these polymorphic chloroplast SSR (cpSSR) was then used to determine the inheritance of chloroplasts in 206 progeny from four control-pollinated, full-sibling P. radiata families. Approximately 99% of the progeny had the cpSSR variant of the pollen parent indicating that in Pinus radiata, like most other conifers, chloroplasts are typically inherited from the paternal parent. These results suggest that polymorphic chloroplast SSRs will be a valuable tool for studying chloroplast diversity, cyto-nuclear disequilibrium, and plastid inheritance in a range of species, and for the analysis of gene flow via pollen and paternity in species with paternal transmission of chloroplasts.

The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

“…However, SSR loci contained in the plant cp genome can provide useful information about plant population genetics (Echt et al, 1998;Powell, 1995a). SSRs in the cp genome were initially reported in studies of Pinus radiata and Oryza sativa (Cato and Richardson, 1996;Powell et al, 1995b;Provan et al, 1996). Kim and Lee (2004) also reported 18 SSR loci in the Panax cp genome and 29 in the Nicotiana cp genome.…”

Somatic stability of microsatellite loci in Eastern white pine, Pinus strobus L.

“…The total vegetative growth separating all sampled cones was determined by summing tree segments a-h. Echt et al (1996). b Cato and Richardson (1996). c Vendramin et al (1996).…”

“…The more highly variables of these loci were selected since they are expected to have the highest mutation rate. DNA sequences of the PCR primers for the loci examined in this study have been published elsewhere (Cato and Richardson, 1996;Echt et al, 1996;Vendramin et al, 1996). The PCR reaction and amplification conditions were as described by Echt et al (1996Echt et al ( , 1999.…”

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

“…SSRs are often used as molecular markers to characterize genetic variability in plant breeding programs and population genetics studies; they usually have high mutation rates compared to other neutral DNA regions due to slipped strand mispairing (slippage) during DNA replication on a single DNA strand. The chloroplast SSRs were initially reported in studies of Pinus radiata and O. sativa (Cato and Richardson, 1996;Powell et al, 1996;Provan et al, 1996), which foreseen the potential use of chloroplast SSR assessments for population genetics. Of the 63 SSR loci characterized in Z. latifolia cp genome, the average rate was 0.46 SSRs/kb (Supplemental Table 4).…”