Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species

Abstract

Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e‐PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker‐assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

“…However, little attention has been given to cpSSRs in the cp genome of Rosa species. Our results revealed a total of 49 candidate cpSSR loci in the cp genome, and most of these markers were located in the non-coding region, which is consistent with the cp genomes of other angiosperms 57,58 . A previous study reported that the variability of cpSSRs in non-coding regions is more abundant than in conserved coding regions 59 .…”

“…Similar results have been found in Prunus mume cultivar and tetraploid alfalfa 82,83 . cpSSR has also been used in individual identification of Cupressaceae species and genetic diversity assessment of cultivated and wild Hevea rubber 84,85 . We believe that the cpSSRs markers of rose could also be applied to further genetic studies.…”

Pollination dynamics in aPlatycladus orientalisseed orchard as revealed by partial pedigree reconstruction

“…Based on P. orientalis previous SSR marker screening and application, we chose 8 nuSSRs (Jin et al 2016) and 4 cpSSRs (Huang et al 2018) for genotyping. PCR was carried out in a total volume of 20 µl including: 10µL 2×Taq PCR Mix, 4µL (4pmol) fluorescent-dye-labeled M13 primer, 2µL (10ng) genomic DNA, and 4µL 4pmolmixed complementary forward and reverse primers.…”

New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes

“…These SSRs could contribute to evolutionary and biogeography knowledge in Lupinus species, which warrants further research. Repeated sequences are thought to cause abnormal replication and repair pathways and have been used extensively for phylogeny, population genetics, genetic mapping, and forensic studies (Huang et al 2018;Bull et al 1999). For example, Li conducted repeated sequence identification of the cp genomes of 7 species of Aristolochiaceae and used them as they can be informative regions for developing genomic markers for phylogenetic analysis (Li et al 2019).…”