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

Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSR s (cp SSR s) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cp SSR s are mostly paternally inherited, thus, they are useful in mating systems and pollen flow st...

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Published in:Ecology and evolution 2018-05, Vol.8 (10), p.4967-4977
Main Authors: Huang, Li‐Sha, Sun, Yan‐Qiang, Jin, Yuqing, Gao, Qiong, Hu, Xian‐Ge, Gao, Fu‐Ling, Yang, Xiao‐Lei, Zhu, Ji‐Jun, El‐Kassaby, Yousry A., Mao, Jian‐Feng
Format: Article
Language:English
Subjects:
Biogeography
Breeding
Chloroplasts
Cupressaceae
Evolution & development
Genetic diversity
Genetics
Genomes
Interspecific
Loci
Markers
Multiculturalism & pluralism
Paternity
Plastomes
Pollen
Pollutants
Polymorphism
Population genetics
Primers
Studies
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Summary:Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSR s (cp SSR s) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cp SSR s 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 cp SSR s 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 cp SSR s and 10 nuclear SSR s, and these individuals were identified with high confidence. The developed cp SSR s 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.
ISSN:2045-7758
2045-7758
DOI:10.1002/ece3.4053