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Genomic SSR and EST‐SSR markers for phylogenetic and pedigree reconstructions—A comparison in sea buckthorn
Author(s) -
Wang LuoYun,
Li ShanShan,
Wang TianYi,
He CaiYun,
Luo HongMei,
Zhang JianGuo,
Zeng YanFei
Publication year - 2021
Publication title -
plant breeding
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.583
H-Index - 71
eISSN - 1439-0523
pISSN - 0179-9541
DOI - 10.1111/pbr.12889
Subject(s) - biology , subspecies , phylogenetic tree , microsatellite , expressed sequence tag , genome , genetics , genetic marker , evolutionary biology , allele , gene , zoology
Abstract Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non‐model species. We identified SSRs from expressed sequence tags (EST‐SSRs) and whole genome sequences (gSSRs), by analysing the transcriptome and genome of the Mongolian sea buckthorn ( Hippophae rhamnoides subsp. mongolica ) cultivar ‘Sunny’. Using the same number of loci, EST‐SSRs showed higher transferability to Hippophae than gSSRs, and phylogenetic trees based on EST‐SSRs demonstrated higher resolution for classifying Hippophae species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST‐SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST‐SSRs and gSSRs would provide insight into the trade‐off between differentiation and polymorphism in marker selection for breeding programs.