Classification of interspecific and intraspecific species by genome-wide SSR markers on Dendrobium

Zhao, Ting-Mei; Zheng, Shiling; Hu, Yiheng; Zhao, Ran; Li, H.J.; Zhang, X.Q.; Chun, Ze

doi:10.1016/j.sajb.2019.08.051

Cited by 12 publications

(17 citation statements)

References 32 publications

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“…In the rhizosphere environment of D. nobile, bacteria play an important role. A previous study showed that some bacterial taxa are involved in the recruitment of genera from the same phylum ( Zhao et al, 2023 ). Orchid root-associated beneficial bacteria can facilitate plant growth, fitness and a number of other ecological or evolutionary processes in orchids ( Kaur & Sharma, 2021 ).…”

Section: Challenges In Applying Orm To Actual Cultivation Of Orchid M...mentioning

confidence: 99%

Perspective and challenges of mycorrhizal symbiosis in orchid medicinal plants

Leng,

Hou,

Xing

et al. 2024

Chinese Herbal Medicines

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Section: Challenges In Applying Orm To Actual Cultivation Of Orchid M...mentioning

confidence: 99%

Perspective and challenges of mycorrhizal symbiosis in orchid medicinal plants

Leng,

Hou,

Xing

et al. 2024

Chinese Herbal Medicines

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“…Molecular markers, such as SSRs, have been used to determine the genetic relationship among individuals within a species, among species, and among genera (Zhao et al 2019;Lee et al 2020;Kim et al 2020;Yun et al 2020). The markers have also been used to aid parental choice in hybridization to generate diverse progenies and support plant breeding activities (Lema 2018;Lamichhane and Thapa 2022).…”

Section: Phylogenetic Analysis Of Subtribe Aeridinaementioning

confidence: 99%

Genetic diversity based on SSR markers of 30 Aeridinae sub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia

Wegadara

Dewanti²,

Diningsih³

et al. 2022

Biodiversitas

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Abstract. Wegadara M, Dewanti M, Diningsih E, Rachmawati F, Sukma D, Sudarsono. 2022. Genetic diversity based on SSR markers of 30 Aeridinaesub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia. Biodiversitas 23: 2943-2956. Advances in molecular biotechnology encourage molecular markers to identify plant diversity to become increasingly common. Using SSR markers, this study will determine the genetic diversity and phylogenetic relationships of 30 accessions from five parental genera of Aeridinaeorchids from the IOCRI genetic resource collection. Molecular characterization of 30 orchid sub-tribes Aeridinaegenetic resources of IOCRI was carried out using 17 polymorphic SSR markers. The resulting binary data was then analyzed using the GenAlEX program to determine Na, Ne, Ho, He, and the PowerMarker V3.25 program to determine the values of MAF, D, and PIC. Molecular characterization using 17 SSR primers generated 240 amplified DNA fragments across 30 accessions, with the fragment sizes ranging from 56-4818 bp. Factorial analysis (PCoA) and phylogenetic tree construction clustered the 30 Aeridinae accessions into three major clusters. Accessions belonging to the Vanda genus are clustered into three clusters (Clusters I, II, and III). The Vascostylisis in Cluster I, along with 12 Vanda accessions. Two accessions of Vanda, two Aranthera, three Arachnis, and one Aerides genera are clustered into Cluster III. This study showed that interspecific hybrids among accessions of Vanda within Cluster I and Cluster II should be possible since they are genetically closely related. Intergeneric hybrids among the accession of Vascostylis and Vanda's genera belonging to Cluster I, should also be possible. Furthermore, intergeneric hybrids among Aerides, Arachnis, Aranthera, and Vanda accessions within Cluster III should also be possible. The generated data from this study should be helpful for future Aeridinae breeding activities intended to generate new hybrid varieties.

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“…ese markers are easy to align but are sometimes too conservative and lack sufficient variability. Consequently, the mentioned genes provide too little phylogenetic information and do not resolve intra-and interspecies relationships (Neubig et al, 2009;Zhao et al, 2019). Studies of their heredity indicate only maternal transmission, with no evidence of paternal or two-parental inheritance (Cafasso et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Potential use of low-copy nuclear gene Xdh at lower taxonomic levels based on phylogenetic analysis of the nominal section of Dendrobium

Burzacka-Hinz,

Dudek,

Szlachetko

2024

Acta Soc Bot Pol

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Dendrobium is a large group of Orchidaceae, counting more than 1,100 species, whose classification, both within the genus and individual sections, is not straightforward. Therefore, the aim of our study was to perform phylogenetic analyses for representatives of a nominal section of Dendrobium and to test the usefulness of a low-copy nuclear gene encoding a xanthine dehydrogenase protein for reconstructing phylogeny. We also wish to compare the utility of two nuclear markers, Xdh and ITS. To realize this, we analyzed the diversity of the two markers and the reliability of the resulting trees. Our results indicate that the nuclear ITS region shows higher variability and clade credibility in trees, in closely related species, and between sections than the low-copy nuclear gene. Xdh may be more reliable at higher taxonomic levels, but confirmation of this requires further research.

show abstract

Classification of interspecific and intraspecific species by genome-wide SSR markers on Dendrobium

Cited by 12 publications

References 32 publications

Perspective and challenges of mycorrhizal symbiosis in orchid medicinal plants

Perspective and challenges of mycorrhizal symbiosis in orchid medicinal plants

Genetic diversity based on SSR markers of 30 Aeridinae sub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia

Potential use of low-copy nuclear gene <i>Xdh</i> at lower taxonomic levels based on phylogenetic analysis of the nominal section of <i>Dendrobium</i>

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