Phylogenetic relationships among cultivars of<i>Prunus persica</i>based on internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA

Yoon, Jihyun; Yang, Deok‐Chun; Liu, D. C.; Song, Won Kyung; Zhang, A. M.; Li, S. H.

doi:10.1080/14620316.2009.11512499

Cited by 3 publications

(4 citation statements)

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“…Albeit the nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were proven to have the strength in distinguishing closely related species and identifying the genetic source of hybrids and cultivars for economic crops (Hidayat et al., 2013; Yonemori et al., 2002; Yoon et al., 2009), the case was different in Polygonatum . An attempt to construct the ITS‐based phylogenetic trees for Polygonatum odoratum accessions in this study resulted in both the ML and BI tree displaying weak backbone structure (Figure 7).…”

Section: Discussionmentioning

confidence: 99%

“…odoratum which is generally 1-4-flowered, but sometimes could be 7-flowered in cultivated individuals (Chen & Tamura, 2000). and cultivars for economic crops (Hidayat et al, 2013;Yonemori et al, 2002;Yoon et al, 2009), the case was different in Polygonatum.…”

Section: Potential Hybrids In Polygonatum Odoratum Cultivarsmentioning

confidence: 99%

“…However, the small sam- odoratum which is generally 1-4-flowered, but sometimes could be 7-flowered in cultivated individuals (Chen & Tamura, 2000). Two closely related species, Asparagus officinalis (KY364194) and Disporopsis fuscopicta (MW248136), were included as outgroups and cultivars for economic crops (Hidayat et al, 2013;Yonemori et al, 2002;Yoon et al, 2009), the case was different in Polygonatum.…”

Section: Potential Hybrids In Polygonatum Odoratum Cultivarsmentioning

confidence: 99%

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Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars

Lee

Chen

et al. 2021

Ecology and Evolution

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Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, P. odoratum and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivar were observed. For genetic aspect, the plastid genome of P. odoratum varies in length from 154,569 bp to 155,491 bp, containing a large single‐copy region of 83,486–84,459 bp, a small single‐copy region of 18,292–18,471 bp, and two inverted repeats of 26,302–26,370 bp. A total of 131 genes were predicted, including 85 protein‐coding, 38 tRNA, and eight rRNA genes. Genome comparisons revealed a slight variation in the sequence across the five accessions, but two highly variable regions (trnC‐petN and rpl32‐trnL) were detected when comparing the four different cultivars. For the RAD‐seq markers, a total of 33.64 Gb of clean data, with an average value of 1.08 Gb per sample, were analyzed for the presence of single nucleotide polymorphisms (SNPs). Well‐resolved phylogenies of the P. odoratum cultivars are constructed; the nonmonophyletic relationship in the plastome‐based phylogenetic trees, yet monophyletic form in the RAD‐based linkage map suggested possibility of hybrid cultivar for P. odoratum “Dazhu” (GDDZ), which was further supported by morphological observations. Quality assessment based on the standards of the Chinese Pharmacopoeia on Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study recorded that PORs from P. odoratum “Zhongzhu” (GDZZ) met the minimum criteria for the acceptance as raw material for medicinal drug production. This study has provided insights on the morphological variations, genetic background, and medicinal qualities of P. odoratum cultivars that could be explored for future genetic improvement as well as breeding programs of P. odoratum for POR production.

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Section: Discussionmentioning

confidence: 99%

Section: Potential Hybrids In Polygonatum Odoratum Cultivarsmentioning

confidence: 99%

Section: Potential Hybrids In Polygonatum Odoratum Cultivarsmentioning

confidence: 99%

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Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars

Lee

Chen

et al. 2021

Ecology and Evolution

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“…Based on such findings, several primers that might be used efficiently were selected and exploited for many purposes in Prunus genetic analyses (Batnini et al 2019;Bortiri et al 2001;Horvath et al 2011;Li et al 2021;Reales et al 2010;Shaw and Small 2004). ITSs are noncoding regions between ribosomal RNA genes, which sequences were efficiently used for phylogenetic analyses in a range of plant taxa including Prunus (Bortiri et al 2001;Gilani et al 2010), for the discrimination among species (Quan and Zhou 2011) and cultivars (Yoon et al 2009).…”

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confidence: 99%

The Self-incompatibility Locus and Chloroplast DNA Regions of Prunus domestica Reflect the Origin and Genetic Diversity of Traditional Cultivars

Halász,

Szendy,

Ivanovska

et al. 2023

J. Amer. Soc. Hort. Sci.

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A traditional cultivar, Besztercei Bt.2, and a clone of an autochthonous landrace (Nemtudom P3) of the hexaploid European plum (Prunus domestica) were studied to highlight their breeding perspectives. Five self-incompatibility ribonuclease (S-RNase) alleles were detected in both cultivars, with one allele shared. DNA sequence analysis confirmed it as a new, previously unidentified allele in P. domestica, which we labeled as S18. This allele was found to share ∼99% identity with the Prunus spinosa SB-RNase allele. Because Prunus species are readily hybridizing, sequence variations in 10 chloroplast DNA regions and nuclear internal transcribed spacers were studied to check if ‘Nemtudom P3’ and ‘Besztercei Bt.2’ are indeed P. domestica. The majority-rule consensus tree of maximum likelihood and Bayesian inferences confirmed it, and also indicated genetic differentiation with ‘Nemtudom P3’ and ‘Besztercei Bt.2’ forming a statistically supported subclade within the P. domestica germplasm. Our results pointed to some regions of the P. domestica chloroplast genome (trnS-trnG-trnG, trnC-ycf6, and trnD-trnT) that can be used to detect intraspecific variations. The proportion of parsimony informative characters compared with the total length of amplified regions was the highest in the case of nrITS with 12.1%. The S-genotyping of 68 wild-growing Nemtudom trees showed the genetic consequences of long-term vegetative propagation and occasional crossing between Besztercei and Nemtudom accessions. Controlled pollinations confirmed the self-compatibility of ‘Nemtudom P3’. By clarifying their phylogenetic position, and characterizing the S-locus, our results will help breeding P. domestica cultivars and pave the way to understanding how the S-locus works in a hexaploid Prunus species.

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High-throughput sequencing of Prunus ferganensis indicates that it is a geographical population of P. persica

Cao

Wang

Zhu

et al. 2018

Tree Genetics & Genomes

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Phylogenetic relationships among cultivars ofPrunus persicabased on internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA

Cited by 3 publications

References 10 publications

Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars

Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars

The Self-incompatibility Locus and Chloroplast DNA Regions of Prunus domestica Reflect the Origin and Genetic Diversity of Traditional Cultivars

High-throughput sequencing of Prunus ferganensis indicates that it is a geographical population of P. persica

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