Association analysis and evaluation of genetic diversity of Teucrium stocksianum Boiss. populations using ISSR markers

Kamali, Mahdiye; Samsampour, Davood; Bagheri, Abdoolnabi; Mehrafarin, A; Homaei, Ahmad

doi:10.1007/s10722-022-01529-w

Cited by 4 publications

(3 citation statements)

References 49 publications

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“…In other Teucrium species, there is a considerable amount of research on population genetics using different marker systems, such as the combination of chloroplast (rpL32-trnL and trnL-trnF) and nuclear regions (ITS) in T. flavum L. [16] and T. scorodonia L. [17], AFLP markers in T. arduini L. [18] or ISSR markers in T. stocksianum Boiss. [19]. There are only a handful of molecular studies on T. capitatum, which usually focus on the systematics of the Teucrium section Polium [20], an entire Teucrium genus [6] as a starting point for conservation [21].…”

Section: Introductionmentioning

confidence: 99%

Joint Identification and Application of Microsatellite Markers in Genetic Diversity Study of Closely Related Species Teucrium montanum, T. capitatum and Their Natural Hybrid

Varga,

Liber,

Turudić

et al. 2024

Diversity

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Teucrium montanum L. and T. capitatum L. are two plant species with overlapping distribution in the Balkan Peninsula, especially in Croatia, where several occurrences of their putative hybrid species T. × rohlenae have been recorded. Next-generation sequencing of both species and de novo assembly was carried out resulting in 120 contigs for T. montanum and 1685 contigs for T. capitatum assembled. The Dig-up primers pipeline was used for SSR mining of both assemblies, applying different criteria that resulted in 112 SSR candidates for testing. A subset of 41 SSRs was selected and after two rounds of testing, twelve SSRs were developed and characterized. A total of 232 alleles were detected with 5 to 29 alleles per locus, based on the test sample. The genetic diversity analysis of three Teucrium taxa from a single location revealed a higher level of diversity in T. montanum than in T. capitatum with intermediate values for the hybrid species. The NeighborNet diagram and genetic structure analysis grouped the taxa into two separate clusters, the first of which consisted exclusively of T. montanum, while the other was composed of intermixed T. capitatum and T. × rohlenae individuals. The availability of SSR markers for two Teucrium taxa will allow in-depth analysis of genetic diversity and structure, as well as molecular identification of their putative hybrids in the future.

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Section: Introductionmentioning

confidence: 99%

Joint Identification and Application of Microsatellite Markers in Genetic Diversity Study of Closely Related Species Teucrium montanum, T. capitatum and Their Natural Hybrid

Varga,

Liber,

Turudić

et al. 2024

Diversity

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“…Among the strategies that can be used to study genetic diversity, the use of ISSR (Inter Simple Sequence Repeats) molecular primers has proved to be a viable tool for various plant species, such as: Teucrium stocksianum Boiss. (Kamali et al 2023), Salvia (Hejazi 2023), Sorghum bicolor (Medraoui et al 2023) and Euphorbia resinifera O. (Abd-dada et al 2023).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity among acerola accessions collected in different states of Brazil using ISSR markers

Nascimento,

Souza,

Souza

et al. 2024

Preprint

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Currently, commercial acerola orchards have been formed using only one or two genotypes, making these crops highly vulnerable to the occurrence of biotic/abiotic stresses. The characterization of available germplasm using molecular primers can identify alleles of interest, useful in the development of new cultivars. Given the above, the aim of this study was to estimate the genetic diversity of a representative sample of acerola germplasm cultivated in Brazil using ISSR primers. Genomic DNA from 96 accessions conserved in Petrolina-PE was extracted and amplified using 15 ISSR primers. The amplifications were annotated for the presence and absence of bands, making it possible to estimate allelic similarity using the Jaccard index and obtaining a dendrogram (UPGMA method). Analysis of molecular variance was used to quantify genetic variability between and within groups. Genes, GenAlex and Cervus software were used. The accessions were grouped into 24 clusters, with ACO01 and MAR12 being the most divergent and Costa Rica and Flor Branca the most similar. The cluster analysis showed that there was greater variation between individuals collected in the same region, a result confirmed by AMOVA and the Shannon-Wiener Index. The ISSR primers were effective in terms of capturing the distribution of the genetic variation present in the studied accessions. Moreover, considering that they are a representative sample of the acerola germplasm in the country, it is understood that this information provides subsidies for decision-making in the management of genetic resources and in the conduction of acerola breeding programs.

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“…A primary conservation goal is to preserve species' evolutionary potential in the face of environmental changes, which necessitates accurate genetic structure analysis and understanding of genetic diversity distribution patterns [7][8][9][10][11]. DNA markers have become an indispensable tool for investigating genetic relationships among plants through the analysis of DNA sequences and allele compositions.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of the Endemic Species Phanera sirindhorniae in the Mekong Basin of Thailand Based on ISSR Markers

Sakulsathaporn,

Choradet,

Roopkham

2023

Trends Sci

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Phanera sirindhorniae, an endemic species to the Mekong Basin’s upper northeastern region in Thailand, is notable for its therapeutic properties in alleviating pain and discomfort. The objective of this study was to assess the genetic diversity of P. sirindhorniae derived from four natural sources, specifically Sakon Nakhon, Nakhon Phanom, Bueng Kan and Mukdahan provinces, utilizing Inter-Simple Sequence Repeat (ISSR) markers. A total of 51 samples were analyzed, and 10 primers exhibited distinct, robust amplified fragments and polymorphism. The amplified fragment sizes ranged from 170 to 1,300 base pairs, identifying a total of 113 amplified fragments, of which 107 (94.69 %) displayed polymorphism. Polymorphic information content (PIC) values spanned between 0.112 and 0.429, while Nei’s gene diversity ranged from 0.2088 ± 0.2184 to 0.2994 ± 0.1912. Assessment of genetic diversity within and among populations revealed the total genetic diversity (Ht = 0.3443 ± 0.0225) and the genetic diversity within populations (Hs = 0.2617 ± 0.0161). The variability among populations (Gst = 0.2401) indicated a significant degree of gene flow (Nm = 1.580). The Analysis of Molecular Variance (AMOVA) results supported this, with 74 % of genetic differentiation occurring within populations and 26 % among populations. Using the Neighbor-Joining (NJ) generated from Nei’s genetic distance-based clustering analysis, Dendrogram construction successfully classified 2 distinct groups. The analysis revealed that P. sirindhorniae from Nakhon Phanom, and Bueng Kan constituted 1 group, whereas P. sirindhorniae from Mukdahan, and Sakon Nakhon formed another. These findings provide essential data for developing genetic conservation initiatives for this valuable genetic resource. HIGHLIGHTS This study presents the inaugural analysis of genetic diversity in wild Phanera sirindhorniae populations, a species designated as endangered, utilizing Inter-Simple Sequence Repeat (ISSR) markers. A group of 10 Inter Simple Sequence Repeat (ISSR) primers showed values for Polymorphism Information Content (PIC), with (AG)8YC (PIC= 0.445) standing out. These results highlight their potential for use in the investigation of genetic diversity. The examination of P. sirindhorniae resulted in the identification of 2 distinct genetic groups, which have the potential to inform and facilitate the development of genetic conservation strategies for this crucial genetic resource. GRAPHICAL ABSTRACT

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Association analysis and evaluation of genetic diversity of Teucrium stocksianum Boiss. populations using ISSR markers

Cited by 4 publications

References 49 publications

Joint Identification and Application of Microsatellite Markers in Genetic Diversity Study of Closely Related Species Teucrium montanum, T. capitatum and Their Natural Hybrid

Joint Identification and Application of Microsatellite Markers in Genetic Diversity Study of Closely Related Species Teucrium montanum, T. capitatum and Their Natural Hybrid

Genetic diversity among acerola accessions collected in different states of Brazil using ISSR markers

Genetic Diversity of the Endemic Species Phanera sirindhorniae in the Mekong Basin of Thailand Based on ISSR Markers

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