SCoT markers provide insight into the genetic diversity, population structure and phylogenetic relationships among three Pistacia species of Iran

Zarei, Abdolkarim; Erfani‐Moghadam, Javad

doi:10.1007/s10722-020-01091-3

Cited by 24 publications

(13 citation statements)

References 58 publications

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“…In our research, the primer ISSR 842 (MI = 1.37, RP = 4.77); UBC 836 (MI = 1.28, RP = 9.27); ISSR 848 (MI = 1.14, RP = 7.22); ISSR 811 (MI = 0.99, Rp = 6.18); and ISSR 11 (MI = 0.91, RP = 7.09) had moderate to high values of marker index and resolving power, suggesting these primers are extremely potential and useful for genetic discrimination of the V. subterranea accessions. These findings have harmony with the previous result reported by Oumer et al 27 ; Zarei and Erfani-Moghadam et al 65 ; Ahmed et al 61 .…”

Section: Discussionsupporting

confidence: 92%

“…The mean of primer efficiency index was comparatively high (RP = 5.30, MI 0.675, D = 0.96) and this matrix indicates the overall efficacy of the tested primers which provides exact differentiation among the accessions. The greater the RP and MI indices refer to the greater efficacy of the respective primer 65 . In our research, the primer ISSR 842 (MI = 1.37, RP = 4.77); UBC 836 (MI = 1.28, RP = 9.27); ISSR 848 (MI = 1.14, RP = 7.22); ISSR 811 (MI = 0.99, Rp = 6.18); and ISSR 11 (MI = 0.91, RP = 7.09) had moderate to high values of marker index and resolving power, suggesting these primers are extremely potential and useful for genetic discrimination of the V. subterranea accessions.…”

Section: Discussionmentioning

confidence: 99%

“…The current finding is consistent with the similar trend of results reported by Rungnoi et al 1 estimated ΔK = 2 using ISSR and RAPD in 363 Bambara groundnut genotypes while Olukolu et al 5 reported ΔK = 4 using DArT assay of 40 Bambara groundnut genotypes. Additionally, other researchers had the parallel statement such as Wu et al 49 found ΔK = 3 using ISSR; Nilkanta et al 42 found ΔK = 3 using ISSR; Zarei and Erfani-Moghadam et al 65 found ΔK = 3 using SCoT; Barbosa et al 71 found ΔK = 3 using ISSR; Zimisuhara et al 51 found ΔK = 2 using ISSR; Li and Zhang 72 found ΔK = 2 using ISSR.…”

Section: Discussionmentioning

confidence: 99%

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DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Khan

Rafii

Ramlee

et al. 2021

Sci Rep

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As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon’s information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei’s genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Khan

Rafii

Ramlee

et al. 2021

Sci Rep

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“…This diploid (2n = 2x = 30), dioecious, wind-pollinated fruit species is believed to originate from the Iranian plateau region spanning from northeast Iran to north Afghanistan and the central Asian republic [2]. Wild pistachio forests still exist in northeast Iran [3]. P. atlantica subsp.…”

Section: Introductionmentioning

confidence: 99%

The First Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Pistachio (Pistacia vera)

et al. 2022

Self Cite

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Pistachio is one of the most economically important nut crops worldwide. However, there are no reports describing the chloroplast genome of this important fruit tree. In this investigation, we assembled and characterized the complete pistachio chloroplast sequence. The Pistacia vera chloroplast genome was 160,598 bp in size, similar to other members of Anacardiaceae (149,011–172,199 bp) and exhibited the typical four section structure, including a large single copy region (88,174 bp), a small single copy region (19,330 bp), and a pair of inverted repeats regions (26,547 bp). The genome contains 121 genes comprised of 87 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Thirteen intron-containing genes were identified in the genome wherein two genes had more than two introns. The genomic patterns of GC content resembled those for other Anacardiaceae. P. vera displayed the highest number of simple sequence repeats (SSRs) among the genera studied, which may be useful for molecular marker development and future population studies. Amino acid analysis revealed that Leucine is the most frequent (10.69%) amino acid in the chloroplast genome followed by Isoleucine (8.53%) and Serine (7.77%). Cysteine (1.30%) and Tryptophan (1.74%) were the least frequent amino acids. Phylogenetic analysis revealed P. vera is most like its taxonomically close relative P. weinmaniifolia, followed by Rhus chinensis; all placed taxonomically in the tribe Rhoeae. Members of Anacardiaceae were most closely related to Rhoeae, followed by members of Spondieae. The reports of this chloroplast genome will be useful for future conservation studies, genetic evaluation and breeding of P. vera, and more comprehensive phylogenetic analysis of the Pistacia species and its closely-related genera.

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“…RP and MI indices refer to the greater efficacy of the respective primers(Zarei et al, 2021).Therefore, the most effective primers are (TC)8C (Rp= 10, MI = 5.51), (GA)8-RC (Rp = 8.7, MI= 3.77), (GA)8 WT (Rp=8.12, MI= 4.05) and (GA)8 SG (Rp= 8, MI = 4.42)Genetic structure based on ISSR markerThe population structure of Onobrychis genus assessed by Bayesian admixture analysis indicated 4 clusters (Fig.4). Based on Q > 0.60, out of 31 Onobrychis species 15 were almost pure and the other species were highly complex, indicating these species were genetically admixture.…”

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confidence: 99%

Relationships of Worldwide Onobrychis species: from seed & pod morphology and molecular perspective

Zarrabian

Dehkordi

Ehtemam

et al. 2022

Preprint

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The present study aimed to investigate the phylogeny of 31 Onobrychis species with the help of seed and fruit macro & micro-morphological traits and ISSR molecular markers. The species were found to be highly variable in their seed and fruit morphological traits. Also, a new type of fruit (O. crista galli type), in addition to the three predefined types of fruit, was introduced. From molecular perspective, a set of 22 ISSR primers were shown to have a good efficiency for genetic discrimination among the species. Bayesian model-based STRUCTURE analysis grouped the genotypes into 4 genetic clusters, and the high value of Fst calculated for these clusters indicated a high level of genetic differentiation among them. On the other hand, based on the Maximum Likelihood phylogenetic tree, our results are in agreement with the subgenus classification (Onobrychis and Sisyrosema), while contrary to Sisyrosema, the Onobrychis subgenus (the Lophobrychis and Onobrychis sections) appears not to be monophyletic. Furthermore, in contrast to the traditional taxonomic classification, species belonging to the Lophobrychis section do not form a coherent group, indicating that this section could be considered as a heterogeneous unit and perhaps could be merge into the Onobrychis section.HighlightThis paper discusses a worldwide phylogenic analysis and population structures of Onobrychis genus. The results of this paper provide a comprehensive answer to complexity of subgenus and section discrimination.

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SCoT markers provide insight into the genetic diversity, population structure and phylogenetic relationships among three Pistacia species of Iran

Cited by 24 publications

References 58 publications

DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

The First Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Pistachio (Pistacia vera)

Relationships of Worldwide Onobrychis species: from seed & pod morphology and molecular perspective

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