Population genetic structure and diversity analysis in economically important Pandanus odorifer (Forssk.) Kuntze accessions employing ISSR and SSR markers

Nasim, Noohi; Sandeep, I. Sriram; Sahoo, Ambika; Das, Sharmistha; Panda, Manoj; Acharya, Laxmikanta; RamaRao, V V; Nayak, Sanghamitra; Mohanty, Sujata

doi:10.1016/j.indcrop.2019.111894

Cited by 33 publications

(10 citation statements)

References 56 publications

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“…SSR markers have been widely used in genetic diversity studies because of their co-dominance, high polymorphism rate, good reproducibility, and rapid excavation at a low cost (Bouck and Vision, 2007;Nasim et al, 2020). Based on 20 highly polymorphic EST-SSR markers developed in our previous study (Liu et al, 2018), we evaluated the genetic structure, bottleneck effect, and effective population size of 10 P. emblica populations distributed in typical dry-hot climate areas and typical humid climate areas.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Liu

Wan

et al. 2020

Front. Plant Sci.

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Phyllanthus emblica L. is a well-known medicinal and edible plant species. Various medicinal compounds in the fruit make it an important medicinal and promising economic material. The plant is widely distributed in Southwestern and Southern China. However, due to massive deforestation and land reclamation as well as deterioration of its natural habitat in recent years, the wild resources of this species have been sharply reduced, and it is rare to see large-scale wild P. emblica forests so far. In order to effectively protect and rationally utilize this species, we investigated the genetic diversity, genetic structure, and population dynamics of 260 individuals from 10 populations of P. emblica sampled from the dry climate area in Yunnan and wet climate area in Guangxi using 20 polymorphic EST-SSR markers. We found high genetic diversity at the species level (He = 0.796) and within populations (He = 0.792), but low genetic differentiation among populations (FST = 0.084). In addition, most genetic variation existed within populations (92.44%) compared with variation among the populations (7.56%). Meanwhile, the NJ tree, STRUCTURE, and hierarchical analysis suggested that the sampled individuals were clustered into two distinct genetic groups. In contrast, the genetic diversity of the dry climate group (He = 0.786, Na = 11.790, I = 1.962) was higher than that of the wet climate group (He = 0.673, Na = 9.060, I = 1.555), which might be attributed to the combined effects of altitude, precipitation, and geographic distance. Interestingly, only altitude and precipitation had significant pure effects on the genetic diversity, and the former was slightly stronger. In addition, DIYABC analysis suggested the effective population size of P. emblica might have contracted in the beginning of the Last Glacial Maximum. These genetic features provided vital information for the conservation and sustainable development of genetic resources of P. emblica, and they also provided new insights and guidelines for ecological restoration and economic development in dry-hot valleys of Yunnan and karst areas in Guangxi.

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Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Liu

Wan

et al. 2020

Front. Plant Sci.

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“…The polymorphic information content and qualitative nature of data (QND) were higher in SSR than RAPD markers. The PIC value and QND were the clear indications of higher efficacy of SSR markers over the dominant markers (Nasim et al, 2020; Zargar et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure analysis of rice false smut pathogen in North India using molecular markers

Masurkar

Bag

Ray

et al. 2021

Journal of Phytopathology

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False smut, caused by Ustilaginoidea virens, is one of the emerging diseases of rice in the world. The fungi show a high degree of morphological and cultural variability and produce diverse symptoms. India is a vast country with 44‐million‐ha rice production area and has only one report on genetic diversity and population analysis of U. virens from the eastern and north‐eastern region. Ten polymorphic RAPD and 21 SSR markers were used to analyse the genetic diversity and population structure of 81 isolates of U. virens from northern India, the second largest rice‐growing region. In this study, higher Polymorphic Information Content (PIC) and Quality Nature of Data (QND) data in simple‐sequence repeats (SSR) markers over random amplified polymorphic DNA (RAPD) revealed its higher efficacy; thus, SSR markers are highly informative and can help to dissect the genetic structures of U. virens. All markers yielded a total of 180 alleles with 1.0 effective alleles per loci. Genetic diversity ranged from 0.1 to 0.39. The principal coordinate analysis (PCoA), and structure analysis identified two genetic clusters of U. virens isolates with some degree of distinctness according to locations. But clusters, PCoA and structure analysis did not group the isolates according to their geographical origin and this may be due to high gene flow (Nm = 1.14).

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“…Microsatellites are ideal for identifying individuals and studying genetic diversity because of their ubiquity, reproducibility, high level of polymorphism, codominant inheritance, and high level of transferability (Nasim et al 2020;Lv et al 2020;Guan et al 2019;Carletti et al 2019). Therefore, SSRs have been used to study genetic diversity, generate genetic linkage maps, and "fingerprinting" many economically important trees (e.g., Ginkgo biloba, Platanus orientalis, Cunninghamia lanceolata (Lamb.)…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

et al. 2021

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Robinia pseudoacacia is an important afforestation tree introduced to China in 1878. In the present study, we examined the genetic diversity among 687 strains representing four improved varieties and two secondary provenances, comprising 641 clones and 46 seedlings. Ninety-one simple sequence repeats (SSRs) were selected through segregation analysis and polymorphism characterization, and all sampled individuals were genotyped using well-characterized SSR markers. After excluding loci with non-neutral equilibrium, missing locus data and null alleles, we used 36 primer pairs to assess the genetic diversity of these germplasm resources, revealing vast genetic differentiation among the samples, with an average of 8.352 alleles per locus and a mean Shannon′s index of 1.302. At the population level, the partitioning of variability was assessed using analysis of molecular variance, which revealed 93% and 7% variation within and among collection sites, respectively. Four clusters were detected using structure analysis, indicating a degree of genetic differentiation among the six populations. Insights into the genetic diversity and structure of R. pseudoacacia provide a theoretical basis for the conservation, breeding and sustainable development in China.

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Population genetic structure and diversity analysis in economically important Pandanus odorifer (Forssk.) Kuntze accessions employing ISSR and SSR markers

Cited by 33 publications

References 56 publications

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Genetic diversity and population structure analysis of rice false smut pathogen in North India using molecular markers

Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

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