New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species

Abstract Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

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Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

BioMed Research International ◽

10.1155/2015/941357 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Yuejin Zhang ◽

Yuanyuan Chen ◽

Ruihong Wang ◽

Ailin Zeng ◽

Michael K. Deyholos ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Gene Diversity ◽

High Genetic Diversity ◽

Information Index ◽

Polyporus Umbellatus ◽

Ssr Primers ◽

Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

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Molecular Assessment of Genetic Diversity among Egyptian Landraces of Wheat (Triticum aestivum L.) Using Microsatellite Markers

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2020/v3i430094 ◽

2020 ◽

pp. 46-58 ◽

Cited By ~ 1

Author(s):

Ahmed Medhat Mohamed Al-Naggar ◽

Mohamed Abd El-Maboud Abd El-Shafi ◽

Mohamed Helmy El-Shal ◽

Ali Hassan Anany

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Ssr Markers ◽

Triticum Aestivum L ◽

Genetic Progress ◽

High Genetic Diversity ◽

Breeding Programs ◽

High Polymorphism Information Content ◽

Wheat Landraces

To increase the genetic progress in wheat (Triticum aestivum L.) yield, breeders search for germplasm of high genetic diversity, one of them is the landraces. The present study aimed at evaluating genetic diversity of 20 Egyptian wheat landraces and two cultivars using microsatellite markers (SSRs). Ten SSR markers amplified a total of 27 alleles in the set of 22 wheat accessions, of which 23 alleles (85.2%) were polymorphic. The majority of the markers showed high polymorphism information content (PIC) values (0.67-0.94), indicating the diverse nature of the wheat accessions and/or highly informative SSR markers used in this study. The genotyping data of the SSR markers were used to assess genetic variation in the wheat accessions by dendrogram. The highest genetic distance was found between G21 (Sakha 64; an Egyptian cultivar) and the landrace accession No. 9120 (G11). These two genotypes could be used as parents in a hybridization program followed by selection in the segregating generations, to identify some transgressive segregates of higher grain yield than both parents. The clustering assigned the wheat genotypes into four groups based on SSR markers. The results showed that the studied SSR markers, provided sufficient polymorphism and reproducible fingerprinting profiles for evaluating genetic diversity of wheat landraces. The analyzed wheat landraces showed a good level of genetic diversity at the molecular level. Molecular variation evaluated in this study of wheat landraces can be useful in traditional and molecular breeding programs.

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Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

10.1101/2021.05.28.446175 ◽

2021 ◽

Author(s):

Tanzeem Fatima ◽

Ashutosh Srivastava ◽

Vageeshbabu S Hanur ◽

M. Srinivasa Rao

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Ssr Markers ◽

Germplasm Conservation ◽

Principal Component ◽

Santalum Album ◽

High Genetic Diversity ◽

Information Index ◽

Genomic Ssr ◽

Santalum Album L

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127 expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

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Characterization of Indian Mustard Germplasm on the Basis of Morphological Traits and SSR Markers

Current Journal of Applied Science and Technology ◽

10.9734/cjast/2020/v39i4831234 ◽

2020 ◽

pp. 300-311

Author(s):

Narendra Singh Rajpoot ◽

M. K. Tripathi ◽

Sushma Tiwari ◽

R. S. Tomar ◽

V. S. Kandalkar

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Morphological Traits ◽

Indian Mustard ◽

Morphological Characters ◽

High Genetic Diversity ◽

Average Value ◽

Seed Crops ◽

High Degree

The genus Brassica is one of the most important oil seed crops in India with high degree of genetic diversity. In present study, genetic diversity was studied in forty germplasm lines and eight cultivars of Indian mustard using morphological traits and SSR markers. Morphological characters were taken for days to 50% flowering, days to maturity, plant height (cm), length of main raceme (cm), number of primary branches/plant, number of secondary branches/plant, number of silique per plant, number of seeds per silique, 1000 seed weight (g) and seed yield per plant (g). Total 50 SSR markers were used for characterization of these lines, out of which 7 SSR markers were highly polymorphic between all the germplasms of mustard. An UPGMA phonogram was constructed for all 48 Germplasms and the similarity coefficient ranged from 0.00 to 0.91. Number of alleles ranged from 3 to 4, genetic diversity ranged from 71% to 65% with average value of 67%, heterozygosity raged from 20 to 10% with average of 12% and PIC value for markers ranged from 0.65 to 0.59 with mean PIC value 0.61. All seven SSR primers showed PIC value above 0.5 (50%) indicating high genetic diversity in the studied plant material.

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Genetic diversity of Ethiopian cocoyam (Xanthosoma sagittifolium (L.) Schott) accessions as revealed by morphological traits and SSR markers

PLoS ONE ◽

10.1371/journal.pone.0245120 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0245120

Author(s):

Eyasu Wada ◽

Tileye Feyissa ◽

Kassahun Tesfaye ◽

Zemede Asfaw ◽

Daniel Potter

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Significant Variation ◽

Morphological Traits ◽

Quantitative Traits ◽

Taxonomic Status ◽

High Genetic Diversity ◽

Xanthosoma Sagittifolium ◽

Ssr Loci ◽

Multiple Routes

Cocoyam (Xanthosoma sagittifolium (L.) Schott) is an exotic species from tropical America that is widely cultivated in Ethiopia for its edible cormels and leaves. There is a dearth of information on the genetic diversity of Ethiopian cocoyam. In order to evaluate and select cocoyam germplasm for breeding and conservation, genetic diversity of 100 Ethiopian cocoyam accessions (65 green- and 35 purple- cocoyam) were analyzed using 29 morphological traits (16 qualitative and 13 quantitative) and 12 SSR loci. Two classes of qualitative traits were observed. ANOVA revealed significant variation in 11 (84.6%) of the 13 studied quantitative traits. The SSR marker analysis showed high genetic diversity. A total of 36 alleles were detected with a range of 2 to 5 (average of 3.273) alleles per locus. The average observed heterozygosity (Ho) and expected heterozygosity (He) values across populations were 0.503 and 0.443, respectively. The analysis of molecular variance showed that the variation among populations, among individuals within populations, and within individuals explained 14%, 18%, and 68% of the total variation, respectively. Cluster analysis grouped the accessions irrespective of the collection sites. A dendrogram based on Nei’s standard genetic distance grouped the green cocoyam accessions together while the purple cocoyam accessions occupied a separate position within the dendrogram. Significant variation in quantitative traits and the high level of genetic diversity revealed by the SSR markers suggest that diverse cocoyam accessions, probably with multiple lineage, were introduced multiple times, through multiple routes and probably by multiple agents, an hypothesis that needs futher testing and analyis. The crop, therefore, needs more research efforts commensurate with its economic and social values than it has been accorded thus far. Further study is recommended to clarify the taxonomic status of Ethiopian cocoyam accesions and to trace their evolutionary relationships with Xanthosoma species elsewhere.

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Exploring the Genetic Diversity of Some Squash (Cucurbita Maxima L.) Germplasm Using Morphological and Molecular Markers in Erzincan

10.21203/rs.3.rs-848708/v1 ◽

2021 ◽

Author(s):

HALIL IBRAHIM OZTURK ◽

Veysel Dönderalp ◽

Hüseyin Bulut ◽

Recep Korkut ◽

Arash HOSSEINPOUR ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Ssr Markers ◽

Molecular Level ◽

Polymorphic Information Content ◽

Plant Genetic Resources ◽

Molecular Characteristics ◽

Cucurbita Maxima ◽

High Genetic Diversity ◽

The Mean

Abstract Background Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. Cucurbita maxima species in the cucurbitaceae family have high genetic diversity, but its genetic diversity at the molecular level is inadequately characterized. Methods and Results To determine the genetic diversity among genotypes of Cucurbita maxima species of squash, which is widely grown in Erzincan, 14 different squash genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple sequence repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. Seven SSR markers yielded a total of 23 polymorphic bands, the number of alleles per marker ranged from 2 to 5, and the mean number of alleles was 3.286. Polymorphic information content (PIC) ranged from 0.00 (GMT-M61) to 0.202 (GMT-P25), and the mean PIC value per marker was 0.130. Cluster analysis using Nei's genetic distance determined that 14 genotypes were divided into 3 major groups. Conclusions The SSR markers used were effective in distinguish among similar winter squash or pumpkin and therefore can be beneficial for consideration of Cucurbita maxima species diversity, screening of genetic resources and their selection.

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Characterization of Lebanese Germplasm of Snake Melon (Cucumis melo subsp. melo var. flexuosus) Using Morphological Traits and SSR Markers

Agronomy ◽

10.3390/agronomy10091293 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1293

Author(s):

Joe Merheb ◽

Magdalena Pawełkowicz ◽

Ferdinando Branca ◽

Hanna Bolibok-Brągoszewska ◽

Agnieszka Skarzyńska ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Skin Color ◽

Cucumis Melo ◽

Environmental Changes ◽

Phenotypic Variability ◽

Morphological Variability ◽

Color Pattern ◽

High Genetic Diversity ◽

Improvement Programs

Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditional crop in the Mediterranean region. Nevertheless, there has been poor interest in assessing snake melon germplasm where its genetic resources have not been surveyed before despite their potential in adaptation to environmental changes. In this study, we assess the genetic diversity of snake melon landraces collected from different Lebanese regions at both morphological and molecular levels. Morphological characterization using a set of 18 descriptors revealed an important phenotypic variability among the landraces studied. Principle component analysis indicated that fruit hair and its consistency, fruit size, and skin color pattern were good criteria for discriminating among landraces. Based on the scatter plot diagram, landraces of snake melon formed five different groups with one being defined as typical var. flexuosus. Ten simple sequence repeat (SSR) markers were used for the molecular characterization. Fifty-six different alleles were detected, with an average of 5.6 alleles per locus. Polymorphism information content of SSR markers ranged from 0.06 to 0.84 (average 0.38). Cluster analysis based on molecular markers showed high genetic diversity and divided the landraces into five distinct genetic groups, confirming thereby the morphological variability. Findings of this study indicate a significant diversity for the Lebanese snake melon germplasm that must be further conserved and considered in improvement programs of this ancient crop.

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Genetic Diversity and Population Structure of Faba Bean (Vicia faba) from Turkey

HortScience ◽

10.21273/hortsci11022-16 ◽

2016 ◽

Vol 51 (8) ◽

pp. 980-983

Author(s):

Şurhan Göl ◽

Sami Doğanlar ◽

Anne Frary

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Vicia Faba ◽

Ssr Markers ◽

Faba Bean ◽

High Efficiency ◽

Starch Content ◽

Molecular Genetic ◽

Distance Matrix ◽

High Genetic Diversity

Faba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation. This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers. A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic. Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history. According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses. Clustering was not correlated with seed size or origin within Turkey. Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization. A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm. This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization.

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Genetic diversity of Picea likiangensis natural population at different altitudes revealed by EST-SSR markers

Silvae Genetica ◽

10.1515/sg-2014-0025 ◽

2014 ◽

Vol 63 (1-6) ◽

pp. 191-197 ◽

Cited By ~ 1

Author(s):

X. Cheng ◽

Y. Jiang ◽

T. Tang ◽

G. Fan ◽

Xiaoxia Huang

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Ssr Markers ◽

Gene Diversity ◽

Population Level ◽

High Elevation ◽

Species Level ◽

High Genetic Diversity ◽

Elevation Gradients ◽

Different Altitudes

AbstractAltitude is thought to have greatly influenced current species distribution and their genetic diversity. However, it is unclear how different altitudes have affected the distribution and genetic diversity of Picea likiangensis, a dominant forestry species in the Qinghai-Tibetan Plateau region (QTP). In this study, we investigated the genetic diversity of Picea likiangensis populations which distributed in different altitudes of QTP using EST-SSR markers. The results suggested that this species has high genetic diversity at species level, with 100% of loci being polymorphic and an average Nei’s gene diversity (He) of 0.7186 and Shannon’s information index (I) of 1.5415. While the genetic diversity of Picea likiangensis at population level was lower than that at species level, with He and I being 0.6562 and 1.3742, respectively. The variation in genetic diversity of all four studied populations indicated a low-high-low pattern along the elevation gradients. The mid-elevation population (3050 m) was more genetically diverse than both low-elevation (2900 m) and high-elevation populations (3200 m and 3350 m). Nei’s genetic diversity (Fst= 0.0809) and AMOVA analysis (Phist = 0.1135) indicated that a low level of genetic differentiation among populations. Gene flow among populations was 2.8384, suggesting that high gene flow is a main factor leading to high levels of the genetic diversity among populations.

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