SSR markers distinguish critically endangered Acer campestre populations from cryptic invading gene pools

Abstract BackgroundVernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidised oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study is initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. ResultsTwenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified across the entire loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations despite low differentiation among populations which accounted for only 11% of the total variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the 150 accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. These analyses showed accessions collected from the same region of origin did not often grouped entirely together within a given major groups. ConclusionsThe result suggested that the markers applied to ten populations, in which East Showa and East Harerghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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Assessment of Genetic Relationship among Male and Female Fig Genotypes Using Simple Sequence Repeat (SSR) Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha45110756 ◽

2017 ◽

Vol 45 (1) ◽

pp. 172-178

Author(s):

Sevin TEOMAN ◽

Meryem IPEK ◽

Umran ERTURK ◽

Nesrin Aktepe TANGU ◽

Erdem DURGUT ◽

...

Keyword(s):

Ssr Markers ◽

Genetic Relationship ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Aegean Sea ◽

Gene Pools ◽

Sequence Repeat ◽

Expected Heterozygosity ◽

Male Tree ◽

Simple Sequence

Fig (Ficus carica L.) is a traditional crop in Turkey and widely cultivated around the Mediterranean areas. The gynodioecious fig species is present in two sexual forms, i.e. the domesticated fig (female tree) and the caprifig (male tree). Caprifigs are crucial for high quality fig production and breeding while, the studies on assessment of genetic relationship among caprifigs is limited. The aim of this study was to determine genetic diversity among 45 caprifigs and 2 female figs collected from four provinces in Marmara and Aegean Sea Regions of Turkey using simple sequence repeat (SSR) markers. In this work, 24 SSR markers were tested, one was monomorphic and the remaining markers amplified 82 alleles. The number of polymorphic alleles per SSR marker ranged from 2 to 7. The observed heterozygosity (Ho) differed from 0.18 to 0.76 and expected heterozygosity (He) ranged between 0.24 and 0.81. The polymorphism information content (PIC) varied from 0.42 to 0.98. A UPGMA analysis based on Dice similarity matrix clustered fig genotypes into two main groups and similarly, STRUCTURE analysis placed fig genotypes into two different gene pools (K=2). Fig genotypes collected from the same region were not clustered together in a group indicating that the fig genotypes did not cluster on the basis of their collection sites. Our results demonstrated that caprifigs and female figs are not genetically distinct and they clustered together in a group. All fig genotypes had distinct SSR marker profiles suggesting that there were no synonyms or homonyms. These results revealed a high genetic variation among fig genotypes and 23 SSR markers were enough to discriminate all fig genotypes analysed in this study demonstrating that SSR marker system is suitable for genetic analysis in figs.

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Genetic diversity and differentiation of the Critically Endangered Hispaniolan palm Coccothrinax jimenezii M.M. Mejía & R.G. García based on novel SSR markers

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2016.04.013 ◽

2016 ◽

Vol 66 ◽

pp. 216-223 ◽

Cited By ~ 3

Author(s):

Brett Jestrow ◽

Brígido Peguero ◽

Francisco Jiménez ◽

William Cinea ◽

Michael Hass ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Critically Endangered

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Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas

Frontiers in Genetics ◽

10.3389/fgene.2020.609603 ◽

2021 ◽

Vol 11 ◽

Author(s):

Reyazul Rouf Mir ◽

Neeraj Choudhary ◽

Vanya Bawa ◽

Sofora Jan ◽

Bikram Singh ◽

...

Keyword(s):

Structural Analysis ◽

Common Bean ◽

Ssr Markers ◽

Allelic Diversity ◽

Genome Wide Association ◽

Gene Pools ◽

Western Himalayas ◽

Genome Wide ◽

Core Set ◽

First Time

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker–trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

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Genetic relationships between Chinese, Japanese, and Brazilian soybean gene pools revealed by simple sequence repeat (SSR) markers

Genetics and Molecular Biology ◽

10.1590/s1415-47572007000100016 ◽

2007 ◽

Vol 30 (1) ◽

pp. 85-88 ◽

Cited By ~ 8

Author(s):

Naoki Yamanaka ◽

Hiroyuki Sato ◽

Zhenyu Yang ◽

Dong He Xu ◽

Lizandra Lucy Catelli ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Gene Pools ◽

Sequence Repeat ◽

Soybean Gene ◽

Simple Sequence

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Intra-population genetic diversity of cultivated carrot (Daucus carota L.) assessed by analysis of microsatellite markers.

Acta Biochimica Polonica ◽

10.18388/abp.2013_2053 ◽

1970 ◽

Vol 60 (4) ◽

Author(s):

Anna Maksylewicz ◽

Rafal Baranski

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Daucus Carota ◽

Allelic Variation ◽

Population Variation ◽

F1 Hybrids ◽

Gene Pools ◽

Homozygous State ◽

Daucus Carota L ◽

Genomic Ssr

Intra-population variation of 18 cultivated carrot (Daucus carota L. ssp. sativus) populations of diverse origins was evaluated using codominant microsatellite (SSR) markers. Using 27 genomic and EST-derived SSR markers, 253 alleles were identified with a mean 9.4 alleles per marker. Most of the alleles (60.5%) were rare i.e., with the frequency ≤ 0.05 while only 3.95% of alleles occurred with frequency > 0.6. EST-derived SSR markers were less polymorphic than genomic SSR markers. Differences in allele occurrence allowed 16 out of 18 populations to be assigned to either the Western or Asian carrot gene pools with high probability. Populations could be also discriminated due to the presence of private alleles (25.3% of all alleles). Most populations had excess of alleles in the homozygous state indicating their inbreeding, although heterozygous loci were common in F1 hybrids. Genetic diversity was due to allelic variation among plants within populations (62% of total variation) and between populations (38%). Accessions originating from continental Asia and Europe had more allelic variants and higher diversity than those from Japan and USA. Also, allelic richness and variability in landraces was higher than in F1 hybrids and open-pollinated cultivars.

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Comparison of genetic diversity between cultivated and wild grape varieties originating from the Near-Caspian zone of Azerbaijan

OENO One ◽

10.20870/oeno-one.2010.44.4.1478 ◽

2010 ◽

Vol 44 (4) ◽

pp. 191

Author(s):

Samira Salayeva ◽

Stéphanie Decroocq ◽

Stéphanie Mariette ◽

Ellada Akhundova

Keyword(s):

Genetic Diversity ◽

Vitis Vinifera ◽

Ssr Markers ◽

Research Work ◽

Similarity Index ◽

Null Alleles ◽

Gene Pools ◽

Wild Grape ◽

Wild Accessions ◽

Grape Varieties

Aim: The Caucasus is considered as a possible primary centre of origin of grapevine. The aim of our research work was to study genetic diversity among cultivated Caucasian grape varieties and wild relatives originating from Near-Caspian areas of Azerbaijan on the basis of simple sequence repeat (SSR) markers.Methods and Results: Microsatellite allele data obtained in 31 local table grape varieties of Vitis vinifera L. ssp. sativa (Absheron region) and 34 wild varieties of Vitis vinifera L. ssp. sylvestris (Nabran, Davachi and Guba regions) were used to estimate population genetic parameters such as the polymorphism information content (PIC), the probability of identity (PI) and the frequency of null alleles (r). The genetic differences among the wild populations and between the wild and the cultivated gene pools were assessed using POPGENE, Arlequin and GENETIX programs. The selected fifteen microsatellite (SSR) markers revealed a high degree of polymorphism within and among the grape populations analyzed. The genetic similarity index ranged from 0.02 to 0.933.Conclusions: Among the selected markers, VVMD28 and VVMD36 displayed the highest diversity level regarding the expected heterozygosity and PIC (highest values) and PI (lowest values). In consequence, we postulate that these two markers are the most appropriate ones for the identification of grape accession and the determination of genetic diversity among cultivated and wild grape genotypes. Clustering analysis based on SSR markers data led to a good separation between cultivated and wild accessions and between wild accessions originating from different regions.Significance and impact of the study: The fifteen microsatellite markers used in this study were highly informative for the identification and analysis of genetic structure of Azerbaijan grapevine populations and clarified the relationships among grape accessions.

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