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

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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Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers

Gene ◽

10.1016/j.gene.2016.07.009 ◽

2016 ◽

Vol 591 (1) ◽

pp. 227-235 ◽

Cited By ~ 19

Author(s):

Xiao Bin Liu ◽

Bang Feng ◽

Jing Li ◽

Chen Yan ◽

Zhu L. Yang

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Flammulina Velutipes ◽

Genomic Ssr ◽

History Of ◽

Breeding History

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Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

Canadian Journal of Plant Science ◽

10.4141/cjps09096 ◽

2010 ◽

Vol 90 (1) ◽

pp. 49-60 ◽

Cited By ~ 13

Author(s):

Z I Talukder ◽

E Anderson ◽

P N Miklas ◽

M W Blair ◽

J Osorno ◽

...

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Allelic Variation ◽

Gene Pools ◽

Gene Sequences ◽

Mineral Contents ◽

Discriminatory Ability ◽

Fe Content ◽

Mapping Populations ◽

Selection Of

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

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Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Genetics Research ◽

10.1017/s0016672307008695 ◽

2007 ◽

Vol 89 (2) ◽

pp. 93-106 ◽

Cited By ~ 37

Author(s):

NOELLE A. BARKLEY ◽

ROB E. DEAN ◽

ROY N. PITTMAN ◽

MING L. WANG ◽

CORLEY C. HOLBROOK ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Data Set ◽

Mini Core Collection ◽

Genomic Ssr ◽

Cultivated Peanut ◽

The Mean ◽

Wild Accessions ◽

Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

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Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes

Mycobiology ◽

10.1080/12298093.2020.1727401 ◽

2020 ◽

Vol 48 (2) ◽

pp. 115-121

Author(s):

Hwa-Yong Lee ◽

Suyun Moon ◽

Hyeon-Su Ro ◽

Jong-Wook Chung ◽

Hojin Ryu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Lentinula Edodes ◽

Genomic Ssr ◽

Wild Strains

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Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L.) cultivars

Electronic Journal of Biotechnology ◽

10.1016/j.ejbt.2016.01.006 ◽

2016 ◽

Vol 21 ◽

pp. 18-25 ◽

Cited By ~ 8

Author(s):

Sulieman A. Al-Faifi ◽

Hussein M. Migdadi ◽

Salem S. Algamdi ◽

Mohammad Altaf Khan ◽

Megahed H. Ammar ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Date Palm ◽

Phoenix Dactylifera ◽

Phoenix Dactylifera L ◽

Genomic Ssr

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Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber

Biologia Plantarum ◽

10.1007/s10535-011-0129-0 ◽

2011 ◽

Vol 55 (3) ◽

pp. 577-580 ◽

Cited By ~ 38

Author(s):

J. Hu ◽

L. Wang ◽

J. Li

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genomic Ssr

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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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Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

10.21203/rs.2.18928/v1 ◽

2019 ◽

Author(s):

Alemneh Mideksa Egu ◽

Kifle Dagne ◽

Kassahun Tesfaye ◽

Xuebo Hu

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Major Gene ◽

In Situ Conservation ◽

Germplasm Conservation ◽

Pharmaceutical Products ◽

Gene Pools ◽

Vernonia Galamensis ◽

Diversity Assessment

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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