scholarly journals Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 31 ◽  
Author(s):  
Shitian Li ◽  
Muthusamy Ramakrishnan ◽  
Kunnummal Kurungara Vinod ◽  
Ruslan Kalendar ◽  
Kim Yrjälä ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
High Throughput ◽  
Regulation Of Gene Expression ◽  
Intact Protein ◽  
Grass Species ◽  
Copy Numbers ◽  
Irap Markers ◽  
Main Class ◽  
Population Genetic Variation

Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.

Invasion Success in Cogongrass (Imperata cylindrica): A Population Genetic Approach Exploring Genetic Diversity and Historical Introductions

2014 ◽  
Vol 7 (1) ◽  
pp. 59-75 ◽  
Author(s):  
Rima D. Lucardi ◽  
Lisa E. Wallace ◽  
Gary N. Ervin
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Biological Invasion ◽  
Propagule Pressure ◽  
Gulf Coast ◽  
The United States ◽  
Parent Material ◽  
Imperata Cylindrica ◽  
Invasion Success ◽  
Grass Species

AbstractPropagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied the tools and theory of population genetics to better understand the dynamics of successful biological invasion. The focal species, cogongrass, is a perennial invasive grass species significantly affecting the Gulf Coast and southeastern region of the United States. The literature indicates separate, allopatric introductions of material from East Asia (Philippines and Japan) into the U.S. states of Mississippi and Alabama. Molecular analysis of samples from those two states utilized amplified fragment length polymorphism (AFLP) markers on 388 individuals from 21 localities. We hypothesized that previously isolated lineages of cogongrass are present and crossing in the Southeast. We observed genetic variation within localities (0.013 ≤ heterozygosity (He) ≤ 0.051, mean = 0.028 ± 0.001) with significant and substantial population structure (FST= 0.534, P < 0.001). Population structure analyses detected two genetically defined and statistically supported populations, which appear to have experienced some admixture. The geographic distribution of those populations was consistent with the two-introduction scenario reported previously. These results are also consistent with contact in the invasive range of previously isolated lineages from the native range.

scholarly journals Genetic Diversity, Population Structure Analysis Using Ultra-High Throughput Diversity array Technology (DArTseq) in Different Origin Sesame (Sesamum indicum L)

2020 ◽  
Author(s):  
TEWODROS TESFAYE NEGASH ◽  
KASSAHUN TESFAYE ◽  
GEMECHU KENENI WAKEYO ◽  
CATHRINE ZIYOMO
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
High Throughput ◽  
Research Work ◽  
Snp Markers ◽  
Diversity Array Technology ◽  
Population Structure Analysis ◽  
Array Technology ◽  
Sesame Genotypes

Abstract BackgroundSesame is an important oil crop widely cultivated in Africa and Asia continent. Characterization of genetic diversity and population structure of sesame genotypes in these continents can be used to designing breeding methods. In the present study, 300 sesame genotypes comprising 209 local, and 75 exotic collection, and 16 released varieties provided from the Ethiopian Biodiversity Institute and research centers were used in the present study.ResultsThe panel was genotyped using two ultra-high-throughput diversity array technology (DArT) markers (silicoDArT and SNP). Both markers were used to identify the genetic diversity and population structure of sesame germplasm. A total of 6115 silicoDArT and 6474 SNP markers were reported, of which 5002 silicoDArT and 4638 SNP markers were screening with quality control parameters. The average polymorphic information content values of silicoDArT and SNP markers were 0.07 and 0.08, respectively. For further analysis, the allele frequency for each SNP site was calculated and purified with MAF < 0.01 and left 2997 high-quality SNPs evenly distributed across the whole genome that could be used for subsequent analysis. All genotypes used in this study were descended from eight 8 geographical origins. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 0.14. Considering the genotypes based on their geographical origin, Africa collections (0.21) as a whole without Ethiopian collection was more diverse than Asia and when further portioned Africa, North Africa (0.23) collection was more diverse than others, but at the continent level, Asia (0.17) was more diverse than Africa (0.14). The genetic distance among the sesame populations was ranged from 0.015 to 0.394, with an average of 0.165. The sesame populations was clustered into four groups. The structure analysis divided the panel into four subgroups and 21 genotypes were clustered as an admixture. These indicates genotypes from the same origin didn’t classify properly on the premise of the country of origin. ConclusionsThe genetic diversity and population structure revealed in this study should guide the future research work to design association studies and the systematic utilization of the genetic variation characterizing the sesame panel.

Genetic diversity and population structure of Populus yunnanensis revealed by SSR markers

2020 ◽  
Vol 52 (6) ◽  
Author(s):  
Anpei Zhou ◽  
Dan Zong ◽  
Peihua Gan ◽  
Yao Zhang ◽  
Dan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers

Genetic diversity and population structure of Bretschneidera sinensis, an endangered species

2014 ◽  
Vol 21 (6) ◽  
pp. 723-731
Author(s):  
Xu Gangbiao ◽  
Liang Yan ◽  
Jiang Yan ◽  
Liu Xiongsheng ◽  
Hu Shangli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Endangered Species

EST-SSR Genetic Diversity and Population Structure of Tea Landraces and Developed Cultivars (Lines) in Zhejiang Province, China

2010 ◽  
Vol 36 (5) ◽  
pp. 744-753 ◽  
Author(s):  
Ting-Ting QIAO ◽  
Chun-Lei MA ◽  
Yan-Hua ZHOU ◽  
Ming-Zhe YAO ◽  
Rao LIU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Zhejiang Province

Genetic Diversity and Population Structure of Germplasm Resources in Sesame (Sesamum indicum L.) by SSR Markers

2013 ◽  
Vol 38 (12) ◽  
pp. 2286-2296 ◽  
Author(s):  
Wen-Di YUE ◽  
Li-Bin WEI ◽  
Ti-De ZHANG ◽  
Chun LI ◽  
Hong-Mei MIAO ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Sesamum Indicum ◽  
Germplasm Resources
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