VNTR typing of the bacterial rice pathogen Burkholderia glumae reveals the coexistence of several diverging lineages in a single field in Colombia.

Plant Disease ◽  
2021 ◽  
Author(s):  
Gilles Bena ◽  
Paola Fory ◽  
Johanna Echeverri ◽  
Gloria Mosquera
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Rice Paddy ◽  
Rice Cultivar ◽  
Bacterial Strains ◽  
Burkholderia Glumae ◽  
Significant Drop ◽  
Origin And Evolution

Bulkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. In order to estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. In order to detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or Variable Number Tandem Repeats, as well as part of the Toxoflavin toxA gene, in all strains. Results show that (i) the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan, (ii) data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, (iii) five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.

Utilisation of wild Cicer in chickpea improvement — progress, constraints, and prospects

2003 ◽  
Vol 54 (5) ◽  
pp. 429 ◽  
Author(s):  
J. S. Croser ◽  
F. Ahmad ◽  
H. J. Clarke ◽  
K. H. M. Siddique
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Biotic Stresses ◽  
Yield And Quality ◽  
Cicer Species ◽  
Cultivated Species ◽  
Wild Cicer Species ◽  
Improvement Programs ◽  
Primary Focus

Efforts to improve the yield and quality of cultivated chickpea (Cicer arietinum L.) are constrained by a low level of intraspecific genetic diversity. Increased genetic diversity can be achieved via the hybridisation of the cultivated species with the unimproved 'wild' relatives from within the 43 species of the Cicer genus. To date, the 8 species sharing an annual growth habit and chromosome number with C. arietinum have been the primary focus of screening and introgression efforts. Screening of these species has uncovered morphological characteristics and resistance to a number of abiotic and biotic stresses that are of potential value to chickpea improvement programs. Detailed analysis of protein and DNA, karyotyping, and crossability studies have begun to elucidate the relationships between the annual Cicer species. In comparison, perennial species have received little attention due to difficulties in collection, propagation, and evaluation. This review discusses the progress towards an understanding of genetic relationships between the Cicer species, and the introgression of genes from the wild Cicer species into the cultivated species.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Runzhi Li ◽  
Shiwen Wang ◽  
Liusheng Duan ◽  
Zhaohu Li ◽  
Michael J. Christoffers ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
The United States ◽  
Mantel Test ◽  
Wild Oat ◽  
Chinese Populations ◽  
Nei's Distance ◽  
The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

scholarly journals Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Masoumeh YOUSEFIAZARKHANIAN ◽  
Ali ASGHARI ◽  
Jafar AHMADI ◽  
Behvar ASGHARI ◽  
Ali Ashraf JAFARI
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphisms ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Variations ◽  
Molecular Techniques ◽  
Wild Populations ◽  
Similarity Coefficients ◽  
The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Nei’s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

scholarly journals Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

2020 ◽  
Vol 24 (5) ◽  
pp. 474-480
Author(s):  
I. I. Suprun ◽  
S. A. Plugatar ◽  
I. V. Stepanov ◽  
T. S. Naumenko
Keyword(s):  
Genetic Diversity ◽  
Bayesian Methods ◽  
Dna Markers ◽  
Wild Species ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
The Other ◽  
Clustering Methods ◽  
Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

scholarly journals Anthropological Genetics Perspectives on the Transatlantic Slave Trade

2020 ◽  
Author(s):  
Cesar Fortes-Lima ◽  
Paul Verdu
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Cultural Landscape ◽  
Slave Trade ◽  
Genetic Relationships ◽  
Anthropological Genetics ◽  
15Th Century ◽  
African Descendants ◽  
Genome Wide Data ◽  
History Of

Abstract During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950’s mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socio-economic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.

scholarly journals Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

2020 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
Zhenqing Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Germplasm Characterization ◽  
2D Barcode ◽  
New Type ◽  
Generation Sequencing ◽  
Kasp Markers ◽  
Selection Of

Abstract Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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