Molecular characterization of Prunus mahaleb L. rootstock canditates by ISSR markers

Prunus mahaleb is widely used as rootstocks particularly on calcareous and dry soils for both sweet and sour cherry cultivars in Turkey. Genetic diversity and relationships among members of Prunus mahaleb including 29 preselected rootstock candidate accessions from Tokat region in Turkey were investigated by using 15 ISSR markers. The study revealed high genetic diversity among accessions, detecting 138 fragments, of which 103 (75%) were polymorphic. The number of polymorphic bands per primer was between 3-13, with average of 6.86. The primers 890 and 891 gave the highest polymorphism ratio (100%). The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation among accessions. Reference rootstock, SL-64 clustered separately. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in Prunus mahaleb rootstock candidate accessions and can contribute to efficient identification, conservation, and utilization of germplasm for rootstock improvement through conventional as well as molecular breeding approaches.

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Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽

10.3390/pathogens10020089 ◽

2021 ◽

Vol 10 (2) ◽

pp. 89

Author(s):

Jiayu Li ◽

Fuxian Yang ◽

Ruobing Liang ◽

Sheng Guo ◽

Yaqiong Guo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Characterization ◽

Zoonotic Potential ◽

Common Occurrence ◽

High Genetic Diversity ◽

Gp60 Gene ◽

The Common ◽

Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

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Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

Microorganisms ◽

10.3390/microorganisms9081612 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1612

Author(s):

Werner Ruppitsch ◽

Andjela Nisic ◽

Patrick Hyden ◽

Adriana Cabal ◽

Jasmin Sucher ◽

...

Keyword(s):

Genetic Diversity ◽

Safety Evaluation ◽

Gene Clusters ◽

Northern Region ◽

Genomic Diversity ◽

High Genetic Diversity ◽

Pathogenic Factors ◽

Flavor Development ◽

Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

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Molecular characterization of echovirus 13 uncovering high genetic diversity and identification of new genotypes in Pakistan

Infection Genetics and Evolution ◽

10.1016/j.meegid.2016.12.017 ◽

2017 ◽

Vol 48 ◽

pp. 102-108

Author(s):

Shahzad Shaukat ◽

Mehar Angez ◽

Tariq Mahmood ◽

Muhammad Masroor Alam ◽

Salmaan Sharif ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

High Genetic Diversity

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Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

Indian Journal of Forestry ◽

10.54207/bsmps1000-2021-xm8ipx ◽

2021 ◽

Vol 43 (1) ◽

pp. 38-42

Author(s):

Kavungal Priya ◽

◽

Indira . ◽

Vadakkethil Balakrishnan Sreekumar ◽

Renuka . ◽

...

Keyword(s):

Genetic Diversity ◽

Western Ghats ◽

Rapd Markers ◽

Gene Diversity ◽

Issr Markers ◽

High Genetic Diversity ◽

Western Ghats Of India ◽

The Mean ◽

Two Parameters ◽

Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

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ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

10.21203/rs.3.rs-666059/v1 ◽

2021 ◽

Author(s):

Lalit Arya ◽

Ramya Kossery Narayanan ◽

Anjali Kak ◽

Chitra Devi Pandey ◽

Manjusha Verma ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Morinda Citrifolia ◽

Species Differentiation ◽

Information Index ◽

Upgma Cluster Analysis ◽

Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

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Characterization of Natural Isolates of Bipolaris maydis Associated with Mating Types, Genetic Diversity, and Pathogenicity in Fujian Province, China

Plant Disease ◽

10.1094/pdis-03-19-0650-re ◽

2020 ◽

Vol 104 (2) ◽

pp. 323-329

Author(s):

Yuli Dai ◽

Lin Gan ◽

Hongchun Ruan ◽

Niuniu Shi ◽

Yixin Du ◽

...

Keyword(s):

Genetic Diversity ◽

Mating Type ◽

Dna Polymorphism ◽

Sweet Corn ◽

Issr Markers ◽

Bipolaris Maydis ◽

Fujian Province ◽

Field Isolates ◽

Rational Distribution

Due to the natural destructiveness and persistence of the southern corn leaf blight (SCLB) fungus Bipolaris maydis (Nisikado et Miyake) Shoem, the characterization of B. maydis field isolates is essential to guide the rational distribution of resistant materials in corn-growing regions. In the present study, 102 field isolates collected from seven locations covering the entire region of Fujian Province, China, were assessed for mating type distribution, genetic diversity, and pathogenicity toward local sweet corn cultivars. Mating type detection via polymerase chain reaction indicated that 36.3 and 63.7% of isolates were MAT1-1 and MAT1-2, respectively; more than 80% of these isolates were confirmed using cross assays with known mating type isolates. Thirteen intersimple sequence repeat (ISSR) markers within and among two mating type populations revealed a high level of DNA polymorphism for all combined isolates and between MAT1-1 and MAT1-2 populations. The MAT1-2 population was more diverse based on DNA polymorphism than the MAT1-1 population. The value of GST was 0.0070, ranging from 0.0399 to 0.3044 based on analysis of combined isolates and individual regional populations, respectively, suggesting the presence of genetic differentiation in the two mating type populations from different locations. Pathogenicity assays revealed that both MAT1-1 and MAT1-2 populations were pathogenic to all 11 local sweet corn cultivars tested in this study. The potential of sexual reproduction, existence of genetic diversity in the two mating type populations, and pathogenicity suggest that B. maydis populations have independently clonally adapted under natural field conditions during corn cultivation.

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High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics

Viruses ◽

10.3390/v10070385 ◽

2018 ◽

Vol 10 (7) ◽

pp. 385 ◽

Cited By ~ 4

Author(s):

Asimina Katsiani ◽

Varvara Maliogka ◽

Nikolaos Katis ◽

Laurence Svanella-Dumas ◽

Antonio Olmos ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

High Throughput Sequencing ◽

Sour Cherry ◽

Prunus Species ◽

Cherry Tree ◽

High Genetic Diversity ◽

Viral Genomes ◽

Virus Diversity ◽

First Time

Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.

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Genetic diversity assessment in winter oilseed rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers

Czech Journal of Genetics and Plant Breeding ◽

10.17221/220/2013-cjgpb ◽

2014 ◽

Vol 50 (No. 3) ◽

pp. 216-225 ◽

Cited By ~ 3

Author(s):

L. Havlíčková ◽

E. Jozová ◽

A. Rychlá ◽

M. Klíma ◽

V. Kučera ◽

...

Keyword(s):

Genetic Diversity ◽

Brassica Napus ◽

Oilseed Rape ◽

Issr Markers ◽

Appropriate Technology ◽

Winter Oilseed Rape ◽

Brassica Napus L ◽

High Genetic Diversity ◽

Diversity Assessment ◽

Breeding Programmes

The genetic diversity of 94 accessions of winter oilseed rape (Brassica napus L.), representing past and contemporary material utilized in the Czech breeding programmes, was determined using microsatellites (SSRs), ISSRs and AFLPs. All three kinds of markers differed in the range of observed polymorphism and differentiated clearly each accession. Altogether 89 SSR, 1003 AFLP and 53 ISSR markers were evaluated. Their average rates of polymorphic bands were 100%, 53.9% and 90.6%, respectively, indicating high genetic diversity among the accessions. The greatest genetic distance was found by ISSRs (62.3%) whereas significantly lower distances of 49.4% in SSRs and 35.5% in AFLPs were observed. The genetic similarity matrix clearly distinguished all accessions. A set of the most distinct varieties was established. The analysis of the genetic pattern of the accessions indicated two groups comprising most of the modern Czech breeding materials, revealing a distinct shift in breeding. Surprisingly, molecular analyses did not support  breeders’ views about a narrow genetic base of the Czech breeding materials. The choice of appropriate technology for different aspects of germplasm evaluation is also discussed.

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