ISSR-Based Genetic Diversity Assessment of Genus Jasminum L. (Oleaceae) from Pakistan

The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon’s information index, polymorphism percentage, effective allele number, Nei’s genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei’s unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species.

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Eficiența unor marcheri moleculari în discriminarea populațiilor de lupoaie originare din China

10.53040/gppb7.2021.35 ◽

2021 ◽

Author(s):

Maria Duca ◽

◽

Ana Mutu ◽

Ina Bivol ◽

Steliana Clapco ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Gene Diversity ◽

Issr Markers ◽

Resolving Power ◽

Information Index ◽

Combined Use ◽

Different Types ◽

High Level ◽

Different Levels

In this study, the effectiveness of different types of molecular markers in assessing genetic diversity of populations of O. cumana from China was determined. ISSR and SSR markers detected different levels of genetic variability among and within broomrape populations. SSR markers analysis showed high level of genetic variation within the populations as revealed by high average values of Nei's gene diversity (H=0,75) and Shannon's information index (I=1,44), while genotyping with ISSR markers showed greater ability to discriminate genotypes according to Resolving power (Rp=7,24). Thus, the combined use of ISSR and SSR markers allowed the detection of higher polymorphism than either set of marker alone.

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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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Genetic diversity assessment and gene expression analysis of prolonged shelf-life genes in Mangalore melon (Cucumis melo ssp. agrestis var. acidulus)

10.21203/rs.3.rs-183494/v1 ◽

2021 ◽

Author(s):

Raghavendra Gunnaiah ◽

Ratnakar M. Shet ◽

Ashwini Lamani ◽

Dattatraya H. Radhika ◽

Rudrappa C. Jagadeesha

Keyword(s):

Genetic Diversity ◽

Shelf Life ◽

Candidate Genes ◽

Cucumis Melo ◽

South India ◽

Ethylene Biosynthesis ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Tree Construction ◽

Diversity Assessment

Abstract Mangalore melon (Cucumis melo ssp. agrestis var. acidulus) is a non-dessert melon, extensively grown in the coastal districts of South India, but hardly known to the rest of the World. Immature or mature fruits of Mangalore melon are used in preparation of delicious dishes such as vegetable stew, chutneys and curries. They are appreciated for nutritional values, long shelf life and biotic stress resistance. Seventy-nine accessions of Mangalore melon were collected from five states of South India and their genetic diversity was assessed using inter simple sequence repeat (ISSR) markers. Putative candidate genes of extended shelf life in Mangalore melon were studied by quantitative reverse transcription polymerase chain reaction in comparison with cantaloupe (Cucumis melo L.). Shelf life varied from 65 days to 300 days at room temperature. Six ISSR primers amplified 142 fragments ranging from 80 bp to 2380 bp with an average of 23.66 bands per marker on a high-resolution capillary electrophoresis system. Neighbor joining phylogenetic tree construction from the ISSR allele similarity based genetic distance revealed two major clusters with 46 and 33 accessions in each cluster. Expression of fruit ripening related genes of ethylene biosynthesis (1-aminocyclopropane-1-carboxylate synthase, 1-aminocyclopropane-1-carboxylate oxidase) and cell wall metabolism (polygalacturonase, xyloglucan endotransglucosylase/hydrolase and expansin) in Mangalore melons was significantly lower than the cantaloupe melon at 180 days after harvest. Mangalore melon is a promising genetic resource for enhancing the shelf life of melons and the putative candidate genes are useful in enhancing shelf life of cantaloupe following validation and conformation.

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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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Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River

Journal of Marine Science and Engineering ◽

10.3390/jmse8060471 ◽

2020 ◽

Vol 8 (6) ◽

pp. 471

Author(s):

Nguyen Thanh Vu ◽

Tran Thi Thuy Ha ◽

Vo Thi Bich Thuy ◽

Vu Thi Trang ◽

Nguyen Hong Nguyen

Keyword(s):

Genetic Diversity ◽

Mekong River ◽

Effective Population ◽

Wild Stock ◽

Pangasianodon Hypophthalmus ◽

Population Genomic ◽

Diversity Assessment ◽

Genomic Analyses ◽

In The Wild ◽

Striped Catfish

The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.

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Genetic Differentiation of Jack Pine (Pinus banksiana) and Red Pine (P. resinosa) Populations From Metal Contaminated Areas in Northern Ontario (Canada) Using ISSR Markers

Silvae Genetica ◽

10.1515/sg-2008-0049 ◽

2008 ◽

Vol 57 (1-6) ◽

pp. 333-340 ◽

Cited By ~ 1

Author(s):

M. Ranger ◽

K. K. Nkongolo ◽

P. Michael ◽

P. Beckett

Keyword(s):

Genetic Diversity ◽

Pinus Banksiana ◽

Metal Accumulation ◽

Gene Diversity ◽

Jack Pine ◽

Issr Markers ◽

Red Pine ◽

Northern Ontario ◽

Polymorphic Loci ◽

Information Index

Abstract Metal accumulation in soil and plant tissues has caused severe ecological damage in forest ecosystems in the Sudbury region. The main objective of the present study was to determine the levels of genetic diversity in jack and red pine populations growing in metal contaminated and uncontaminated areas. Newly introduced populations were compared to 40 to 60 old populations. For jack pine, the percentage of polymorphic loci (P %) ranged from 14.6% to 45.8% with a mean of 31.6%. Nei’s gene diversity (h) varied from 0.046 to 0.169 with an average of 0.100, and Shannon’s index (I) ranged from 0.070 to 0.250 with an average of 0.153. The level of genetic variation was much lower in the red pine populations. For this species, the level of polymorphic loci varied from 4.55% to 27.27%. The mean for Nei’s gene diversity and Shannon’s information index, were 0.034 and 0.053, respectively. The highest genetic diversity values were observed in new plantations being developed by the Sudbury reforestation program. Overall, the genetic distance among the Pinus banksiana populations revealed that all the populations analyzed were genetically close to each other. There was no association between metal accumulation and genetic diversity for both species.

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ASSESSMENT OF GENETIC DIVERSITY AND RELATIONSHIPS AMONG GRAPEVINE CULTIVARS ORIGINATING IN CENTRAL AND EASTERN EUROPE AND NORTH AMERICA USING ISSR MARKERS

Acta Scientiarum Polonorum Hortorum Cultus ◽

10.24326/asphc.2019.5.14 ◽

2019 ◽

Vol 18 (5) ◽

pp. 141-152

Author(s):

Anna Lisek ◽

Jerzy Lisek

Keyword(s):

Genetic Diversity ◽

North America ◽

Polymorphic Information Content ◽

Issr Markers ◽

Molecular Techniques ◽

Resolving Power ◽

Vitis Vinifera L ◽

Phenotypic Differences ◽

High Degree ◽

Issr Primers

The study shows genetic diversity of 38 Vitis vinifera L. cultivars and hybrids originating in North America and Europe, including cultivars selected in Poland, which have not been characterized with the use of DNA markers yet. The agrobiological features of the genotypes selected for testing, indicate that they may be useful for the breeding of new cultivars and grape production. The use of 12 ISSR primers allowed to obtain 94.4% of polymorphism. The polymorphic information content (PIC) value was high and varied between 0.829 and 0.953 with an average of 0.897. The resolving power (Rp) ranged between 3.678 and 8.892 with an average of 6.347. Primers UBC 809, UBC 810, UBC 812, UBC 855, UBC 891 and UBC 810 were found to be highly effective (informative). Similarity coefficient ranged between 0.167 and 1.0, which indicates high degree of diversity of tested grape cultivars. Tested cultivars were grouped in 3 main clusters; one of them was further divided into 6 subclusters. ‘Pannonia Kincse’ and ‘Danmarpa Polonia’ were not differentiated. Phenotypic differences among those two cultivars suggest that ‘Danmarpa Polonia’ might be a clone of ‘Pannonia Kincse’ and other molecular techniques must be used to differentiate them. Morphological and agrobiological characters of cultivars support the results obtained by ISSR markers.

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Genetic diversity assessment among Corema album (L.) D. Don (Ericaceae) genotypes based on ISSR markers and agro-morphological traits

Genetic Resources and Crop Evolution ◽

10.1007/s10722-019-00849-8 ◽

2019 ◽

Vol 67 (3) ◽

pp. 715-726

Author(s):

João Jacinto ◽

Pedro Brás de Oliveira ◽

Teresa Valdiviesso ◽

Jorge Capelo ◽

Pedro Arsénio ◽

...

Keyword(s):

Genetic Diversity ◽

Morphological Traits ◽

Issr Markers ◽

Diversity Assessment

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Molecular characterization of some landraces and varieties of Date palm (Phoenix dactylifera L.) from Afar region of Ethiopia using ISSR markers

10.21203/rs.2.10762/v1 ◽

2019 ◽

Author(s):

Meera Indracanti ◽

Dawud Takele Mekonnen ◽

Mesfin Tsegaw

Keyword(s):

Genetic Diversity ◽

Date Palm ◽

Polymorphic Information Content ◽

Phoenix Dactylifera ◽

Issr Markers ◽

Snp Markers ◽

Discrimination Power ◽

Information Index ◽

Phoenix Dactylifera L ◽

Afar Region

Abstract Back ground Date palm (Phoenix dactylifera L.) is one of the oldest fruit trees in hot arid region of the world including North Africa. In some areas of Afar region of Ethiopia, date palm grow as landraces, are in danger due to introduction of improved cultivars. Present study was carried out to fill knowledge gap about molecular diversity of this crop in Afar region. Molecular studies of 5 landraces and 3 introduced cultivars of date palm from Afar region of Ethiopia were tested using 21 randomly selected ISSR primers for amplification and polymorphism detection using genomic DNA. ISSR markers across 8 date palm varieties were scored for their presence (1) or absence (0). Shannon's Information index (I) and polymorphic information content (PIC) were analyzed by popGENE 32 and online PIC calculator respectively. Results 17 out of 21 ISSR markers used for this study produced a total of 557 scorable DNA fragments with average of 33.52 per marker and 61.68, 43.93 and 68.22% polymorphism were obtained within local landraces, introduced varieties and among all samples respectively. The genetic distance among all samples ranged from 0.1402 to 0.5953; and the dendrogram separated date palm varieties into seven clusters. ISSR markers used for this study have high discrimination power and the average values of Shannon's information index and PIC were 0.318 and 0.76 respectively. Conclusion Genetic diversity was observed among all date palms studied in this investigation. To have better understanding on genetic diversity of date palm in the Afar region, further research should be done using SNP markers and landraces should be registered.

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