Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

Comparative assessment of SCoT and ISSR markers for analysis of genetic diversity and population structure in some Aegilops tauschii Coss. accessions

2021 ◽  
pp. 1-9
Author(s):  
Atefeh Nouri ◽  
Maryam Golabadi ◽  
Alireza Etminan ◽  
Abdolmajid Rezaei ◽  
Ali Ashraf Mehrabi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Aegilops Tauschii ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Start Codon ◽  
D Genome ◽  
Breeding Programmes ◽  
High Level ◽  
Effective Multiplex Ratio

Abstract Aegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCoT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (Ht) and genetic diversity within populations (Hs) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCoT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCoT (2.13 versus 8.62). Cluster analysis and population structure of SCoT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCoT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.

Genetic diversity of ten Moroccan populations of Tetraclinis articulata as revealed by Inter Simple Sequence Repeat (ISSR) markers

2020 ◽  
Vol 345 ◽  
pp. 15-25
Author(s):  
Meryem MAKKAOUI ◽  
Younes ABBAS ◽  
Salwa EL ANTRY-TAZY ◽  
Leila MEDRAOUI ◽  
Mohammed ALAMI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Mantel Test ◽  
Conservation Strategies ◽  
Sequence Repeat ◽  
Tetraclinis Articulata ◽  
High Level ◽  
Simple Sequence

Tetraclinis articulata (Vahl) Masters is one of Morocco's most important forest species. It is also found occasionally in Malta and Spain, showing significant adaptability to different bio-climatic conditions. However, the species is being affected by anthropogenic fragmentation, logging and neglect from authorities, which could lead to the irretrievable loss of this resource. In this study, the genetic diversity and genetic structure of ten Moroccan populations of T. articulata were assessed. Fifteen Inter-Simple Sequence Repeat (ISSR) markers were used. These generated 271 polymorphic fragments with an average of 18.06 per primer and showed 79.59% of polymorphism. The 129 individuals revealed a high level of genetic diversity (Hs = 0.221; Ht = 0.254) and 85% of genetic variation within populations. However, the genetic differentiation level was low (Gst = 0.13), which is consistent with the lack of correlation between genetic and geographic distances revealed by the Mantel test, resulting in a high level of gene flow (Nm = 3.294). Based on PCoA and neighbour-joining methods, the ten populations clustered under the effect of continental and marine climates. Compared with other conifers, the current genetic diversity and the pattern of T. articulata population structure indicate an important gene pool requiring efficient conservation strategies.

scholarly journals Genetic variability of Colletotrichum lindemuthianum isolates from Turkey and resistance of Turkish bean cultivars

2020 ◽  
Vol 18 (3) ◽  
pp. e1005
Author(s):  
Gulsum Palacioglu ◽  
Harun Bayraktar ◽  
Goksel Ozer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Common Bean ◽  
Issr Markers ◽  
Genetic Distances ◽  
Colletotrichum Lindemuthianum ◽  
Pathogen Populations ◽  
High Level ◽  
Pathogenic Diversity

Aim of study: To evaluate genetic variability and population structure of C. lindemuthianum isolates in Turkey and to record the reactions of some common bean cultivars to the pathogen isolates representing different genetic groups.Area of study: The study was performed in seven provinces of Turkey.Material and methods: Genetic diversity of 91 C. lindemuthianum isolates obtained from different provinces of Turkey was characterized by 27 iPBS and 30 ISSR primers. Also, the resistance of 40 common bean cultivars was scored against three isolates representing different genetic groups.Main results: The dendrogram based on the combined dataset of iPBS and ISSR markers classified the isolates into two main groups with a genetic similarity of 72%, which closely associated with the geographic distribution of the isolates. The dendrogram of Nei’s genetic distances and Structure analysis supported the clustering of C. lindemuthianum isolates according to the geographical provinces. The results indicated that high level of genetic diversity (GST= 0.4) and low level of gene flow (NM=0.748) exist among the populations. AMOVA analysis showed that 58.7% of total genetic variability resulted from genetic differences between the isolates within populations, while 41.29% was among populations. Four cultivars showed resistant reaction to three isolates, while the other cultivars were susceptible to at least one isolate.Research highlights: The results indicated that iPBS and ISSR markers were reliable and effective tools for analyzing population structure of C. lindemuthianum and revealed high level of genetic and pathogenic diversity among pathogen populations in Turkey.

scholarly journals Research Genetic diversity of Ottelia acuminata (Hydrocharitaceae) from the Eastern Himalayas, revealed by ISSR markers

1970 ◽  
Vol 7 ◽  
pp. 56-63 ◽  
Author(s):  
Chunlin Long ◽  
Zhutan Jiang ◽  
Zhiling Dao
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Natural Populations ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Ex Situ ◽  
Eastern Himalayas ◽  
Average Value ◽  
Geographical Distances ◽  
High Level

Ottelia acuminata (Gagnep.) Dandy (Hydrocharitaceae), an endangered aquatic species, was investigated in the Eastern Himalayas, especially in Yunnan Province of Southwest China. The genetic diversity among seven populations was examined using inter-simple sequence repeat (ISSR) amplification markers. The field survey showed that 43.5% natural populations of O. acuminata have become extinct during the last 30 years. Among 13 remaining wild populations, eight (61.5%) are on the edge of extinction and only five (38.5%) were unaffected. For the study on seven populations based on ten primers, 147 clear and reproducible DNA fragments were generated, of which 144 (97.96%) were polymorphic. Within populations, however, the polymorphic bands (PPB) generated by ISSRs was 53 and occupied 36.05% in population B, and similarly within population J (51 and 34.69%, respectively). The results showed that genetic variation is much higher among populations of O. acuminata than within populations. Analyses of Nei’s gene diversity, genetic distance and Shannon’s index also agreed with these results. The average value of Nei’s gene diversity (h) equaled 0.3710. The coefficient of genetic differentiation (Gst) equaled 0.5487, which means that 54.87% of the total molecular variance existed among populations. Such a high level of divergence present among populations may be caused by the complex topography and separated habitats which effectively restrict gene flow. Moreover, there is a lack of significant association between genetic and geographical distances (r = 0.28889, P > 0.05) in the populations of O. acuminata. Therefore, we proposed an appropriate strategy for conserving the genetic resources of O. acuminata in the Eastern Himalayas; namely, rescuing and conserving the core populations in situ, while selecting and preserving more populations with fewer individuals from each population ex situ. Key-words: Ottelia acuminata, genetic diversity, conservation, Eastern Himalayas, Yunnan Plateau, China DOI: 10.3126/botor.v7i0.4374Botanica Orientalis – Journal of Plant Science (2010) 7: 56-63

scholarly journals Molecular analysis of genetic diversity in population of Silybum marianum (L.) Gaertn in Egypt

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Marwa Hamouda
Keyword(s):  
Genetic Diversity ◽  
Electrophoretic Pattern ◽  
Issr Markers ◽  
Silybum Marianum ◽  
Inter Simple Sequence Repeats ◽  
Sds Page ◽  
Dna Pattern ◽  
Pharmaceutical Properties ◽  
High Level ◽  
Rapd And Issr

Abstract Background Silybum marianum L. Gaertn is a medicinal plant of unique pharmaceutical properties in the treatment of liver disorders and diabetic nephropathy. Biochemical (SDS-PAGE) and molecular markers such as randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) technologies were used in this work to detect genetic diversity of 14 collections of Silybum marianum population in Egypt. Results The electrophoretic pattern of seed protein gave different molecular weight bands, ranging from 24 to 111 KDa with the presence of unique bands. RAPD results revealed a high level of polymorphism (73.2%) using 12 RAPD primers, but only eight of them gave reproducible polymorphic DNA pattern. Sixteen primers were used in the ISSR method; only ten of them yielded clearly identifiable bands. The percentage of polymorphism is about 80% of the studied samples. Conclusion The obtained data confirmed that SDS-protein, RAPD, and ISSR markers are important tools for genetic analysis for Silybum marianum and recommended to give accurate results.

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

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.

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

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.

scholarly journals Analysis of Genetic Diversity in three Kazakh Sheep using 12 Microsatellites

2018 ◽  
Vol 7 (4.38) ◽  
pp. 122
Author(s):  
Kairat Dossybayev ◽  
Aizhan Mussayeva ◽  
Bakytzhan Bekmanov ◽  
Beibit Kulataev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mean Value ◽  
Fixation Index ◽  
Merino Sheep ◽  
Str Markers ◽  
Sheep Breeds ◽  
Str Loci ◽  
High Level ◽  
Two Populations

The genetic structure of three Kazakh sheep breeds was examined by using 12 microsatellite loci. A total of 144 alleles were detected from the 12 STR loci, with a mean value of 12.0. The highest allele diversity was found at the locus CSRD247 (16 alleles). PIC value showed that all studied STR markers are more informative and appropriate for genetic analysis of three Kazakh sheep populations. Beside of INRA006, all markers had high level of genetic variability. As Fixation index shows, the excess of the heterozygosity was observed only in loci MAF065. Obtained number of private alleles in Edilbai, Kazakh Arkhar Merino and Kazakh Fine-wool sheep were 25, 17 and 15 respectively. Genetic diversity was higher in Edilbai population than in other two populations. The genetic variability was lower in Kazakh Arkhar Merino sheep than in the Edilbai and Kazakh Fine-wool sheep breeds. The genetic distance was the largest between Edilbai and Kazakh Arkhar Merinos. Also, the moderate differentiation was observed between Edilbai and Kazakh Arkhar Merinos.   

scholarly journals Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

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