Genetic Diversity and Selection of Suitable Molecular Markers for Characterization of Indigenous Zizyphus Germplasm

Co-dominant markers’ data are often analysed as if they were dominant markers, an over-simplification that may be misleading. Addressing this, the present paper aims to provide a practical guide to the analysis of co-dominant data and selection of suitable software. An overview is provided of the computational methods and basic principles necessary for statistical analyses of co-dominant molecular markers to determine genetic diversity and molecular characterization of germplasm collections. The Hardy–Weinberg principle is at the base of statistical methods to determine genetic distance, genetic diversity, and its distribution among and within populations. Six statistical software packages named GenAlEx, GDA, Power Marker, Cervus, Arlequin, and Structure are compared and contrasted. The different software packages were selected based on: (i) The ability to analyze co-dominant data, (ii) open access software, (iii) ease of downloading, and (iv) ease of running using a Microsoft Window interface. The software packages are compared analyzing the same dataset. Differences among parameters are discussed together with the comments on some of the software outputs.

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Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

Research Journal of Biotechnology ◽

10.25303/1611rjbt147154 ◽

2021 ◽

Vol 16 (11) ◽

pp. 147-154

Author(s):

Anjali Uniyal ◽

Akhilesh Kumar ◽

Sweta Upadhyay ◽

Vijay Kumar ◽

Sanjay Gupta

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Fragment Length Polymorphism ◽

Dna Polymorphisms ◽

Inter Simple Sequence Repeats ◽

Pharmaceutical Industries ◽

Endangered Medicinal Herb ◽

Identification And Characterization ◽

Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

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Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽

10.1017/s0031182002002020 ◽

2002 ◽

Vol 125 (7) ◽

pp. S51-S59 ◽

Cited By ~ 50

Author(s):

J. CURTIS ◽

R. E. SORENSEN ◽

D. J. MINCHELLA

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Molecular Markers ◽

Microsatellite Markers ◽

Natural Populations ◽

Mitochondrial Marker ◽

Tropical Regions ◽

Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

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Selection of ISSR Primers to Study the Genetic Diversity of Myrciaria floribunda O. Berg

Current Journal of Applied Science and Technology ◽

10.9734/cjast/2020/v39i1630730 ◽

2020 ◽

pp. 23-28

Author(s):

Luiz Sergio Costa Duarte Filho ◽

Danielson Ramos Ribeiro ◽

Allison Vieira da Silva

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

South America ◽

Central America ◽

Dna Extraction ◽

Endemic Species ◽

Germplasm Bank ◽

Slow Growing ◽

Selection Of ◽

Issr Primers

The species Myrciaria floridunda O. Berg, popularly known as cambuí, belongs to the Myrtaceae family. Cambui is a native, non-endemic species that occur in diverse environments in Central America and South America. They are slow-growing plants with a shrub or sub-shrub habit. The fruits, the product of interest of the species, are small, spherical berries orange or red in colorturning to wine colorwhen they are ripe. The exploitation of the species is still mostly extractivist, carried out by traditional local families who, in times of fruiting of the species, leverage their income by selling fruits at fairs. The fruits can be eaten fresh, in the form of jellies, liquor or wine. To study the genetic diversity of the species using ISSR-type molecular markers, it is necessary to first isolate DNA in sufficient quality and quantity. Here, leaves for DNA extraction were collected from the active germplasm bank of the Federal University of Alagoas, Brazil. The DNA of the species was extracted using CTAB detergent methodology with modifications adapted to the species. Twelve ISSR primers were tested on DNA from two cambui genotypes. Of the twelve primers, eight were selected due to their polymorphism index above 50%, namely: UFAL-2, UFAL-3, UFAL-5, UFAL-6, UFAL-7, UFAL-8, UFAL-9 and UFAL-10.

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GENETIC CHARACTERIZATION OF GALOBA DURIAN (AMONUM SPP.) IN AMBON ISLAND BASED ON RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD)

AgroTech Journal ◽

10.31327/atj.v3i1.524 ◽

2018 ◽

Vol 3 (1) ◽

pp. 27-33

Author(s):

Fuadiska Salamena ◽

Cecilia Anna Seumahu

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Characterization ◽

Kidney Diseases ◽

Random Amplified Polymorphic Dna ◽

Quantitative Result ◽

Dna Amplification ◽

Polymorphic Band ◽

Qualitative And Quantitative

Galoba durian is one of the endemic floras from Maluku. Galoba durian is a species belonging to the Amomum genera Zingiberaceae family. It is also used as a medicinal plant for waist and kidney diseases. Based on the color of the fruit, galoba durian is divided into two nmely red galoba durian and green galoba durian. Distribution of this plant in Ambon can found in a few places such as highland and coastal area. Different locations influence phenotypic of plants, but may not show different genetic characteristic. Genetic diversity can detected by molecular markers. Genetic characterization from galoba durian using RAPD markers has not been done before. This study aimed to analyze genetic diversity from galoba durian using molecular markers RAPD. Samples of plants are used red galoba durian from Hatu and green galoba durian from Hatalae. The result of the first study, characterization of the morphology of the galoba durian, showed that both galoba have almost similar characteristics. Further DNA was tested by qualitative and quantitative. Result shows good qualitative and quantitative of DNA genomic. The second study was amplification by PCR-RAPD. DNA amplifications were performed using 3 primers out of 9 screened random primers. The primers selection was based on hight polymorphism. DNA amplification has 36 bands which were 100% polymorphic. The size of each bands from visualization of agarose was determined by linear regression. Number of band amplified was range from 120 to 1612 bp. Polymorphic band of RAPD showed the highest genetic diversity. It can be concluded that the two plants of galoba durian are different species

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Characterization of Genetic Diversity Using Molecular Markers

10.1007/978-3-030-76649-8_5 ◽

2021 ◽

pp. 77-90

Author(s):

Lalith Perera ◽

R. Manimekalai

Keyword(s):

Genetic Diversity ◽

Molecular Markers

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Morphological and Genetic Diversity of Rhizobia Nodulating Cowpea (Vigna unguiculataL.) from Agricultural Soils of Lower Eastern Kenya

International Journal of Microbiology ◽

10.1155/2017/8684921 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Damaris K. Ondieki ◽

Evans N. Nyaboga ◽

John M. Wagacha ◽

Francis B. Mwaura

Keyword(s):

Genetic Diversity ◽

Developing Countries ◽

Crop Production ◽

Agricultural Soils ◽

Repetitive Element ◽

Morphological Characteristics ◽

Soil Samples ◽

Cowpea Rhizobia ◽

Selection Of

Limited nitrogen (N) content in the soil is a major challenge to sustainable and high crop production in many developing countries. The nitrogen fixing symbiosis of legumes with rhizobia plays an important role in supplying sufficient N for legumes and subsequent nonleguminous crops. To identify rhizobia strains which are suitable for bioinoculant production, characterization of rhizobia is a prerequisite. The objective of this study was to assess the morphological and genetic diversity of rhizobia that nodulates cowpea in agricultural soils of lower eastern Kenya. Twenty-eight rhizobia isolates were recovered from soil samples collected from farmers’ fields in Machakos, Makueni, and Kitui counties in lower eastern Kenya and characterized based on morphological characteristics. Thirteen representative isolates were selected and characterized using BOX repetitive element PCR fingerprinting. Based on the dendrogram generated from morphological characteristics, the test isolates were distributed into two major clusters at a similarity of 75%. Phylogenetic tree, based on BOX repetitive element PCR, grouped the isolates into two clusters at 90% similarity level. The clustering of the isolates did not show a relationship to the origin of soil samples, although the isolates were genetically diverse. This study is a prerequisite to the selection of suitable cowpea rhizobia to develop bioinoculants for sustainable crop production in Kenya.

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Genetic diversity of Albanian pea (Pisum sativum L.) landraces assessed by morphological traits and molecular markers

Czech Journal of Genetics and Plant Breeding ◽

10.17221/227/2013-cjgpb ◽

2014 ◽

Vol 50 (No. 2) ◽

pp. 177-184 ◽

Cited By ~ 7

Author(s):

B. Gixhari ◽

M. Pavelková ◽

H. Ismaili ◽

H. Vrapi ◽

A. Jaupi ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Morphological Traits ◽

Principal Component ◽

Morphological Characters ◽

Insertion Polymorphism ◽

Growing Seasons ◽

And Cluster Analysis

In order to investigate the genetic diversity present in the pea germplasm stored in the Albanian genebank, we analyzed 28 local pea genotypes of Albanian origins for 23 quantitative morphological traits, as well as 14 retrotransposon-based insertion polymorphism (RBIP) molecular markers. The study of morphological characters carried out during three growing seasons (2010, 2011 and 2012) had the objective of characterization of traits useful in breeding programs. RBIP marker analysis revealed the genetic similarity in range from 0.06 to 0.45. ANOVA, principal component analysis (PCA) and cluster analysis was used to visualize the association among different traits. Most of the quantitative morphological traits showed significant differences. PCA and cluster analysis (Ward’s method) carried out for morphological traits divided the local pea genotypes into three clusters. Finally, the study identified the agronomicaly important traits which will facilitate the maintenance and agronomic evaluation of the collections.

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Time for a paradigm shift in the use of plant genetic resources

Genome ◽

10.1139/gen-2019-0141 ◽

2020 ◽

Vol 63 (3) ◽

pp. 189-194

Author(s):

François Belzile ◽

Amina Abed ◽

Davoud Torkamaneh

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Candidate Genes ◽

Paradigm Shift ◽

Large Scale ◽

Plant Genetic Resources ◽

Phenotypic Characterization ◽

Novel Traits ◽

The World

For all major crops, sizeable genebanks are maintained across the world and serve as repositories of genetic diversity and key sources of novel traits used in breeding. Although molecular markers have been used to characterize diversity in a broad sense, the most common approach to exploring these resources has been through phenotypic characterization of subsets of these large collections. With the advent of affordable large-scale genotyping technologies and the increasing body of candidate genes for traits of interest, we argue here that it is time for a paradigm shift in the way that we explore and exploit these considerable and highly useful resources. By combining dense genotypic information in and around candidate genes, it is possible to classify accessions based on their haplotype, something approximating the actual alleles at these genes of interest.

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Characterization of the Populations of Botrytis cinerea Infecting Plastic Tunnel-Grown Strawberry and Tomato in Hubei Province of China

Plant Disease ◽

10.1094/pdis-01-20-0164-re ◽

2020 ◽

Author(s):

Rui Yang ◽

Na Li ◽

Ziliang Zhou ◽

Guoqing Li

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Nicotiana Benthamiana ◽

Agar Medium ◽

Hubei Province ◽

Mating Types ◽

Highly Sensitive ◽

Overall Ratio ◽

Highly Virulent

A total of 707 isolates of Botrytis were collected from plastic tunnel-grown strawberry and tomato in Hubei province of China. They were identified based on the specific molecular markers. Diversity of the B. cinerea (Bc) isolates was evaluated by typing the transposable elements or TE (Boty, Flipper) and the mating types (MAT1-1, MAT1-2), as well as by determining virulence on tobacco (Nicotiana benthamiana) and fenhexamid sensitivity in agar medium. The results showed that 706 isolates (accounting for 99.9%) belonged to Bc, one isolate (accounting for 0.1%) belonged to B. pseudocinerea. The Bc isolates fell into four TE types, Vacuma, Boty, Flipper and Transposa, which accounted for 3.1%, 9.6%, 18.4% and 68.8% (n = 706), respectively. The strawberry and tomato sub-populations of Bc differed significantly (P < 0.05) in composition of the four TE types. The overall ratio of MAT1-1 to MAT1-2 deviated from 1:1 (n = 706, P = 0.0002), MAT1-2 (accounting for 56.9%) predominated over MAT1-1 (accounting for 43.1%). However, in 7 out of 12 geographic sub-populations, the ratio of MAT1-1 to MAT1-2 matched 1:1, whereas in the remaining five geographic sub-populations, the ratio of MAT1-1 to MAT1-2 did not match 1:1. Results of the biological characterizations showed that most Bc isolates were highly sensitive or sensitive to fenhexamid, and the majority of Bc isolates were highly virulent or virulent on tobacco. Moreover, relationship between genetic diversity and biological characteristics was analyzed. The results achieved in this study are helpful for understanding of the populations of B. cinerea.

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