scholarly journals iMAF - Index of Major Allele Frequency

2018 ◽  
Vol 2 (2) ◽  
pp. 78
Author(s):  
Naris Pojskić
Keyword(s):  
Allele Frequency ◽  
Major Allele Frequency ◽  
Major Allele

scholarly journals A Study of GluK1 Kainate Receptor Polymorphisms in Down Syndrome Reveals Allelic Non-Disjunction at 1173(C/T)

2009 ◽  
Vol 27 (2) ◽  
pp. 45-54 ◽  
Author(s):  
Debarati Ghosh ◽  
Swagata Sinha ◽  
Anindita Chatterjee ◽  
Krishnadas Nandagopal
Keyword(s):  
Down Syndrome ◽  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Brain Regions ◽  
Parental Origin ◽  
Heterozygous Parent ◽  
Major Allele Frequency ◽  
Hardy Weinberg Equilibrium ◽  
Patient Families ◽  
Major Allele

Mechanisms underlying Down syndrome (DS)-related mental retardation (MR) remain poorly understood. In trisomic offspring, non-disjunction may result in the reduction to homozygosity of a susceptibility allele inherited from a heterozygous parent. Accordingly, we sought evidence for allelic non-disjunction in the GluK1 gene that encodes the critical kainite-binding glutamate receptor subunit-5, maps to chromosome 21q22.1 in the DS critical region and is expressed in brain regions responsible for learning and memory. Three polymorphisms of GluK1 [522(A/C) rs363538; 1173(C/T) rs363430 and 2705(T/C) rs363504] were genotyped in 86 DS patient families by means of PCR-coupled RFLP assays and evaluated with respect to allele frequency, heterozygosity, linkage disequilibrium, stage and parental origin of allelic non-disjunction. We report that the distribution of allele frequencies is in Hardy-Weinberg equilibrium. Moderate heterozygosity (0.339) and a major allele frequency of 0.78 render the 1173(C/T) marker informative. Pair-wise comparisons reveal that 522(A/C)-1173(C/T) [χ2= 31.2,df= 1,p= 0.0001;D’ = 0.42] and 1173(C/T)-2705(T/C) [χ2= 18.3,df= 1,p= 0.0001;D’ = 0.34] are in significant linkage disequilibrium of weak magnitude. The estimated ratio of meiosis-I to meiosis-II errors arising from allelic non-disjunction of 1173(C/T) is 4:1 in maternal cases and 2:1 in paternal cases. Studies including additional markers and patient samples are warranted to further substantiate present findings.

scholarly journals Microsatelite diversity of Bosnian-Herzegovinian-Croatian shepherd dog Tornjak

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 49-56
Author(s):  
Almira Softic ◽  
Katica Velija ◽  
Jasmin Ramic ◽  
Kasim Bajrovic ◽  
Gabrijela Radosavljevic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Allele Frequency ◽  
Bosnia And Herzegovina ◽  
Microsatellite Loci ◽  
Weinberg Equilibrium ◽  
Major Allele Frequency ◽  
Hardy Weinberg Equilibrium ◽  
Major Allele ◽  
High Level ◽  
Diversity Studies

This paper presents the first estimation of polymorphism of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak in Bosnia and Herzegovina using 10 microsatellite loci, which are an integral part of StockMarks? for Canine Genotyping Kit (Applied Biosystems, Foster City, CA, USA). Ten microsatellite loci used in this study are appropriate for assessing the genetic diversity for this breed. Measures of genetic diversity were estimated based on allelic and genotypic calculations, observed (HO) and expected (HE) heterozygosities, deviations from Hardy-Weinberg equilibrium and polymorphism information content (PIC). The lowest genetic diversity was estimated for locus PEZ20, and the highest for PEZ6 locus. Observed and expected mean heterozygosities were 0.7261 and 0.7392, respectively. Statistically significant deviation (p<0.05) from Hardy-Weinberg equilibrium was found for PEZ1, PEZ12, PEZ3 and PEZ6 loci. The PIC values suggested that all markers (100%) are very informative (PIC > 0.5) in terms of their suitability for genetic diversity studies. When all observed parameters are taken into account (observed and expected heterozygosities, PIC, number of detective and effective alleles, number of detected and maximum possible genotypes, major allele frequency and major allele frequency index), we can conclude that PEZ6 locus shows the highest genetic diversity while PEZ3 displays the lowest. However, assuming values of observed and expected heterozygosities, as well as PIC, we consider loci PEZ20 to be the least diverse, but this locus has more effective alleles and more genotypes present than PEZ3. These preliminary results are the first genetic diversity survey of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak in Bosnia and Herzegovina and could be useful to the dog breeders in designing and managing breeding strategies. Summarizing the information above, we can conclude that the population of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak from B&H is not affected by substantial loss of genetic diversity. Results of our study indicate presence of reasonably high level of genetic variability and lead to a better understanding of this dog breed.

scholarly journals Morphological and Molecular Characterization of Tropical Strawberry

2019 ◽  
Vol 29 (2) ◽  
pp. 267-276
Author(s):  
Ripa Rani Bhowal ◽  
M. Mofazzal Hossain ◽  
Emrul Kayesh ◽  
Mehfuz Hasan
Keyword(s):  
Molecular Characterization ◽  
Molecular Level ◽  
Gene Diversity ◽  
Polymorphic Markers ◽  
Major Allele Frequency ◽  
Ssr Primers ◽  
Major Allele ◽  
Genetic Dissimilarity ◽  
Morphological And Molecular Characterization

The experiment was conducted to assess five tropical strawberry genotypes at phenotypic and molecular level. Among the five strawberry genotypes (BARI Strawberry 1, BARI Strawberry 2, BARI Strawberry 3, FA 005 and Festival), BARI Strawberry 2 was found to be the best in respect of fruit per plant (32.42), fruit yield per plant (594.73 gm) and yield per hectare (19.39 ton). Ten SSR primers were initially screened for molecular characterization and finally MFv104, ARSFL-10 and ARSFL-15 markers were selected for the analysis. EMFv104 and ARSFL-15 produced the maximum number of polymorphic alleles (4) while ARSFL-10 produced three polymorphic alleles. The major allele frequency at each locus ranged from 0.4 (EMFv104) to 0.6 (ARSFL-10). The PIC values varied from 0.4992 on ARSFL-10 to 0.672 on EMFv104. The gene diversity ranged from 0.56 (ARSFL-10) to 0.72 (EMFv104 and ARSFL-15). BARI Strawberry 1 and Festival were the closest genotypes with the lowest genetic dissimilarity value of 0.16667. EMFv104 and ARSFL-15 can be used as polymorphic markers for assessing genetic diversity of different strawberry genotypes.

Development of a core SNP panel for cacao (Theobroma cacao L.) identity analysis

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Amrita Mahabir ◽  
Lambert A. Motilal ◽  
David Gopaulchan ◽  
Saila Ramkissoon ◽  
Antoinette Sankar ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
Allele Frequency ◽  
Theobroma Cacao ◽  
Nucleotide Polymorphisms ◽  
Major Allele Frequency ◽  
Concomitant Reduction ◽  
Minimum Number ◽  
Snp Panel ◽  
Snp Panels ◽  
Theobroma Cacao L

Single nucleotide polymorphisms (SNPs) are preferred markers for DNA fingerprinting and diversity studies in cacao (Theobroma cacao L.). Yet, a consensus SNP panel with a minimum number of SNPs for optimal identity analysis is unavailable for cacao. An initial set of 146 SNP panels of varying sizes were assembled based on heterozygosity, linkage disequilibrium (LD), linkage group (LG) distribution, major allele frequency, minor allele frequency (MiAF), polymorphism information content (PIC), and random distribution. These panels were assessed to determine their ability to distinguish among a training set of 155 accessions. The panels with the best separation ability were supplemented with additional SNPs to create 16 designer panels, which separated all 155 accessions. The 16 designer SNP panels were then assessed on a dataset of 1220 accessions coming from 10 ancestral groups. Increasing the number of SNPs generally yielded improved resolution of genetic identities with concomitant reduction of synonymous groups. The number and choice of SNPs were critical factors with LD, MiAF, and PIC being important selection attributes but an even LG distribution was unnecessary. A robust set of 96 SNPs is recommended as a minimal core SNP panel for cacao DNA fingerprinting to the international cacao community.

Genetic diversity of selected accessions for seed protein among pigeonpea minicore collection

2016 ◽  
Author(s):  
L. G. Jaggal ◽  
B. R. Patil ◽  
P. M. Naik ◽  
K. Priya
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Core Collection ◽  
Seed Protein ◽  
Polymorphic Information Content ◽  
Efficient System ◽  
Major Allele Frequency ◽  
Entire Collection ◽  
Major Allele ◽  
Simple Sequence

Protein is an important part of our diet and legumes viz., pigeonpea, chickpea, groundnut, cowpea, blackgram, greengram, etc are very rich source of protein. Among them, pigeonpea consists of about 20 to 22% of seed protein. Minicore collection set is consisted of approximately 10 % of core collection and 1% of entire collection with lot of diversity present in it. Nitrogen content of pigeonpea minicore collection set was estimated using Micro-Kjeldhal method and was ranged from 9.82 to 21.45 %. Based on per cent seed protein, twelve accessions of high and twelve accessions of low seed protein were selected for molecular characterization using 23 simple sequence repeat (SSR) markers. The PowerMarker result depicted that, among twenty three amplified markers, twenty markers generated polymorphism with mean polymorphic information content (PIC), major allele frequency (MAF) and genetic diversity of 0.479, 0.589 and 0.525 respectively. Based on molecular characterization, the dendrogram was constructed using DARwin 5.0 software distinguished the selected accessions of both high and low seed protein separately into different clusters showing diversity The results illustrate the potential of marker systems to distinguish the content of seed protein in pulses crop at genus level. Use of these markers also offers an efficient system for the assessment of genetic diversity within minicore set of pigeonpea.

scholarly journals Evaluation of Diversity among Soybean Genotypes via Yield Attributing Traits and SSR Molecular Markers

2021 ◽  
pp. 9-24
Author(s):  
Nishi Mishra ◽  
Manoj Kumar Tripathi ◽  
Sushma Tiwari ◽  
Niraj Tripathi ◽  
Neha Gupta ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Microsatellite Markers ◽  
Physiological Traits ◽  
Design Data ◽  
Major Allele Frequency ◽  
Major Cluster ◽  
Soybean Genotypes ◽  
Physiological Analysis ◽  
Major Allele ◽  
High Yielding Varieties

Introduction: As an important source of nutrients to humans and animals, soybean is considered to be a major crop. Objective: The present study has been executed to identify diverse soybean genotypes on account of different morpho-physiological and microsatellite molecular markers. Study Design: Data for Morpho-physiological traits were recorded from experiment conducted under field conditions in RBD design whereas molecular work was conducted in Laboratory. Place and Duration of the Study: The present study was conducted at College of Agriculture, Gwalior, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, M.P., India during Kharif 2018-19. Methodology: The study was conducted to document different morphological and physiological traits related to the yield and its attributing traits in soybean. Total 32 microsatellite markers were also used in laboratory to analyze the variability among soybean genotypes. Results: Morpho-physiological analysis among 53 genotypes revealed the presence of considerable level of variability. Phylogenetic tree based on morpho-physiological traits grouped the genotypes into major and minor cluster. Major cluster had fifty genotypes while minor cluster had only three genotypes. Among polymorphic 32 microsatellite markers, the highest genetic diversity (0.66) was recorded in Satt520 whilst lowest (0.037) was in Satt557 with an average of 0.35. The highest PIC value was 0.59 prearranged by Satt520 and lowest 0.036 by Satt557. An average major allele frequency was 0.69 while, an average PIC value was 0.32. Microsatellite markers-based data also grouped the genotypes into one major and one minor cluster. Conclusion: Molecular analysis based on microsatellite markers confirms the presence of genetic variability among genotypes under the investigation. Data obtained in the present investigation may contribute towards improvement of soybean genotypes to develop high yielding varieties by considering diverse genotypes with good agronomical traits in hybridization programme.

Molecular diversity and phenotypic characterization of A, B and R lines in Pigeonpea [Cajanus cajan (L.) Millsp.]

2017 ◽  
Author(s):  
Yamanura . ◽  
R. Lokesha ◽  
S. Muniswamy ◽  
G. Girish ◽  
M. Mahiboobsa ◽  
...  
Keyword(s):  
Molecular Diversity ◽  
Growth Habit ◽  
Phenotypic Variability ◽  
Phenotypic Characterization ◽  
Polymorphic Markers ◽  
Male Sterile ◽  
Major Allele Frequency ◽  
Major Allele ◽  
B Lines

An experiment was carried out with 17 CGMS lines and their maintainers along with 22 diversified restorer (R) lines to obtain information on molecular diversity and phenotypic characterization. All exhibited enormous phenotypic variability. Anthocynin pigmentation on hypocotyls was present in 50 genotypes and it was absent in six genotypes viz., ICPA 2043, ICPB 2043, GT 307A, GT 307B, RAJA and BSMR 736. Determinate type of growth habit was found in three genotypes viz., ICPA 2078, ICPB 2078 and GC 11-39. A total of 30 SSR markers were used across 56 genotypes. The polymorphic markers amplified a total of 76 alleles with an average of 2.93 alleles per markers and number of alleles ranged from 2 to 4 per marker. Major allele frequency ranged from 0.34 (CcM0057) to 0.79 (CcM0402) with an average of 0.47 per marker. Molecular diversity among 17 male sterile (A) lines and their maintainer (B) lines yielded three main clusters. All the ‘A’ and ‘B’ lines found isogenic, as indicated by close clusters, except for the genotypes GRGA/B 2, GRGA/B 4, GRGA/B 6 and GT 307A/B. Hence more number of back crosses are needed to make them as isonuclear lines.

scholarly journals Phylogenetic analysis of Colchicum (Colchicaceae) genus by molecular markers from nuclear and chloroplast genome

2020 ◽  
Vol 4 (1) ◽  
pp. 1
Author(s):  
Abdurrahman Umut Tüyel ◽  
Ezgi Çabuk Şahin ◽  
Funda Şentürk Akfirat ◽  
Yıldız Aydin ◽  
Ahu Altınkut Uncuoğlu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Rapd Analysis ◽  
Rapd Marker ◽  
Haplotype Network ◽  
Sequence Length ◽  
Discrimination Power ◽  
Major Allele Frequency ◽  
Major Allele ◽  
The Relationship

We evaluated the patterns of genetic variation of 16 Colchicum species, including 37 different genotypes, using RAPD marker and trnL–trnF chloroplast DNA sequence. A total of 861 polymorphic alleles through RAPDs showed a mean of 33.88 ± 3.80 alleles per primer, while mean major allele frequency was 0.067 ± 0.05. The sequence length of trnL–trnF ranged from 1022 bp to 1081 bp. The phylogenetic tree was constructed to understand the relationship between Colchicum species and the discrimination power of the nuclear and chloroplast genome for species. The results showed that trnL–trnF gene region grouped Colchicum species well in comparison with RAPD analysis. This data was also supported by haplotype network analysis, structure analysis and PCA (Principle Component Analysis). This study showed that there is a need for a characterization that contains more molecular and morphological methods to correctly distinguish Colchicum species.

scholarly journals Preprocessing Tools for Data Preparation

2022 ◽  
pp. 35-70
Author(s):  
Osval Antonio Montesinos López ◽  
Abelardo Montesinos López ◽  
Jose Crossa
Keyword(s):  
Machine Learning ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Data Preparation ◽  
Statistical Machine Learning ◽  
Major Allele Frequency ◽  
Major Allele ◽  
Best Linear Unbiased

AbstractThis data preparation chapter is of paramount importance for implementing statistical machine learning methods for genomic selection. We present the basic linear mixed model that gives rise to BLUE and BLUP and explain how to decide when to use fixed or random effects that give rise to best linear unbiased estimates (BLUE or BLUEs) and best linear unbiased predictors (BLUP or BLUPs). The R codes for fitting linear mixed model for the data are given in small examples. We emphasize tools for computing BLUEs and BLUPs for many linear combinations of interest in genomic-enabled prediction and plant breeding. We present tools for cleaning, imputing, and detecting minor and major allele frequency computation, marker recodification, frequency of heterogeneous, frequency of NAs, and three methods for computing the genomic relationship matrix. In addition, scaling and data compression of inputs are important in statistical machine learning. For a more extensive description of linear mixed models, see Chap. 10.1007/978-3-030-89010-0_5.

scholarly journals Genetic Variation in Pawpaw Cultivars Using Microsatellite Analysis

2011 ◽  
Vol 136 (6) ◽  
pp. 415-421 ◽  
Author(s):  
Li Lu ◽  
Kirk W. Pomper ◽  
Jeremiah D. Lowe ◽  
Sheri B. Crabtree
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Information Content ◽  
Polymorphism Information Content ◽  
State University ◽  
The Public ◽  
Asimina Triloba ◽  
Major Allele Frequency ◽  
High Polymorphism Information Content ◽  
Major Allele

Pawpaw (Asimina triloba) is a tree fruit native to eastern North America, which is in the early stages of domestication. Most early 20th century pawpaw cultivars have been lost; however, recent cultivar releases and potential new releases may have enhanced genetic diversity. The objective of this study was to compare the genetic variation exhibited among older and new pawpaw cultivars and Kentucky State University (KSU) advanced selections using simple sequence repeat (SSR) markers. Polymorphic microsatellite marker analysis was conducted with nine older pawpaw cultivars, six recently released PawPaw Foundation (PPF) cultivars, and nine KSU advanced selections. Using 18 microsatellite loci, a total of 179 alleles were amplified in the set of 24 genotypes. The major allele frequency (0.13 to 0.96), number of genotypes (two to 23), and allele size (96 to 341 bp) varied greatly by locus. Eighteen loci were highly polymorphic, as indicated by high expected heterozygosity (He = 0.71) and observed heterozygosity (Ho = 0.65) values as well as high polymorphism information content (polymorphism information content = 0.69). The dinucleotide SSR (GA and CA motifs) loci were more polymorphic than trinucleotide (ATG and AAT motifs) SSRs. The PPF cultivars and KSU advanced selections were more closely grouped genetically than with older cultivars. Older cultivars displayed the greatest genetic diversity (Ho = 0.69). The pawpaw cultivar base of older and PPF cultivars does appear to be genetically diverse. However, KSU advanced selections contain unique pawpaw germplasm that should enhance the genetic base of cultivars if these selections are released to the public.

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