scholarly journals Single Nucleotide Polymorphisms in the Promoter of CYP19 Gene in Cattle Bred in Iraq

2020 ◽  
Vol 33 (1) ◽  
pp. 89-97
Author(s):  
Salah H. Faraj ◽  
Asaad Y. Ayied ◽  
Khalaf A. H. Al-Rishdy
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Diversity ◽  
Animal Species ◽  
Haplotype Diversity ◽  
Evolutionary Relationship ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cyp19 Gene

The present study was undertaken to characterize the genetic diversity of the aromatase cytochrome P450 (CYP19) gene in 34 cows (15 local, 14 Holstein, and 5 Crosses) in Iraq. The objectives of the present study are to detect SNPs (mutations) in promoter p1.1 of the CYP19 gene in cattle bred in Iraq using sequencing techniques. We identified five single-nucleotide polymorphisms (SNP) loci of the CYP19 gene that were detected, namely G933T, G994C, A1044G, A1062T, and C1468A. The results showed the presence of 3, 4, and 2 polymorphic sites leading to the construction of 4, 5, and 3 different haplotypes for Holstein, local, and crosses respectively. Haplotype diversity were 0.791, 0.752, and 0.700 respectively. While nucleotide diversity was 0.0017, 0.0022, and 0.0013 respectively. Besides, we carried out a phylogenetic analysis of these sequences to address the evolutionary relationship between the animal species. These fragments were assigned in the GenBank database under the accession numbers: LC490756, LC490757, LC491437, LC491438, LC491439, LC491588, and LC491589.

scholarly journals Single-Nucleotide Polymorphisms in Soybean

Genetics ◽  
2003 ◽  
Vol 163 (3) ◽  
pp. 1123-1134 ◽  
Author(s):  
Y L Zhu ◽  
Q J Song ◽  
D L Hyten ◽  
C P Van Tassell ◽  
L K Matukumalli ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genomic Dna ◽  
Nucleotide Diversity ◽  
Genomic Sequence ◽  
Haplotype Diversity ◽  
Pcr Primers ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cultivated Soybean

Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

scholarly journals A Comparison of Genetic Diversity of COX-III Gene in Lowland Chickens and Tibetan Chickens

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Xueqin Liu ◽  
Pu Zhang ◽  
Gongying Zhang ◽  
Sichen Li ◽  
Long Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Low Genetic Diversity ◽  
Hydropathy Index ◽  
Altitude Adaptation ◽  
Nucleotide Divergence ◽  
Tibetan Chicken

To obtain a full understanding of the genetic diversity of the cytochrome oxidase III gene(COX-III)and its association with high altitude adaptation in Tibetan chickens, we sequencedCOX-IIIin 12 chicken populations (155 Tibetan chickens and 145 other domestic chickens). We identified a total of 11 single nucleotide polymorphisms (SNPs) and 12 haplotypes (Ha1–Ha12). Low genetic diversity (haplotype diversity = 0.531 ± 0.087, nucleotide diversity = 0.00125) was detected forCOX-III, and haplotype diversity of Tibetan chicken populations (0.750 ± 0.018) was markedly higher than lowland chicken populations (0.570 ± 0.028). Obvious genetic differentiation (nucleotide divergence = 0.092~0.339) and conspicuous gene communication (gene flow = 0.33~32.22) among 12 populations suggested that Tianfu black-bone fowl (white feather) was possibly introduced from Tibetan chicken. SNP m.10587 T>C affects the specific functions of the COX enzyme. Haplotype Ha3 was found in Tibetan chickens, and SNP m.10115G>A caused an amino acid substitution (Val62Ile) associated with phospholipid binding, while mutations m.10017C>A and m.10555G>A and the previously reported SNP m.10065T>C reduced the hydropathy index to some extent. Together, this indicates that the mitochondrial membrane is more hydrophobic in Tibetan chickens.

scholarly journals Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

2016 ◽  
Vol 141 (1) ◽  
pp. 62-65 ◽  
Author(s):  
Michael J. Havey ◽  
Yul-Kyun Ahn
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Characteristics ◽  
Single Nucleotide ◽  
Germplasm Collections ◽  
Indel Markers ◽  
Production Environments ◽  
Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

Effect of single-nucleotide polymorphisms in the CYP19 gene on response to Letrozole among breast cancer patients

2008 ◽  
Vol 26 (15_suppl) ◽  
pp. 22096-22096 ◽  
Author(s):  
l. Kadouri ◽  
D. Bercovich ◽  
Y. Rottenberg ◽  
S. Korem ◽  
A. Elimelech ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Cancer Patients ◽  
Nucleotide Polymorphisms ◽  
Breast Cancer Patients ◽  
Single Nucleotide ◽  
Cyp19 Gene

scholarly journals Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

2018 ◽  
Vol 20 (1) ◽  
pp. 17-22
Author(s):  
TETY HARTATIK ◽  
DWI NUR HAPPY HARIYONO ◽  
YUDI ADINATA
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Gene Sequences ◽  
Cattle Breeds ◽  
Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs)

2020 ◽  
Vol 63 (1) ◽  
pp. 193-201
Author(s):  
Heli Xiong ◽  
Xiaoming He ◽  
Jing Li ◽  
Xingneng Liu ◽  
Chaochao Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Structure Analysis ◽  
Genetic Background ◽  
Nucleotide Polymorphisms ◽  
Genetic Origin ◽  
Single Nucleotide ◽  
Sheep Breeds ◽  
Genome Wide ◽  
Nj Tree

Abstract. Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population FST, which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

scholarly journals Analysis of the genetic diversity of Phalaenopsis orchids with single nucleotide polymorphisms and snap markers derived from the Pto gene

2021 ◽  
Vol 53 (4) ◽  
pp. 620-631
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Functional Link ◽  
Single Nucleotide ◽  
Functional Changes ◽  
Interspecies Variability

The Pto gene is a plant gene that has been reported to be involved in resistance to bacterial pathogens. A partial genomic sequence corresponding to Pto (~449 bp) was isolated from 16 species and four hybrids of Phalaenopsis during 2017 at the Department of Agronomy and Horticulture, IPB University, Bogor, Indonesia. Multiple sequence analysis was performed to find putative single nucleotide polymorphisms (SNPs) and design the corresponding single nucleotide-amplified polymorphism (SNAP) markers, which were in turn used to estimate the genetic diversity of 25 Phalaenopsis species. In total, 20 SNPs, of which 14 were nonsynonymous, were identified from the partial Pto sequences. Eighteen SNAP primers were then developed based on these 14 nonsynonymous and four synonymous SNPs. Validation results showed that 15 SNAP primers showed a polymorphism information content exceeding 0.3, suggesting the existence of more than two alleles for this locus. Upon their use, the SNAP markers described 86% of all interspecies variability. The Pto 52, Pto 349, Pto 229, and Pto 380 SNAP markers were very informative in the determination of genetic diversity. Notably, the existence of these nonsynonymous SNPs implied the possibility of functional changes within the amino acid sequence of the putative PTO protein. Thus, the resulting differences in the activity of the PTO protein may be used to breed tolerance to pathogen infection. Further work may be required to establish a functional link between tolerance to pathogens and the presence of Pto-SNAP markers in Phalaenopsis properly.

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