scholarly journals Genome-Wide Identification of Sequence Variations and SSR Marker Development in the Munake Grape Cultivar

2021 ◽  
Vol 9 ◽  
Author(s):  
Haixia Zhong ◽  
Fuchun Zhang ◽  
Xiaoming Zhou ◽  
Mingqi Pan ◽  
Juan Xu ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Agronomic Traits ◽  
Entire Genome ◽  
Single Nucleotide ◽  
Grape Cultivar ◽  
Insertion And Deletion ◽  
Genome Wide ◽  
Sequence Variations ◽  
Polymerase Chain ◽  
Simple Sequence

The Munake grape cultivar produces uniquely flavored and high-quality fruits. Despite the numerous beneficial agronomic traits of Munake, there are few genetic resources available for this cultivar. To address this knowledge gap, the entire genome was sequenced using whole-genome sequencing approaches and compared with a Vitis vinifera L. reference genome. This study describes more than 3 million single nucleotide polymorphism (SNP), 300,000 insertion and deletion (InDel), 14,000 structural variation (SV), and 80,000 simple sequence repeat (SSR) markers (one SSR per 4.23 kb), as well as their primers. Among the SSRs, 44 SSR primer pairs were randomly selected and validated by polymerase chain reaction (PCR), allowing discrimination between the different Munake cultivar genotypes. The genetic data provided allow a deeper understanding of Munake cultivar genomic sequence and contribute to better knowledge of the genetic basis behind its key agronomic traits.

scholarly journals Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1792
Author(s):  
Hongyang Wang ◽  
Yang Fu ◽  
Peng Gu ◽  
Yingying Zhang ◽  
Weilong Tu ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Growth And Development ◽  
Miniature Pig ◽  
Sequencing Data ◽  
Pig Breeds ◽  
Polymorphic Ssrs ◽  
Repeat Units ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Simple Sequence

Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.

Exact word matches in rice pseudomolecules

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 1047-1051 ◽  
Author(s):  
Shaolin Liu ◽  
Nicholas A Tinker ◽  
Diane E Mather
Keyword(s):  
High Frequency ◽  
Genomic Sequence ◽  
Oryza Sativa L ◽  
Rice Genome ◽  
Low Frequency ◽  
Nucleotide Position ◽  
Genome Wide ◽  
Transposon Activity ◽  
Simple Sequence ◽  
Oligonucleotide Sequence

Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones. Low-frequency zones contained occasional high-frequency spikes; these may represent footprints of RIM2 transposon activity. BLASTn searches of high-frequency non-SSR (simple sequence repeat) 18 bp oligos returned few sequences from species other than rice. These results demonstrate that, in rice, words are not randomly used between different regions within the same genome, and indicate that words that are frequently repeated within the rice genome tend to be unique to rice.Key words: oligonucleotide, sequence repetition, word match frequency, rice.

Interleukin 7 receptor alpha polymorphism rs6897932 and susceptibility to multiple sclerosis in the Western Balkans

2010 ◽  
Vol 16 (5) ◽  
pp. 533-536 ◽  
Author(s):  
Aleksandra Stanković ◽  
Evica Dinčić ◽  
Smiljana Ristić ◽  
Luca Lovrečić ◽  
Nada Starčević Cizmarević ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Western Balkans ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Receptor Alpha ◽  
Interleukin 7 ◽  
Genome Wide ◽  
Significant Difference ◽  
Polymerase Chain ◽  
Genome Variants

The interleukin 7 receptor alpha single nucleotide polymorphism rs6897932 was identified as a multiple sclerosis susceptibility-modifying polymorphism in genome-wide and gene scan studies, mainly in populations in western countries. The aim of this study was to investigate the association of interleukin 7 receptor alpha rs6897932 with multiple sclerosis in populations from the Western Balkans: Serbia, Croatia, and Slovenia. A total of 678 unrelated white patients and 597 unrelated, ethnically matched healthy controls were included in the study. Genotyping was performed by real-time polymerase chain reaction. We found no significant difference in genotype or allele frequencies between controls and patients with multiple sclerosis either separately in Serbian, Croatian, and Slovenian populations or in the whole sample from the Western Balkans. The odds ratio for multiple sclerosis in this study was 1.04 (0.86—1.25) for the C allele. It is known that demographic as well as environmental factors have a substantial role in multiple sclerosis development, as well as population genetic background. The results of this study indicate that other types of genome variants should be required for the development and/or progression of multiple sclerosis, which may vary among populations.

scholarly journals Intergenic interactions and genetic polymorphism in increasing the probability of alcoholic dependence

2021 ◽  
pp. 92-105
Author(s):  
Evgenii V. Snytkov ◽  
Vyacheslav N. Kipen ◽  
Aleksandr V. Kazachok ◽  
Sergei B. Melnov
Keyword(s):  
Alcohol Dependence ◽  
Association Studies ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Pcr Rflp ◽  
Polymerase Chain

The results of molecular genetic analysis of 13 polymorphic variants of genes, according to the data of genome-wide association studies (GWAS) associated with the development of addictive states, in the group of persons with alcohol dependence (n = 142) and in the comparison group (n = 211) are presented. The main genotyping method is polymerase chain reaction (PCR) followed by high resolution melting (HRM) and clustering of melting profiles; the melting results are validated using the restriction fragment length polymorphism (PCR-RFLP) method. As a result, single nucleotide polymorphisms associated with an increased likelihood of alcohol dependence are genotype GG (rs7085104, AS3MT); genotype GG (rs7590720, PECR); allele C (rs11191580, NT5C2); allele T (rs17504622); allele A (rs73229090, EPHX2); allele A (rs1109501, MUC7 ). 

Genetic Analysis of Ulcerative Colitis in Japanese Individuals Using Population-specific SNP Array

2020 ◽  
Vol 26 (8) ◽  
pp. 1177-1187
Author(s):  
Daisuke Okamoto ◽  
Yosuke Kawai ◽  
Yoichi Kakuta ◽  
Takeo Naito ◽  
Takehiro Torisu ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Lower Probability ◽  
Healthy Controls ◽  
Single Nucleotide ◽  
Kaplan Meier ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain

Abstract Background To clarify the genetic background of ulcerative colitis (UC) in the Japanese population, we conducted a genome-wide association study (GWAS) using a population-specific single nucleotide polymorphism (SNP) array. Methods We performed a GWAS and replication study including 1676 UC patients and 2381 healthy controls. The probability of colectomy was compared between genotypes of rs117506082, the top hit SNP at HLA loci, by the Kaplan-Meier method. We studied serum expression of miR-622, a newly identified candidate gene, from 32 UC patients and 8 healthy controls by quantitative reverse-transcription polymerase chain reaction. Results In the GWAS, only the HLA loci showed genome-wide significant associations with UC (rs117506082, P = 6.69E-28). Seven nominally significant regions included 2 known loci, IL23R (rs76418789, P = 6.29E-7) and IRF8 (rs16940202, P = 1.03E-6), and 5 novel loci: MIR622 (rs9560575, P = 8.23E-7), 14q31 (rs117618617, P = 1.53E-6), KAT6B (rs12260609, P = 1.81E-6), PAX3-CCDC140-SGPP2 (rs7589797, P = 2.87E-6), and KCNA2 (rs118020656, P = 4.01E-6). Combined analysis revealed that IL23R p.G149R (rs76418789, P = 9.03E-11; odds ratio [OR], 0.51) had genome-wide significant association with UC. Patients with GG genotype of rs117506082 had a significantly lower probability of total colectomy than those with the GA+AA genotype (P = 1.72E-2). Serum expression of miR-622 in patients with inactive UC tended to be higher than in healthy controls and patients with active UC (inactive UC vs healthy controls, P = 3.03E-02; inactive UC vs active UC, P = 6.44E-02). Conclusions IL23R p.G149R is a susceptibility locus for UC in Japanese individuals. The GG genotype of rs117506082 at HLA loci may predict a better clinical course.

Analysis of SNP markers for chicken blue-shelled gene using PCR-SSCP

2007 ◽  
Vol 4 (1) ◽  
pp. 53-56 ◽  
Author(s):  
Zhao Rui ◽  
Liu Zhen-Zhen ◽  
Xu Gui-Yun ◽  
Yang Ning
Keyword(s):  
Close Association ◽  
Marker Locus ◽  
Snp Markers ◽  
Chromosome 1 ◽  
Nucleotide Polymorphism ◽  
Single Strand Conformational Polymorphism ◽  
Single Nucleotide ◽  
Polymerase Chain ◽  
Chelating Complex ◽  
Simple Sequence

AbstractThe oocyan (O) gene determines blue shell pigmentation of domesticated chicken. The O locus is closely linked to ALEV1 on chromosome 1 with a genetic distance of 2.3 cM. Blue eggshells contain a protoporphyrin, biliverdin and zinc biliverdin chelating complex, which belongs to the porphyrin metabolic pathway. A bio-informatic approach was first used to BLAST for the genes of the enzymes in the porphyrin pathway; no gene was detected to specify the O locus. Due to a limited number of simple sequence repeat (SSR) markers around the O locus, polymerase chain reaction–single-strand conformational polymorphism (PCR-SSCP) was then employed to search for candidate single nucleotide polymorphism (SNP) markers. The sequence bearing a marker was found to consist of two transversions at Chr1:61754089T→A and Chr1:61754175A→T, respectively. Population screening showed that 81% of homozygous blue-shelled layers (OO) were classified as AA genotype at the SNP loci, while 89% of heterozygous blue-shelled layers (Oo) were AB genotype and 93% of tinted layers (oo) were BB genotype. The results indicated that there is a close association between O locus and SNP locus, suggesting that the marker locus could be used as a molecular marker in breeding for blue-shelled chickens.

scholarly journals Molecular markers and their application for DNA fingerprinting and genetic diversity studies in Coffea species Marka molekuler dan penerapannya untuk studi sidik jari DNA dan keragaman genetik pada spesies Coffea

2016 ◽  
Vol 82 (1) ◽  
Author(s):  
. PRIYONO ◽  
Riza Arief PUTRANTO
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Dna Fingerprinting ◽  
Fragment Length ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Polymerase Chain ◽  
Simple Sequence

AbstrakStrategi klasik yang meliputi perbandingan anatomi, fisiologi dan sitogenetika telah banyak diterapkan untuk mengidentifikasi karakter tertentu serta untuk menentukan keragaman dan hubungan antar dan intra spesies. Namun, saat ini penanda molekuler telah melengkapi strategi sebelumnya dengan sangat cepat. Berbagai jenis penanda molekuler digunakan untuk menilai tingkat polimorfisme DNA. Penanda molekuler ini diklasifikasikan sebagai penanda berbasis hibridisasi dan berbasis Polymerase Chain Reaction (PCR). Dalam beberapa tahun terakhir, sistem penanda DNA yang berbeda seperti Restriction Fragment Length Polymorphisms (RFLPs), Random Amplied Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats (SSRs) yang juga disebut Mikrosatelit, Single Nucleotide Polymorphims (SNPs) dan lain-lain telah dikembangkan dan diterapkan pada berbagai spesies tanaman. Penanda molekuler ini dapat digunakan untuk sidik jari DNA dan studi keragaman genetik. Sidik jari berdasarkan DNA telah banyak digunakan dalam ilmu forensik, juga memiliki berbagai aplikasi dalam pemuliaan tanaman. Tulisan ini memberikan overview tentang berbagai penanda molekuler dan aplikasinya untuk sidik jari dan kajian keragaman genetik tanaman berdasarkan DNA pada berbagai spesies tanaman, dan secara khusus pada Coffea sp.AbstractConventional strategies including comparative anatomy, physiology and cytogenetics were applied to identify the certain character as well as to determine inter- and intra-species diversity and relationships. However, more recently molecular markers have very rapidly complemented the previous strategies. Various types of molecular markers are used to assess DNA polymorphism. They are classified as hybridization-based markers and polymerase chain reaction (PCR) based markers. In recent years, different DNA marker systems such as Restriction Fragment Length Polymorphisms (RFLPs), Random Amplied Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats (SSRs) which also called as microsatellites, Single Nucleotide  Polymorphims  (SNPs)  and  others  have been developed and applied to a range of plant species. These molecular markers can be used for DNA fingerprinting and genetic diversity study. DNA fingerprinting has been widely used in forensic science, but is has also a variety of application in plant breeding. This paper provides an overview about various molecular markers and their application for DNA plant fingerprinting and genetic diversity, especially in Coffea sp.

scholarly journals Molecular markers and their application for DNA fingerprinting and genetic diversity studies in Coffea species Marka molekuler dan penerapannya untuk studi sidik jari DNA dan keragaman genetik pada spesies Coffea

2016 ◽  
Vol 82 (1) ◽  
Author(s):  
. PRIYONO ◽  
Riza Arief PUTRANTO
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Dna Fingerprinting ◽  
Fragment Length ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Polymerase Chain ◽  
Simple Sequence

AbstrakStrategi klasik yang meliputi perbandingan anatomi, fisiologi dan sitogenetika telah banyak diterapkan untuk mengidentifikasi karakter tertentu serta untuk menentukan keragaman dan hubungan antar dan intra spesies. Namun, saat ini penanda molekuler telah melengkapi strategi sebelumnya dengan sangat cepat. Berbagai jenis penanda molekuler digunakan untuk menilai tingkat polimorfisme DNA. Penanda molekuler ini diklasifikasikan sebagai penanda berbasis hibridisasi dan berbasis Polymerase Chain Reaction (PCR). Dalam beberapa tahun terakhir, sistem penanda DNA yang berbeda seperti Restriction Fragment Length Polymorphisms (RFLPs), Random Amplied Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats (SSRs) yang juga disebut Mikrosatelit, Single Nucleotide Polymorphims (SNPs) dan lain-lain telah dikembangkan dan diterapkan pada berbagai spesies tanaman. Penanda molekuler ini dapat digunakan untuk sidik jari DNA dan studi keragaman genetik. Sidik jari berdasarkan DNA telah banyak digunakan dalam ilmu forensik, juga memiliki berbagai aplikasi dalam pemuliaan tanaman. Tulisan ini memberikan overview tentang berbagai penanda molekuler dan aplikasinya untuk sidik jari dan kajian keragaman genetik tanaman berdasarkan DNA pada berbagai spesies tanaman, dan secara khusus pada Coffea sp.AbstractConventional strategies including comparative anatomy, physiology and cytogenetics were applied to identify the certain character as well as to determine inter- and intra-species diversity and relationships. However, more recently molecular markers have very rapidly complemented the previous strategies. Various types of molecular markers are used to assess DNA polymorphism. They are classified as hybridization-based markers and polymerase chain reaction (PCR) based markers. In recent years, different DNA marker systems such as Restriction Fragment Length Polymorphisms (RFLPs), Random Amplied Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats (SSRs) which also called as microsatellites, Single Nucleotide  Polymorphims  (SNPs)  and  others  have been developed and applied to a range of plant species. These molecular markers can be used for DNA fingerprinting and genetic diversity study. DNA fingerprinting has been widely used in forensic science, but is has also a variety of application in plant breeding. This paper provides an overview about various molecular markers and their application for DNA plant fingerprinting and genetic diversity, especially in Coffea sp.

scholarly journals Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

2020 ◽  
Author(s):  
Hanna Amoanimaa-Dede ◽  
Jiacheng Zhang ◽  
Chuntao Su ◽  
Hongbo Zhu
Keyword(s):  
Ssr Markers ◽  
Ipomoea Batatas ◽  
Genomic Sequence ◽  
Average Frequency ◽  
Genetic Studies ◽  
Germplasm Identification ◽  
Cultivar Development ◽  
Genome Wide ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Background: Sweetpotato is a multifunctional root crop with many essential nutrients and bioactive compounds. Due to its genetic complexity and lack of genomic resources, efficient genetic studies, and cultivar development lags far behind other major crops. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweetpotato. Results: To further explore new SSR markers and accelerate its use in sweetpotato genetic studies, genome-wide characterization and development of SSR markers were performed using the recently published genome of sweetpotato cultivar, Taizhong6. In this study, a set of 2,431 primer pairs were developed from 133,727 SSRs identified in the sweetpotato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. 50% of the 100 randomly selected primer pairs amplified 251 alleles and the average number of alleles was 5.02 alleles per locus with a range of 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweetpotato materials into four clusters at a similarity coefficient of 0.68. Conclusion: The SSR markers currently developed will provide valuable genetic resources for germplasm identification, genetic diversity analysis, and functional genomics studies in sweetpotato and related species.

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