SNPs genotyping technologies and their applications in farm animals breeding programs: review

Koopaee, Hamed Kharrati; Koshkoiyeh, Ali Esmailizadeh

doi:10.1590/s1516-89132014000100013

Cited by 38 publications

(27 citation statements)

References 37 publications

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“…Knowledge of the genetic architecture can also be leveraged in artificial selection. Agricultural breeding programs currently make prodigious use of a technique known as genomic selection to improve plant and animal breeding (Meuwissen et al 2001;Koopaee and Koshkoiyeh 2014). The approach first uses GWAM to find associations between molecular markers and the phenotype(s) of interest in crops or livestock.…”

Section: Impacts Of Epigenetics Researchmentioning

confidence: 99%

“…The approach first uses GWAM to find associations between molecular markers and the phenotype(s) of interest in crops or livestock. Then, individuals with unknown phenotype or pedigree are genotyped at the same SNP sites (using a low-cost SNP chip) to forecast their phenotype(s) from the effect sizes associated with each allele from the GWAM study (Koopaee and Koshkoiyeh 2014). In this way, superior stock can be selected for breeding and development without further measuring of phenotype.…”

Section: Impacts Of Epigenetics Researchmentioning

confidence: 99%

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Quantitative epigenetics and evolution

Banta

Richards

2018

Heredity

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Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited. To explicate these points, we show that epigenetics can influence all aspects of the phenotypic variance formula: V (total phenotypic variance) = V (genetic variance) + V (environmental variance) + V (genotype-by-environment interaction) + 2COV (the genotype-environment covariance) + V (residual variance), requiring new strategies to account for different potential sources of epigenetic effects on phenotypic variance. We also demonstrate how each of the components of phenotypic variance not only can be influenced by epigenetics, but can also have evolutionary consequences. We argue that no sources of epigenetic effects on phenotypic variance can be easily cast aside in a quantitative genetic research program that seeks to understand evolutionary processes.

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Section: Impacts Of Epigenetics Researchmentioning

confidence: 99%

Section: Impacts Of Epigenetics Researchmentioning

confidence: 99%

Quantitative epigenetics and evolution

Banta

Richards

2018

Heredity

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“…Genomic selection using SNPs is a new tool for choosing the best breeding animals. In addition, the high density maps using SNPs can provide useful genetic tools to study quantitative traits genetic variations (Koopaee and Koshkoiyeh, 2014;Yılmaz et al, 2015).…”

Section: Modern Types Of Molecular Markermentioning

confidence: 99%

A Comparison of Old and Modern Type DNA Marker Technologies and Their Impact on Animal Breeding Programs

Gündüz¹,

Yılmaz²,

Cemal³

et al. 2016

jist

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In recent years, molecular genetic technologies allowed to identify genetic structure in farm animals have great advantages for animal breeding. Especially, in developed countries these methods began to be widely used to assist animal breeding studies. It can be said that there are various molecular genetic markers. These markers can be classified by taking into consideration a number of factors such as the principle of the detection technique, type of polymorphism. Although old type molecular genetic markers such as RFLP, AFLP, microsatellites are widely used today, the information obtained from them is more limited than modern molecular genetic markers. SNP chip technologies, which known as modern molecular markers and are one of the most important developments in the molecular genetics field, have provided genomic breeding value estimation and genomic selection in farm animals. In this review, old and new types of molecular markers were compared and their usage in animal breeding were discussed.

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“…Oxidative stress analysis was an analysis of the changes in oxidant and antioxidants balance that caused damage of cell structure and even DNA structure (Birben et al, 2012). The detection of single nucleotide polymorphism was the detection of a single nucleotide variation in a specific sequence of genomic DNA (Cui et al, 2018 (Koopaee and Koshkoiyeh, 2014).…”

Section: Introductionmentioning

confidence: 99%

IDENTIFICATION OF -308 TNF-α PROMOTER SINGLE NUCLEOTIDE POLYMORPHISM IN ACTIVE AND PASSIVE SMOKERS

Pollo

Rumende

Tallei

2019

JIS

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IDENTIFICATION OF -308 TNF-α PROMOTER SINGLE NUCLEOTIDE POLYMORPHISM IN ACTIVE AND PASSIVE SMOKERS ABSTRACTTumour necrosis factor-α (TNF-α) is one of the pro-inflammatory cytokines that play a role in the inflammatory process, immune system development, and apoptosis. This protein is encoded by the TNF-α gene. Several studies had linked the presence of polymorphisms in the TNF-α promoter region with susceptibility to the onset of chronic obstructive pulmonary disease (COPD) in active and passive smokers. This study aimed to identify and analyze the nucleotide polymorphism in TNF-α gene promoter regions in active and passive smokers in Manado. The method used in this study included blood sampling, DNA extraction, amplification of -308 TNF-α promoter region, sequencing and data analysis. The softwares used for data analysis were Geneious, Multalin, Clustal Omega and DnaSP. DnaSP was used to compute the level of polymorphism based on haplotype statistics. The results did not show single nucleotide polymorphism at position -308 in TNF-α gene promoters in active and passive smokers. This was because at that position, the nucleotides were both in the form of guanosine monophosphate and there were no mutation caused by cigarette smoke exposure.Keywords: active smoker, passive smoker, single nucleotide polymorphism, TNF-α promoter DETEKSI POLIMORFISME NUKLEOTIDA TUNGGAL-308 PROMOTERTNF-α PADA PEROKOK AKTIF DAN PASIF ABSTRAKTumor necrosis factor-α (TNF-α) merupakan salah satu sitokin pro-inflamasi yang berperan dalam proses inflamasi, perkembangan sistem imun, dan apoptosis. Protein ini dikode oleh gen TNF-α. Beberapa penelitian telah mengkaitkan adanya polimorfisme pada daerah promoter TNF-α dengan kerentanan terhadap timbulnya chronic obstructive pulmonary disease (COPD) pada perokok aktif maupun pasif. Penelitian ini bertujuan untuk mengidentifikasi dan menganalisis polimorfisme nukleotida tunggal pada posisi -308 dari promoter gen TNF-α perokok aktif dan pasif. Metode yang digunakan dalam penelitian ini meliputi pengambilan sampel darah, ekstraksi DNA, amplifikasi daerah -308 promoter gen TNF-α, sekuensing serta analisis data. Analisis data menggunakan perangkat lunak Geneious, BLAST, Multalin, Clustal Omega dan DnaSP. Perangkat DnaSP akan mengkomputasi tingkat polimorfisme berdasarkan statistik haplotype-based. Hasil yang didapatkan menunjukkan bahwa polimorfisme nukleotida tunggal pada posisi -308 dari promoter gen TNF-α antara perokok aktif dan pasif tidak ditemukan. Hal ini dikarenakan oleh pada posisi tersebut, nukleotidanya sama-sama berbentuk guanosin monofosfat dan tidak terjadi mutasi akibat pengaruh paparan asap rokok.Kata kunci: perokok aktif, perokok pasif, single nucleotide polymorphism, TNF-α promoter

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SNPs genotyping technologies and their applications in farm animals breeding programs: review

Cited by 38 publications

References 37 publications

Quantitative epigenetics and evolution

Quantitative epigenetics and evolution

A Comparison of Old and Modern Type DNA Marker Technologies and Their Impact on Animal Breeding Programs

IDENTIFICATION OF -308 TNF-α PROMOTER SINGLE NUCLEOTIDE POLYMORPHISM IN ACTIVE AND PASSIVE SMOKERS

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