التفاصيل البيبلوغرافية
| العنوان: |
RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs |
| المؤلفون: |
Pierzchała, Mariusz, Ogłuszka, Magdalena, Polawska, Ewa, Blicharski, Tadeusz, Roszczyk, Agnieszka, Nawrocka, Agata, Urbański, Paweł, Stepanow, Kamila, Ciepłoch, Aleksandra, Goluch, Dorota, Sachajko, Mateusz, Juszczuk-Kubiak, Edyta, Szczepański, Adrian, Buszewska-Forajta, Magdalena, Szczepanek, Joanna, Pareek, Chandra Shekhar |
| المصدر: |
Translational Research in Veterinary Science; Vol. 2 No. 1 (2019); 51-65 ; Translational Research In Veterinary Science; Tom 2 Nr 1 (2019); 51-65 ; 2657-4489 |
| بيانات النشر: |
Nicolaus Copernicus University in Toruń |
| سنة النشر: |
2019 |
| المجموعة: |
Akademicka Platforma Czasopism (APCZ) |
| مصطلحات موضوعية: |
Single nucleotide variations, SNPs, paired-end, genetic markers, RNA-seq, illumina, paired-end read, GATK, SAMtools, mapping, bioinformatics, NGS, transcriptome, gluteus medius muscle, Landrace, pig, Omega-6 and omega-3 polyunsaturated fatty acid |
| الوصف: |
BackgroundSingle nucleotide polymorphisms (SNPs) are the well-known molecular markers in genetics and breeding studies applied to veterinary sciences and livestock production. Advancement of next generation sequencing (NGS) provides a high-throughput means of potential putative SNP discovery. The aim of the study was to identify the putative genetic variants in gluteus medius muscle transcriptome of Polish Landrace pigs.MethodsRNA-seq based NGS experiment was performed on Polish Landrace pigs fed with omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) and normal diets. Isolation of total RNA from gluteus medius muscle was performed on low PUFAs (n=6) and High PUFAs dietary group of Polish Landrace pigs. The RNA-seq libraries were constructed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control of raw RNA-seq data was performed using the Trimmomatic and FastQC tools. High QC paired-end RNA-seq data of gluteus medius muscle transcriptome were mapped to the reference genome Sus scrofa v.10.2. Finally, the SNPs discovery was performed using GATK and SAMtools bioinformatics SNPs caller tools.ResultsThe Fastq RNA-seq data generated from two pooled paired-end libraries (151bp) of gluteus medius muscle tissue of Polish Landrace pigs were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Study identified a total of 50.5 million paired-end reads (32.5 million low PUFAs dietary group and 18 million reads high PUFAs dietary group) of gluteus medius muscle transcriptome of Polish Landrace pigs. SNP discovery identified a total of 35436 homozygous and 28644 heterozygous cSNPs in gluteus medius muscle transcriptomes representing both dietary groups of Polish Landrace pig. Moreover, a total of 25187 and 5488 cSNP were identified as synonymous SNPs, and 18005 and 4780 cSNP were ... |
| نوع الوثيقة: |
article in journal/newspaper |
| وصف الملف: |
application/pdf |
| اللغة: |
English |
| Relation: |
https://apcz.umk.pl/TRVS/article/view/TRVS.2019.004/18171; https://apcz.umk.pl/TRVS/article/view/TRVS.2019.004 |
| الاتاحة: |
https://apcz.umk.pl/TRVS/article/view/TRVS.2019.004 |
| Rights: |
Prawa autorskie (c) 2019 Translational Research In Veterinary Science |
| رقم الانضمام: |
edsbas.C103B51 |
| قاعدة البيانات: |
BASE |