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Whole genome SNPs discovery in Nero Siciliano pig
- Source :
- Genetics and Molecular Biology, Genetics and Molecular Biology, Volume: 42, Issue: 3, Pages: 594-602, Published: 14 NOV 2019
- Publication Year :
- 2019
- Publisher :
- SOC BRASIL GENETICA, 2019.
-
Abstract
- Autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical products. To explore its genetic variability, here we present for the first time whole genome sequencing data and SNPs discovered in a male domestic Nero Siciliano pig compared to the last pig reference genome Sus scrofa11.1.A total of 346.8 million paired reads were generated by sequencing. After quality control, 99.03% of the reads were mapped to the reference genome, and over 11 million variants were detected.Additionally, we evaluated sequence diversity in 21 fitness-related loci selected based on their biological function and/or their proximity to relevant QTLs. We focused on genes that have been related to environmental adaptation and reproductive traits in previous studies regarding local breeds. A total of 6,747 variants were identified resulting in a rate of 1 variant every ~276 bases. Among these variants 1,132 were novel to the dbSNP151 database. This study represents a first step in the genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Whole genome sequencing
Genetics
whole genome sequencing
variant calling
Environmental adaptation
Single-nucleotide polymorphism
Biology
SNPs discovery
01 natural sciences
Genome
Nero Siciliano pig
03 medical and health sciences
030104 developmental biology
fitness genes
Nero Siciliano pig, whole genome sequencing, Variant calling, SNPs discovery, Fitness genes
Genetic variability
Molecular Biology
Gene
Animal Genetics
010606 plant biology & botany
Reference genome
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Genetics and Molecular Biology, Genetics and Molecular Biology, Volume: 42, Issue: 3, Pages: 594-602, Published: 14 NOV 2019
- Accession number :
- edsair.doi.dedup.....fa66a2f0c210cbe483109c913d962e38