ArticleAnimal genetics2017
Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing.
Article in Animal genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Whole-genome resequencing revealed genetic structure and specific breed identification loci of Ningxia Jingyuan chicken breed (Gallus gallus).BMC genomics · 2025Article
- Detection of Copy Number Variations in Woori-Heukdon Populations with the Illumina PorcineSNP60 Bead-Chip Array.Animals : an open access journal from MDPI · 2025Article
- Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses.Genes · 2023Article
- Article
- Genetic Evaluation and Population Structure of Jiangsu Native Pigs in China Revealed by SINE Insertion Polymorphisms.Animals : an open access journal from MDPI · 2022Article
- Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs.Frontiers in veterinary science · 2022Article
- Improving read alignment through the generation of alternative reference via iterative strategy.Scientific reports · 2020Article
- Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes Under Selection in Chinese Indigenous Pigs in the Taihu Lake Region.Frontiers in genetics · 2020Article
- Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays.Frontiers in genetics · 2020Article
- Identification of copy number variations using high density whole-genome SNP markers in Chinese Dongxiang spotted pigs.Asian-Australasian journal of animal sciences · 2019Article
- Optimal sequencing depth design for whole genome re-sequencing in pigs.BMC bioinformatics · 2019Article
- Detection of genome-wide structural variations in the Shanghai Holstein cattle population using next-generation sequencing.Asian-Australasian journal of animal sciences · 2019Article
- Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs.PloS one · 2019Article
- A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.Frontiers in genetics · 2019Article
- Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization.GigaScience · 2018Article
- Genome-wide analysis of structural variants reveals genetic differences in Chinese pigs.PloS one · 2017Article
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13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large-effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed-specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.
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