SNP genotyping analyses for the Chinese indigenous pig breeds and commercial pig breeds
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE46733 | GEO | 2013/05/09
SECONDARY ACCESSION(S): PRJNA202205
REPOSITORIES: GEO
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Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification. 9 Chinese indigenous pig, 4 commercial pigs and 1 wild pig were genotyped by PorcineSNP60 array (Illumina) for exploring the phylogeny relationships among them.
2013-05-09 | E-GEOD-46733 | biostudies-arrayexpress
Project description:Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)
2013-05-15 | GSE46847 | GEO
Project description:Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)
2015-06-29 | GSE49299 | GEO
Project description:Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2) 9 Chinese indigenous pig, 2 commercial pigs, 1 wild pig were detected using one pig of Duroc as reference.
2013-05-15 | E-GEOD-46847 | biostudies-arrayexpress
Project description:Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2) 9 Chinese indigenous pig, one Chinese wild boar and 2 commercial pigs were detected using one pig of Duroc as reference. These 12 animals include 1 wild pig, 2 pigs each from Yorkshire and Landrace as the representatives of modern commercial breeds and 9 unrelated individuals selected from 6 Chinese indigenous breeds (2- Tibetan pig, 2- Diannan small-ear pig, 2-Meishan pig, 1- Min pig, 1-Daweizi pig, and 1-Rongchang pig).
2015-06-29 | E-GEOD-49299 | biostudies-arrayexpress
Project description:SNP genotyping of various breeds
| PRJNA508513 | ENA
Project description:BackgroundModern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood.ResultsWe identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively.ConclusionsIn this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.
| S-EPMC3898232 | biostudies-literature
Project description:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128372 | GEO
Project description:Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68-98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.
| S-EPMC9880450 | biostudies-literature
Project description:Chinese indigenous chickens (CICs) constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.
| S-EPMC6383742 | biostudies-literature