Dataset Information

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data.

ABSTRACT: In this study, we investigated the genetic variants, including SNPs and indels (short insertions or deletions, less than 50 bp in length), in the genomes and genetic structures of five pig populations (in the northern Taihu Lake region, Jiangsu Province) using the genotyping by genome reducing and sequencing (GGRS) approach. A total of 581 million good reads with an average depth of 11× and an average coverage of 2.16% were used to call variants. In general, 202 106 SNPs and 34 415 indels were obtained, of which 2690 SNPs and 224 indels were capable of inducing protein-coding changes. The genes containing these variants were extracted for functional annotation. The results of gene enrichment analysis revealed that the SNPs under investigation may be associated with reproduction, disease resistance, meat quality and adipose tissue traits, whereas the indels were associated mainly with adipose tissue and disease. Analysis of the genetic structure showed that each population displayed comparable, large differentiations from the others, indicating their uniqueness. In conclusion, the results of our study provide the first genomic overview of the genetic variants and population structures of five Chinese indigenous pig populations.

SUBMITTER: Xiao Q

PROVIDER: S-EPMC5638066 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data.

Xiao Q Q Zhang Z Z Sun H H Yang H H Xue M M Liu X X Zhang W W Zhen Y Y Zhu M M Wang Q Q Pan Y Y

Animal genetics 20170522 5

In this study, we investigated the genetic variants, including SNPs and indels (short insertions or deletions, less than 50 bp in length), in the genomes and genetic structures of five pig populations (in the northern Taihu Lake region, Jiangsu Province) using the genotyping by genome reducing and sequencing (GGRS) approach. A total of 581 million good reads with an average depth of 11× and an average coverage of 2.16% were used to call variants. In general, 202 106 SNPs and 34 415 indels were o ...[more]

PMID: 28543043

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Project description:BackgroundMetabolic syndrome (MetS), a condition of metabolic disorders, is now causing large disease burden around the world. This study aimed to update the prevalence of MetS in Jiangsu Province of China and evaluate the predicting value of five anthropometric measures including waist circumference (WC), body mass index (BMI), waist-to-height ratio (WHtR), a body shape index (ABSI) and body roundness index (BRI) in MetS.Methods8040 participants from 12 survey sites were enrolled into this cross-sectional study by multi-stage stratified cluster random sampling method from 2014 nutrition and diet investigation project in Jiangsu Province. The transformation of sex-specific z-score made the comparison meaningful when conducting the logistic analysis between anthropometric indices and MetS. The abilities of anthropometric indices to predict MetS were evaluated by the receiver operating characteristic curve (ROC). Delong test was applied to compare area under different ROC curves.ResultsThe prevalence of MetS in Jiangsu Province was 35.2% and the standardized prevalence was 34.8%. WC, BMI, WHtR, ABSI and BRI z-scores were positively related to MetS and its components. WC, WHtR and BRI z-score had stronger associations with MetS than BMI and ABSI in both male and female population. WC, WHtR and BRI had larger area under ROC curve than BMI and ABSI in male and female. WC in men had the largest area under the ROC curve, significantly higher than the other four measures of BMI, WHtR, ABSI and BRI (Z value = 9.08, 2.88, 16.73, 2.75 respectively). Among women, WC, WHtR and BRI had larger area under the ROC curve than BMI and ABSI, but the area under the WC, WHtR and BRI curve were not significantly different after the pairwise comparison by the Delong test. The optimal cut-off values of WC, WHtR and BRI for predicting MetS was 85.25 cm, 0.52 and 3.61 in male, 80.05 cm, 0.51 and 3.83 in female.ConclusionMetS has become one of the major chronic diseases in Jiangsu Province. WC was better than other four indices in predicting MetS among male population in Jiangsu. WC, WHtR and BRI had superior abilities than BMI/ABSI in predicting MetS among female population.

Dataset Information

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data.

Publications

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data.

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