Project name: Pleiotropic architectures of porcine immune and growth trait pairs revealed by a self-product-based transcriptome method

Description: Pleiotropy is an important biological phenomenon with complicated genetic architectures for multiple traits. To date, pleiotropy was mainly identified by multi-trait GWAS, but GWAS method has its disadvantages, and new developments for pleiotropy detection methods are needed. Here we defined a novel metric, self-product, and based on it, we developed a transcriptome method to identify candidate pleiotropic genes and revealed the genetic architectures of immune and growth trait pairs in pigs.In statistics, the well-known covariance is used to quantify the co-variation between two variables. Suppose that X and Y represent two traits with individual records of xi and yi and corresponding means of μx and μy. We defined the individual-level product (xi − μx)(yi − μy) as self-product. Obviously, self-product is an individual-level measurement for the co-variation between two traits of the ith individual, and the covariance Cov(X , Y) is the mean of the self-product (xi − μx)(yi − μy).The self-product-based transcriptome method was tested using immune and growth trait pairs in pigs.We identify candidate pleiotropic genes using the Affymetrix Porcine Genechip.Result:Comparative transcriptome analyses identified dozens of candidate pleiotropic genes related to 8 trait pairs from two tails of self-product distribution. GO enrichment analysis indicated that most of identified pleiotropic genes were involved in both immune- and growth-related biological processes. We established pleiotropic genes interaction network to exhibit core genes shared by 8 trait pairs, of which CCL5 and IL-10 genes were hub genes. Genetic association analyses showed that SmaI-polymorphisms of CCL5 and IL-10 genes had significant associations with phenotypic co-variations of multiple trait pairs, indicating that the variants in pleiotropic genes were also pleiotropic variants.Conclusions:The validity of our proposed method was preliminarily verified, and our findings provide new insights into the genetic basis of pleiotropic architectures of immune and growth trait pairs in pigs.Overall design: A total of 8 immune and growth trait pairs were selected, including CD4+--W35, CD8+--W35, IFN-alpha--W35, IL-10--W35, CD4+--IFN-alpha, CD4+--IL-10, CD8+--IFN-alpha, and CD8+--IL-10, where W35 refers to the weight on day 35. After calculation, each trait pair has a self-product measurement. For each trait pair, all individuals were ordered according to the values of self-product. Five extreme individuals were separately selected from two tails of the self-product distribution in each trait pair, and the selected individuals were divided into high and low groups for subsequent transcriptome experiments. The total RNAs were extracted from blood samples with Trizol reagent following supplier’s recommendation. RNA tagging and hybridization were performed at a commercial Affymetrix array service company (GeneTech Biotechnology Limited Company, Shang Hai, China).In our study, CEL files were one-to-one with individuals, because the same individuals appeared repeatedly in different experimental groups, so the same CEL files were also shared by multiple experimental groups. CEL files have been named so that all CEL files have unique names but the raw data contained in these files are identical. For example, raw data in CD4+--W35_low_2240.CEL are identical to raw data contained in IFN-alpha--W35_low_2240.CEL.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Agricultural

Last updated: 2022-07-05