Abstract
BackgroundIt has been shown that hematological traits are strongly associated with the metabolism and the immune system in domestic pig. However, little is known about the genetic architecture of hematological traits. To identify quantitative trait loci (QTL) controlling hematological traits, we performed single marker Genome-wide association studies (GWAS) and haplotype analysis for 15 hematological traits in 495 Chinese Sutai pigs.ResultsWe identified 161 significant SNPs including 44 genome-wide significant SNPs associated with 11 hematological traits by single marker GWAS. Most of them were located on SSC2. Meanwhile, we detected 499 significant SNPs containing 154 genome-wide significant SNPs associated with 9 hematological traits by haplotype analysis. Most of the identified loci were located on SSC7 and SSC9.ConclusionsWe detected 4 SNPs with pleiotropic effects on SSC2 by single marker GWAS and (or) on SSC7 by haplotype analysis. Furthermore, through checking the gene functional annotations, positions and their expression variation, we finally selected 7 genes as potential candidates. Specially, we found that three genes (TRIM58, TRIM26 and TRIM21) of them originated from the same gene family and executed similar function of innate and adaptive immune. The findings will contribute to dissection the immune gene network, further identification of causative mutations underlying the identified QTLs and providing insights into the molecular basis of hematological trait in domestic pig.
Highlights
It has been shown that hematological traits are strongly associated with the metabolism and the immune system in domestic pig
3610 SNPs with call rates < 90%, 16242 SNPs with minor allele frequency (MAF) < 0.05, 64 SNPs severely departing from Hardy Weinberg Equilibrium (HWE) (P-value < 10−5) and 149 makers exhibiting Mendelian inconsistency were excluded, remained a total of 44650 SNPs
Sutai pigs included two kinds of LD: LD between breeds created by intercross and LD within each breed created in the ancestor history, and they become very good experimental population for quantitative trait loci (QTL) mapping and single marker Genome-wide association studies (GWAS) analysis
Summary
It has been shown that hematological traits are strongly associated with the metabolism and the immune system in domestic pig. White blood cell count is a strong indicator of infectious and inflammatory diseases, such as leukaemia and lymphoma. Platelets play important roles in hemostasis, the initiation of wound repair and can be the strong effector cells of innate immune response [8,9,10,11]. Accompanying with reduction of platelet count, idiopathic thrombocytopenic purpura (ITP), often an idiopathic immune thrombocytopenia, may result in lower gastrointestinal bleeding or other internal bleeding in human [12]. Speaking, they are routinely measured as important clinical indicators to diagnose and monitor hematologic diseases and ascertain overall patient health condition
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