杜长大猪、二花脸猪和莱芜猪3个群体25种血液性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2016.04.013

Abstract

Abstract: 【Objective】 The genome-wide association of 25 hematological traits in Western DLY pigs and two Chinese Erhualian and Laiwu populations was analyzed in this study. The findings would benefit the final identification of causative genes, and provide insights into the potential molecular basis on hematological traits and provide clues for pig anti-disease breeding and production. 【Method】 A total of 610 DLY ternary hybrid pigs at (180±5) days, 336 Erhualian pigs and 333 Laiwu pigs at (300 ±5) days after birth were slaughtered at Guohong commercial abattoir. Blood samples at 2mL of each pig were immediately collected in anticoagulation tubes at slaughter. Twenty-five hematological traits were determined with commercial kits. Genomic DNA was extracted from ear tissues using a standard phenol/chloroform method, the concentration and quality were determined by NANODROP 1000 analyzer. All individuals were genotyped with Illumina porcineSNP60 Bead-Chip. After the genotype quality control by PLINK software, the GWAS were performed with the mixed linear model using GenABEL package in the R software.【Result】 After quality control of phenotype and genotype, there were 552 DLY, 325 Erhualian and 281 Laiwu left for the study, respectively; and there were 56 216 SNPs left for DLY pigs, 49 343 SNPs for Laiwu pigs, 35 974 SNPs for Erhualian pigs and 32 967 SNPs for Meta analysis. The GWAS identified 610 significant loci for 25 hematological traits, of which 135 SNPs were at the genome significant level and 475 SNPs were at the suggestive level, on all pig chromosomes in three populations. In DLY ternary hybrid pigs, 32 genome significant SNPs were identified in 8 traits (LYM，LYMR，BAS，BASR，MCV，RDW_CV，MCH and PDW) and other 85 suggestive level SNPs were also identified. In Erhualian pigs, 33 genome significant SNPs were identified in 9 traits (LYM, MCH, MCHC, MON, MONR, MPV, NEUR, P_LCC and PCT) and other 139 suggestive level SNPs were also identified. In Laiwu pigs, 54 genome significant SNPs were identified in 6 traits (BASR, HCT, MCH, MCHC, MCV and RBC) and other 169 suggestive level SNPs were also identified. In Meta results, 16 genome significant SNPs were identified in 6 traits (RBC, HCT, MCH, MCHC, MCV and MON) and other 82 suggestive level SNPs were also identified. Five promising candidate genes were found in the neighboring region of the lead SNPs at the genome-wide significant loci, such as F13A1 for BASR, SPTA1 for HCT, DBNL for LYM. SLC25A28 for MCHC and CTSC for NEUR. 【Conclusion】 A total of 610 loci surpassing the suggestive significant level were identified for 25 hematological traits on all pig chromosomes in Western DLY pigs and two Chinese Erhualian and Laiwu populations, revealing the complex genetic architecture of hematological traits. Neighboring the lead SNPs at the 54 genome-wide significant loci, five promising candidate genes were found, such as F13A1 for BASR, SPTA1 for HCT, DBNL for LYM, SLC25A28 for MCHC and CTSC for NEUR, and thus providing clues for analysis of the hematological traits and immune disease of commercial pigs and pure indigenous breeds.

Key words: pig, hematological traits, genome-wide association study, candidate gene

LIU Chen-long, YANG Hui, ZHANG Hui, ZHANG Zhi-yan, DUAN Yan-yu. Genome-Wide Association Study of 25 Hematological Parameters in Western DLY Pigs and Two Chinese Erhualian and Laiwu Populations[J].Scientia Agricultura Sinica, 2016, 49(4): 739-753.

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Genome-Wide Association Study of 25 Hematological Parameters in Western DLY Pigs and Two Chinese Erhualian and Laiwu Populations

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