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Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population

Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of an...

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Autores principales: Luo, Weizhen, Chen, Shaokang, Cheng, Duxue, Wang, Ligang, Li, Yong, Ma, Xiaojun, Song, Xin, Liu, Xin, Li, Wen, Liang, Jing, Yan, Hua, Zhao, Kebin, Wang, Chuduan, Wang, Lixian, Zhang, Longchao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Ivyspring International Publisher 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385009/
https://www.ncbi.nlm.nih.gov/pubmed/22745577
http://dx.doi.org/10.7150/ijbs.4027
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author Luo, Weizhen
Chen, Shaokang
Cheng, Duxue
Wang, Ligang
Li, Yong
Ma, Xiaojun
Song, Xin
Liu, Xin
Li, Wen
Liang, Jing
Yan, Hua
Zhao, Kebin
Wang, Chuduan
Wang, Lixian
Zhang, Longchao
author_facet Luo, Weizhen
Chen, Shaokang
Cheng, Duxue
Wang, Ligang
Li, Yong
Ma, Xiaojun
Song, Xin
Liu, Xin
Li, Wen
Liang, Jing
Yan, Hua
Zhao, Kebin
Wang, Chuduan
Wang, Lixian
Zhang, Longchao
author_sort Luo, Weizhen
collection PubMed
description Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of animals such as pigs. QTLs for hematological parameters (hematological traits) have been detected in pig chromosomes, although these are often mapped by linkage analysis to large intervals making identification of the underlying mutation problematic. Single nucleotide polymorphisms (SNPs) are the common form of genetic variation among individuals and are thought to account for the majority of inherited traits. In this study, a genome-wide association study (GWAS) was performed to detect regions of association with hematological traits in a three-generation resource population produced by intercrossing Large White boars and Minzhu sows during the period from 2007 to 2011. Illumina PorcineSNP60 BeadChip technology was used to genotype each animal and seven hematological parameters were measured (hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC) and red blood cell volume distribution width (RDW)). Data were analyzed in a three step Genome-wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) method. A total of 62 genome-wide significant and three chromosome-wide significant SNPs associated with hematological parameters were detected in this GWAS. Seven and five SNPs were associated with HCT and HGB, respectively. These SNPs were all located within the region of 34.6-36.5 Mb on SSC7. Four SNPs within the region of 43.7-47.0 Mb and fifty-five SNPs within the region of 42.2-73.8 Mb on SSC8 showed significant association with MCH and MCV, respectively. At chromosome-wide significant level, one SNP at 29.2 Mb on SSC1 and two SNPs within the region of 26.0-26.2 Mb were found to be significantly associated with RBC and RDW, respectively. Many of the SNPs were located within previously reported QTL regions and appeared to narrow down the regions compared with previously described QTL intervals. In current research, a total of seven significant SNPs were found within six candidate genes SCUBE3, KDR, TDO, IGFBP7, ADAMTS3 and AFP. In addition, the KIT gene, which has been previously reported to relate to hematological parameters, was located within the region significantly associated with MCH and MCV and could be a candidate gene. These results of this study may lead to a better understanding of the molecular mechanisms of hematological parameters in pigs.
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spelling pubmed-33850092012-06-28 Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population Luo, Weizhen Chen, Shaokang Cheng, Duxue Wang, Ligang Li, Yong Ma, Xiaojun Song, Xin Liu, Xin Li, Wen Liang, Jing Yan, Hua Zhao, Kebin Wang, Chuduan Wang, Lixian Zhang, Longchao Int J Biol Sci Research Paper Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of animals such as pigs. QTLs for hematological parameters (hematological traits) have been detected in pig chromosomes, although these are often mapped by linkage analysis to large intervals making identification of the underlying mutation problematic. Single nucleotide polymorphisms (SNPs) are the common form of genetic variation among individuals and are thought to account for the majority of inherited traits. In this study, a genome-wide association study (GWAS) was performed to detect regions of association with hematological traits in a three-generation resource population produced by intercrossing Large White boars and Minzhu sows during the period from 2007 to 2011. Illumina PorcineSNP60 BeadChip technology was used to genotype each animal and seven hematological parameters were measured (hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC) and red blood cell volume distribution width (RDW)). Data were analyzed in a three step Genome-wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) method. A total of 62 genome-wide significant and three chromosome-wide significant SNPs associated with hematological parameters were detected in this GWAS. Seven and five SNPs were associated with HCT and HGB, respectively. These SNPs were all located within the region of 34.6-36.5 Mb on SSC7. Four SNPs within the region of 43.7-47.0 Mb and fifty-five SNPs within the region of 42.2-73.8 Mb on SSC8 showed significant association with MCH and MCV, respectively. At chromosome-wide significant level, one SNP at 29.2 Mb on SSC1 and two SNPs within the region of 26.0-26.2 Mb were found to be significantly associated with RBC and RDW, respectively. Many of the SNPs were located within previously reported QTL regions and appeared to narrow down the regions compared with previously described QTL intervals. In current research, a total of seven significant SNPs were found within six candidate genes SCUBE3, KDR, TDO, IGFBP7, ADAMTS3 and AFP. In addition, the KIT gene, which has been previously reported to relate to hematological parameters, was located within the region significantly associated with MCH and MCV and could be a candidate gene. These results of this study may lead to a better understanding of the molecular mechanisms of hematological parameters in pigs. Ivyspring International Publisher 2012-06-15 /pmc/articles/PMC3385009/ /pubmed/22745577 http://dx.doi.org/10.7150/ijbs.4027 Text en © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited.
spellingShingle Research Paper
Luo, Weizhen
Chen, Shaokang
Cheng, Duxue
Wang, Ligang
Li, Yong
Ma, Xiaojun
Song, Xin
Liu, Xin
Li, Wen
Liang, Jing
Yan, Hua
Zhao, Kebin
Wang, Chuduan
Wang, Lixian
Zhang, Longchao
Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population
title Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population
title_full Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population
title_fullStr Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population
title_full_unstemmed Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population
title_short Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population
title_sort genome-wide association study of porcine hematological parameters in a large white × minzhu f2 resource population
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385009/
https://www.ncbi.nlm.nih.gov/pubmed/22745577
http://dx.doi.org/10.7150/ijbs.4027
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