Immunogenetic basis of chicken’s Heterophil/Lymphocyte ratio revealed by genome-wide indel variants analysis

doi:10.1016/j.jia.2022.12.012

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ZHANG Jin¹^*, WANG Jie²^*, WANG Qiao¹, CUI Huan-xian¹, DING Ji-qiang¹, WANG Zi-xuan¹, Mamadou Thiam¹, LI Qing-he¹, ZHAO Gui-ping¹

¹Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing100193, P.R.China

²Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan 250023, P.R.China

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摘要

增强宿主免疫力是降低鸡发病率的有效途径。异嗜性粒细胞与淋巴细胞比率（H/L）与鸟类的抗病性有关。具有不同H/L表型的鸡只表现出抗病性的差异。然而，H/L作为免疫功能指标的有效性仍需进一步分析。本研究构建了H/L定向选育系（京星黄鸡），该品系已培育了12个世代。我们比较了异嗜性粒细胞的功能，并结合统计学分析方法来探索与H/L相关的候选基因和调控途径。与非选择系（NS）相比，从H/L选择系（G12）分离的异嗜性粒细胞的氧化爆发功能较强（P=0.044）。基于全基因组选择性清除分析，选择系第九世代（G9，n = 92）相比于非选择系（NS，n = 92），有22.44 Mb基因组区域受到选择，注释到300个蛋白编码基因。其中，包含与细胞内受体信号通路相关的解旋酶C结构域1（IFIH1）和moesin（MSN）诱导的干扰素，与白细胞趋化性负调节相关的C-C基序趋化因子受体6（CCR6），二肽基肽酶4（DPP4）和溶血补体（HC）以及与肌动蛋白细胞骨架组织相关的紧密连接蛋白1（TJP1）等基因。此外，基于全基因组关联分析（GWAS），还鉴定出了45个indels与H/L相关，共注释到29个蛋白编码基因。北京油鸡肝脏转录组验证发现，蛋白酪氨酸磷酸酶非受体5型（PTPN5）（r=0.75，P=0.033）和氧甾醇结合蛋白5（OSBPL5）（r=0.89，P=0.0027）基因的表达量与H/L呈正相关。与高H/L组相比，北京油鸡低H/L组PTPN5和OSBPL5的表达量较低（P<0.05）。OSBPL5基因上indel位点 5_13108985（P=3.85E-06）的A/A等位基因频率从NS到G5和G9逐渐增加，且A/A个体的H/L低于杂合子A/ATCT（P=4.28E-04）和纯合ATCT/ATCT个体（P=3.40E-05）。以上结果表明，H/L经过定向选育，异嗜性粒细胞的氧化爆发功能增强，基因组22.44 Mb区域受到定向选择。另外PTPN5和OSBPL5基因被鉴定为H/L相关候选基因。这些发现揭示了H/L与免疫相关的复杂遗传机制，基于H/L进行遗传选育有助于提高鸡的免疫力。

Abstract

Enhancing host immunity is an effective way to reduce morbidity in chickens. Heterophil/lymphocyte (H/L) ratio is associated with host disease resistance in birds. Chickens with different H/L ratio levels show different disease resistances. However, the utility of the H/L ratio as an indicator of immune function remains to be analyzed. In this study, a H/L directional breeding chicken line (Jingxing yellow chicken) was constructed, which has been bred for 12 generations. We compared the function of heterophils, and combined statistical analysis to explore the candidate genes and pathways related to H/L ratio. The oxidative burst function of the heterophils isolated from the H/L selection line (G12) was increased (P=0.044) compared to the non-selection line (NS). The 22.44 Mb genomic regions which annotated 300 protein-coding genes were selected in the genome of G9 (n=92) compared to NS (n=92) based on a genome-wide selective sweep. Several selective regions were identified containing genes like interferon induced with helicase C domain 1 (IFIH1) and moesin (MSN) associated with the intracellular receptor signaling pathway, C-C motif chemokine receptor 6 (CCR6), dipeptidyl peptidase 4 (DPP4) and hemolytic complement (HC) associated with the negative regulation of leukocyte chemotaxis and tight junction protein 1 (TJP1) associated with actin cytoskeleton organization. In addition, 45 genome-wide significant indels containing 29 protein-coding genes were also identified as associated with the H/L ratio based on genome-wide association study (GWAS). The expression of protein tyrosine phosphatase non-receptor type 5 (PTPN5) (r=0.75, P=0.033) and oxysterol binding protein like 5 (OSBPL5) (r=0.89, P=0.0027) were positively correlated with H/L ratio. Compared to the high H/L ratio group, the expression of PTPN5 and OSBPL5 were decreased (P<0.05) in the low H/L group of Beijing-You chicken. The A/A allelic frequency of indel 5_13108985 (P=3.85E-06) within OSBPL5 gradually increased from the NS to G5 and G9, and the individuals with A/A exhibited lower H/L ratio than individuals with heterozygote A/ATCT (P=4.28E-04) and homozygous ATCT/ATCT (P=3.40E-05). Above results indicated oxidative burst function of heterophils were enhanced, and 22.44 Mb genomic regions were selected with the directional selection of H/L ratio. In addition, PTPN5 and OSBPL5 genes were identified as H/L ratio related candidate genes. These findings revealed the complex genetic mechanism of H/L ratio related to immunity and will allow selection for improving chicken immunity based on the H/L ratio.

Keywords: H/L ratio heterophil indel selective sweep GWAS

Online: 31 December 2022

Fund:

This research was supported by grants from the National Natural Science Foundation of China (32072708), the National Key R&D Program of China (2018YFE0128000) and the Major scientific research projects of Chinese Academy of Agricultural Sciences (CAAS-ZDRW202005).

About author: Correspondence ZHAO Gui-ping, E-mail: zhaoguiping@caas.cn *These authors have contributed equally to this work

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ZHANG Jin, WANG Jie, WANG Qiao, CUI Huan-xian, DING Ji-qiang, WANG Zi-xuan, Mamadou Thiam, LI Qing-he, ZHAO Gui-ping. 2022. Immunogenetic basis of chicken’s Heterophil/Lymphocyte ratio revealed by genome-wide indel variants analysis. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2022.12.012

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