Brief note

The major quantitative trait loci related to host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) and weight gain have been identified by genome-wide association studies.^1–3 In addition, the viral load and weight gain traits of PRRSV-infected pigs have strong negative phenotypic and genetic correlations.^3,4 Several studies have shown that SNPs (rs712180276, WUR10000125, and rs340943904) in the guanylate binding protein 1 (GBP1) and 5 (GBP5) genes have significant correlations with the viral load and weight gain of PRRSV-infected pigs.^2,5–7 In particular, WUR10000125 in GBP1 and rs340943904 in GBP5 have complete or strong linkage disequilibrium (LD; r² > 0.70) in many pig breeds^8–10 and individual with homozygous recombinant haplotypes have so far not been reported. This precludes an estimation of additive genetic effects of the GBP1 and GBP5 SNPs.

This study analyzed, in 113 Korean native pigs (KNPs), associations of the three SNPs (Table S1) with three phenotypes of days to 90 kg, backfat thickness (BF), and average daily gain (ADG; Table S2), considering sex and genotype as fixed effects and slaughter age as a covariate. The degree of LD between GBP5 (rs340943904) and GBP1 (WUR10000125) SNPs, D′, and r² between the variations were estimated.¹¹

Individuals with rs340943904 genotype GT genotyped pigs grew more slowly than those with GG genotype (Tables S3, S4; TT has not been observed). Two SNPs (rs712180276 and WUR10000125) in GBP1 were also in complete LD in our KNPs. The WUR10000125 GG genotype had a significant effect on ADG and BF (P < 0.05). Unlike in previous studies, the two SNPs GBP5: rs340943904 and GBP1: WUR10000125 showed very low LD (r² = 0.203, Tables S5, S6a). The frequencies of haplotype (ht) 1 (-GA-), ht2 (-GG-), and ht3 (-TG-) were 0.814, 0.142, and 0.044, respectively (Table S5b). Ht1 confers a significantly better BF (P = 0.021) than ht2, while it had faster growth in days to 90 kg and ADG than ht3 (Table 1). Ht2 showed clearly faster growth than ht3 (P < 0.001), suggesting that individuals with the rs340943904 SNP T and WUR10000125 SNP G alleles, which are associated with high resistance to PRRSV, grow more slowly.

Table 1. Differences in phenotypes between the GBP5 (rs340943904) and GBP1 (WUR10000125) haplotypes in 113 Korean native pigs.

Haplotype estimate	D90 (days)	BF (mm)	ADG (kg)
	least squares means ± S.E (p-value)
ht1 (GA) vs. ht2 (GG)	4.54 ± 2.37 (0.336)	0.15 ± 0.03 (0.021)	–0.02 ± 0.01 (0.107)
ht1 (GA) vs. ht3 (TG)	–20.06 ± 4.02 (0.004)	–0.22 ± 0.05 (0.012)	0.04 ± 0.01 (0.010)
ht2 (GG) vs. ht3 (TG)	–24.60 ± 6.49 (0.002)	–0.36 ± 0.09 (<0.001)	0.05 ± 0.01 (<0.001)

• D90, days to 90 kg; BF, backfat thickness; ADG, average daily gain (kg); SE, standard error; ht, haplotype structure in GBP5 (rs340943904) and GBP1 (WUR10000125) polymorphisms.

Lack of LD in KNP results indicated rs340943904 and WUR10000125 SNPs have independent effects on growth traits, with the allele effect size of GBP5 is larger than for GBP1. Hence, we suggest that the KNP is a suitable population for studies of the mechanism of PRRSV resistance.

中文翻译：

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韩国本地猪与猪繁殖与呼吸综合征病毒易感性相关的 GBP1 和 GBP5 SNP 单倍型的连锁不平衡和加性效应的新见解

简要说明

全基因组关联研究已确定与宿主对猪繁殖与呼吸综合征病毒（PRRSV）的抗性和体重增加相关的主要数量性状位点。^1-3此外，PRRSV 感染猪的病毒载量和增重性状具有很强的负表型和遗传相关性。^{3 , 4}多项研究表明，鸟苷酸结合蛋白 1 ( GBP1 ) 和5 ( GBP5 ) 基因中的 S​​NP（rs712180276、WUR10000125 和 rs340943904）与 PRRSV 感染猪的病毒载量和体重增加具有显着相关性。^{2 , 5–7}特别是，GBP1中的 WUR10000125和GBP5中的 rs340943904在许多猪品种^8–10中具有完全或强连锁不平衡（LD；r ² > 0.70） ，并且迄今为止尚未报道具有纯合重组单倍型的个体。这排除了GBP1和GBP5 SNP的附加遗传效应的估计。

本研究在 113 头韩国本土猪 (KNP) 中分析了三个 SNP（表 S1）与 3 个表型（天数至 90 公斤）、背膘厚度 (BF) 和平均日增重 (ADG；表 S2) 的关联，并考虑了性别基因型作为固定效应，屠宰年龄作为协变量。估计了GBP5 (rs340943904) 和GBP1 (WUR10000125) SNP、D ' 和变异之间的r ²之间的 LD 程度。¹¹

具有rs340943904基因型GT基因型猪的个体比具有GG基因型的猪生长得更慢（表S3、S4；尚未观察到TT）。GBP1中的两个 SNP（rs712180276 和 WUR10000125）在我们的 KNP 中也处于完全 LD 状态。WUR10000125 GG 基因型对 ADG 和 BF 有显着影响（P  < 0.05）。与之前的研究不同，两个 SNP GBP5：rs340943904 和GBP1：WUR10000125 显示出非常低的 LD（r ² = 0.203，表 S5、S6a）。单倍型（ht）1（-GA-）、ht2（-GG-）和ht3（-TG-）的频率分别为0.814、0.142和0.044（表S5b）。Ht1 的 BF ( P  = 0.021) 显着优于 ht2，同时其在达到 90 kg 的天数和日增重方面比 ht3 具有更快的生长速度（表 1）。Ht2 的生长速度明显快于 ht3 ( P  < 0.001)，这表明具有 rs340943904 SNP T 和 WUR10000125 SNP G 等位基因（与 PRRSV 高抗性相关）的个体生长速度更慢。

表 1. 113 头韩国本土猪的GBP5 (rs340943904) 和GBP1 (WUR10000125) 单倍型之间的表型差异。

单倍型估计	D90（天）	高炉（毫米）	日增重（公斤）
	最小二乘法平均值 ± SE（p值）
ht1 (GA) 与 ht2 (GG)	4.54±2.37（0.336）	0.15±0.03（0.021）	–0.02 ± 0.01 (0.107)
ht1 (GA) 与 ht3 (TG)	–20.06 ± 4.02 (0.004)	–0.22 ± 0.05 (0.012)	0.04±0.01（0.010）
ht2 (GG) 与 ht3 (TG)	–24.60 ± 6.49 (0.002)	–0.36 ± 0.09 (<0.001)	0.05±0.01（<0.001）

• D90，天到90斤；BF，背膘厚度；ADG，平均日增重（公斤）；SE，标准误；ht，GBP5 (rs340943904) 和GBP1 (WUR10000125) 多态性中的单倍型结构。

KNP结果中缺乏LD表明rs340943904和WUR10000125 SNP对生长性状具有独立影响， GBP5的等位基因效应大小大于GBP1。因此，我们认为KNP是研究PRRSV耐药机制的合适人群。