The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

中文翻译：

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对 PRRSV 疫苗接种的总抗体反应的进一步宿主基因组特征及其与商业母猪繁殖性能的关系：全基因组单倍型和接合性分析

使用抗体反应（S / P 比）在杂交商业小母猪中测量的 PRRSV 疫苗接种作为接种杂交母猪繁殖性能的遗传指标的可能性已经激发了对该性状的基因组基础的进一步研究。在这项研究中，我们调查了单倍型和纯合性 (ROH) 和杂合性 (ROHet) 与 S/P 比的关联及其对繁殖性能的影响。S/P 比率与 ROH 或 ROHet 的百分比，或与整个基因组或主要组织相容性复合体 (MHC) 区域中的杂合性百分比没有关联（P 值≥0.18）。然而，特定的 ROH 和 ROHet 区域与 1、4、5、7、10、11、13 和 17 号染色体上的 S/P 比显着相关（P 值 ≤ 0.01），但不（P 值 ≥ 0.10）与繁殖性能。通过基于单倍型的全基因组关联研究 (GWAS)，在 4、7 和 9 号染色体上发现了与 S/P 比率相关的其他基因组区域。这些区域包含免疫相关基因，例如 SLA-DOB、TAP2、 TAPBP、TMIGD3 和 ADORA。7 号染色体上已识别区域的四种单倍型也与多种生殖性状有关。与先前鉴定的单核苷酸多态性 (SNP) (H3GA0020505) 相比，位于 MHC 区域的与 S/P 比率显着相关的单倍型可能与数量性状基因座 (QTL) 处于更强的连锁不平衡 (LD) 给定更大的估计由单倍型解释的遗传变异比由 SNP 解释。特定的 ROH 和 ROHet 区域与 S/P 比显着相关。基于单倍型的 GWAS 鉴定了第 4、7 和 9 号染色体上 S/P 比率的新 QTL，并证实了 MHC 区域中至少存在一个 QTL。7号染色体区域也与生殖性能有关。这些结果缩小了对该区域因果基因的搜索范围，并表明 SLA-DOB 和 TAP2 作为与 7 号染色体上 S/P 比率相关的潜在候选基因。这些结果为标记辅助选择和 S/P 比率的基因组选择提供了额外的机会作为商品猪种群产仔数的遗传指标。