Bovine paratuberculosis is a contagious disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), with adverse effects on animal welfare and serious economic consequences. Published results on host genetic resistance to MAP are inconsistent, mainly because of difficulties in characterizing the infection status of cows. The objectives of this study were to identify quantitative trait loci (QTL) for resistance to MAP in Holstein and Normande cows with an accurately defined status for MAP. From MAP-infected herds, cows without clinical signs of disease were subjected to at least four repeated serum ELISA and fecal PCR tests over time to determine both infected and non-infected statuses. Clinical cases were confirmed using PCR. Only cows that had concordant results for all tests were included in further analyses. Positive and control cows were matched within herd according to their birth date to ensure a same level of exposure to MAP. Cows with accurate phenotypes, i.e. unaffected (control) or affected (clinical or non-clinical cases), were genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were imputed to whole-genome sequences using the 1000 Bull Genomes reference population (run6). A genome-wide association study (GWAS) of MAP status of 1644 Holstein and 649 Normande cows, using either two (controls versus cases) or three classes of phenotype (controls, non-clinical and clinical cases), revealed three regions, on Bos taurus (BTA) chromosomes 12, 13, and 23, presenting significant effects in Holstein cows, while only one of those was identified in Normande cows (BTA23). The most significant effect was found on BTA13, in a short 8.5-kb region. Conditional analyses revealed that only one causal variant may be responsible for the effects observed on each chromosome with the ABCC4 (BTA12), CBFA2T2 (BTA13), and IER3 (BTA23) genes as good functional candidates. A sequence-based GWAS on cows for which resistance to MAP was accurately defined, was able to identify candidate variants located in genes that were functionally related to resistance to MAP; these explained up to 28% of the genetic variance of the trait. These results are very encouraging for efforts towards implementation of a breeding strategy aimed at improving resistance to paratuberculosis in Holstein cows.

中文翻译：

---

从荷斯坦和诺曼德奶牛中基于序列的GWAS鉴定对副结核病抗性的ABCC4，IER3和CBFA2T2候选基因

牛副结核病是一种传染性疾病，由鸟分枝杆菌亚种引起。副结核病（MAP），对动物福利产生不利影响，并产生严重的经济后果。关于宿主对MAP的遗传抗性的已发表结果不一致，主要是因为难以确定母牛的感染状况。这项研究的目的是确定具有精确定义的MAP状态的荷斯坦和诺曼德奶牛对MAP的抗性的定量性状基因座（QTL）。对于经过MAP感染的牛群，对无临床疾病迹象的母牛进行至少四次反复的血清ELISA和粪便PCR测试，以确定其感染和未感染状态。使用PCR证实了临床病例。进一步的分析只包括所有测试结果一致的奶牛。阳性和对照母牛根据出生日期在畜群中进行匹配，以确保相同水平的MAP暴露。使用Illumina BovineSNP50 BeadChip对具有精确表型的母牛进行基因型分型，即未受影响（对照）或受影响（临床或非临床病例）。使用1000个Bull基因组参考人群（run6）将基因型推算为全基因组序列。使用两个（对照与病例）或三类表型（对照，非临床和临床病例）的1644荷斯坦奶牛和649诺曼德牛的MAP状态的全基因组关联研究（GWAS），揭示了Bos上的三个区域金牛座（BTA）的12、13和23号染色体在荷斯坦奶牛中表现出显着影响，而诺曼德（BTA23）牛只鉴定出其中一个。在短的8.5-kb区域中发现了对BTA13的最大影响。条件分析表明，只有一个因果变体可能是每个染色体上观察到的效应的原因，ABCC4（BTA12），CBFA2T2（BTA13）和IER3（BTA23）基因是良好的功能候选者。准确定义了对MAP的抗性的基于序列的奶牛GWAS能够鉴定出与MAP抗性功能相关的基因中的候选变体。这些解释了该性状遗传变异的28％。这些结果对于实施旨在提高荷斯坦奶牛对肺结核副抗性的育种策略的努力非常令人鼓舞。准确定义了对MAP的抗性的基于序列的奶牛GWAS能够鉴定出与MAP抗性功能相关的基因中的候选变体。这些解释了该性状遗传变异的28％。这些结果对于实施旨在提高荷斯坦奶牛对肺结核副抗性的育种策略的努力非常令人鼓舞。准确定义了对MAP的抗性的基于序列的奶牛GWAS能够鉴定出与MAP抗性功能相关的基因中的候选变体。这些解释了该性状遗传变异的28％。这些结果对于实施旨在提高荷斯坦奶牛对肺结核副抗性的育种策略的努力非常令人鼓舞。