A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle

Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle has been recently reported to have an influence on the rearing success of calves. The affected animals show untreatable diarrhea accompanied by hypocholesterolemia and hypolipoproteinemia and usually die within the first weeks or months of life. Here we show that whole genome sequencing combined with knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred bull carrying one copy of the critical 2.24 Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the inbred animal. The genetic makeup of this key inbred animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3 kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low density lipoproteins and therefore the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia-1 (FBHL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle.

近日有研究报道，荷斯坦奶牛（Holstein cattle）中存在一种新型常染色体隐性遗传缺陷——胆固醇缺乏症，该病症会对犊牛的饲养成活率产生负面影响。患病个体表现出无法治愈的腹泻症状，同时伴有低胆固醇血症（hypocholesterolemia）和低脂蛋白血症（hypolipoproteinemia），通常在出生后数周或数月内死亡。本研究表明，全基因组测序（whole genome sequencing）结合家畜种群的系谱信息与近交状态数据，可助力致病突变的定位鉴定。我们对一头患病犊牛与一头健康的部分近交公牛进行了全基因组重测序：该健康公牛携带一份祖先型的关键11号染色体2.24 Mb片段，以及一份携带胆固醇缺乏症突变的同源片段。我们仅检测到一处结构变异：患病个体为纯合突变型，近交公牛则为杂合突变型。该关键近交个体的遗传背景为该突变的致病性提供了极强的佐证。该突变表现为载脂蛋白B（APOB）基因编码区插入了一段长1.3 kb的可转座长末端重复序列（LTR）元件ERV2-1，这会导致转录本截短与异常剪接。通过对患病犊牛肝脏转录组的RNA测序（RNA sequencing），进一步验证了这一发现。其编码的载脂蛋白B是乳糜微粒与低密度脂蛋白上的关键载脂蛋白，因此该突变属于功能丧失型突变，与人类的常染色体隐性遗传性家族性低β脂蛋白血症1型（FBHL1）类似。本研究结果可为荷斯坦奶牛群体开发直接的基因检测手段，助力针对该有害突变的选育淘汰工作。