The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland.
Genet Sel Evol. 2019 Mar 5;51(1):9. doi: 10.1186/s12711-019-0452-z.
In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals.
In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production.
We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype.
We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.
在畜牧业中，有害的隐性等位基因可能通过多种方式导致纯合个体的经济性能下降，例如早期胚胎死亡、出生后不久死亡，或不完全外显的半致死性导致存活能力降低。虽然死亡是一个容易评分的表型，但存活能力降低并不那么容易识别。然而，它有时可以表现为受孕率降低、产犊间隔延长或活产动物的存活率降低。
在本文中，我们在来自五个品种（阿伯丁安格斯、夏洛莱、海福特、利木赞和西门塔尔）的 132725 头爱尔兰肉牛的基因型中搜索了可能携带隐性致死或半致死等位基因的单倍型。我们在基因组上的滑动窗口中对基因型进行相位划分，并使用五种测试来识别不存在或减少纯合性的单倍型。然后，我们将鉴定出的单倍型与 44351 条指示早期胚胎死亡和产后存活的授精记录相关联。最后，我们通过估计对 15 个在牛肉生产中具有经济重要性的性状的育种值的替代效应来评估单倍型的多效性。
我们发现了一个携带隐性致死（西门塔尔 16 号染色体）和两个携带半致死等位基因（阿伯丁安格斯 14 号染色体和夏洛莱 19 号染色体）的单倍型的支持，其群体频率分别为 8.8%、15.2%和 14.4%。这三个单倍型对牛肉生产中具有经济重要性的性状表现出多效性效应。它们的等位基因替代效应分别为终端指数的€2.30、€3.42 和€1.47，以及替代指数的€1.03、-€3.11 和-€0.88，终端指数的标准差分别为€22.52、€18.65 和€22.70，替代指数的标准差分别为€31.35、€29.82 和€35.79。我们确定 ZFAT 为阿伯丁安格斯半致死性的候选基因，确定了几个携带隐性致死性西门塔尔单倍型的候选基因，以及没有携带隐性致死性夏洛莱单倍型的候选基因。
我们分析了基因型、繁殖、存活和生产数据，以检测爱尔兰肉牛中可能携带隐性致死或半致死等位基因的单倍型，并鉴定出一个致死和两个半致死单倍型，它们对牛肉生产中具有经济重要性的性状具有多效性效应。
