Cliona A. Ryan, Deirdre C. Purfield, Daragh Matthews, Carla Canedo-Ribeiro, Ainhoa Valldecabres, Donagh P. Berry
Aneuploidy is a genetic condition characterized by the loss or gain of one or more chromosomes. Aneuploidy affecting the sex chromosomes can lead to infertility in otherwise externally phenotypically normal cattle. Early identification of cattle with sex chromosomal aneuploidy is important to minimize the costs associated with rearing infertile cattle and futile breeding attempts. As most livestock breeding programs routinely genotype their breeding populations using single nucleotide polymorphism (SNP) arrays, this study aimed to assess the feasibility of integrating an aneuploidy screening tool into the existing pipelines that handle dense SNP genotype data. A further objective was to estimate the prevalence of sex chromosome aneuploidy in a population of 146,431 juvenile cattle using available genotype intensity data. Three genotype intensity statistics were used: the LogR Ratio (LRR), R-value (the sum of X and Y SNP probe intensities), and B-allele frequency (BAF) measurements. Within the female-verified population of 124,958 individuals, the estimated prevalence rate was 0.0048% for XO, 0.0350% for XXX, and 0.0004% for XXY. The prevalence of XXY in the male-verified population was 0.0870% (i.e., 18 out of 20,670 males). Cytogenetic testing was used to verify 2 of the XXX females who were still alive. The proposed approach can be readily integrated into existing genomic pipelines, serving as an efficient, large-scale screening tool for aneuploidy. Its implementation could enable the early identification of infertile animals with sex-chromosome aneuploidy.
非整倍体是一种遗传病,其特征是一条或多条染色体缺失或增殖。影响性染色体的非整倍体可导致外部表型正常的牛不育。及早发现性染色体非整倍体牛对于最大限度地降低饲养不育牛和徒劳的育种尝试所带来的成本非常重要。由于大多数家畜育种项目都会使用单核苷酸多态性(SNP)阵列对育种群体进行常规基因分型,因此本研究旨在评估将非整倍体筛选工具整合到处理高密度 SNP 基因分型数据的现有管道中的可行性。研究的另一个目的是利用现有的基因型强度数据估算146,431头幼牛群体中性染色体非整倍体的发生率。研究中使用了三种基因型强度统计量:对数比(LRR)、R 值(X 和 Y SNP 探针强度之和)和 B 等位基因频率(BAF)测量值。在由 124 958 人组成的女性验证人群中,XO 的患病率估计为 0.0048%,XXX 为 0.0350%,XXY 为 0.0004%。男性验证人群中的 XXY 患病率为 0.0870%(即 20,670 名男性中有 18 名 XXY 患者)。细胞遗传学检测用于验证 2 名仍在世的 XXX 女性。所提出的方法可以很容易地集成到现有的基因组管道中,成为一种高效、大规模的非整倍体筛查工具。采用这种方法可以及早发现患有性染色体非整倍体的不育动物。
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Markus Schmid, Ramona Weishaar, Jana Seifert, Amélia Camarinha-Silva, Markus Rodehutscord, Jörn Bennewitz
Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations. Blood urea nitrogen (BUN) levels in the pig are suitable to predict the NUE and, therefore, might be an indicator trait for NUE because BUN is a relatively easy-to-measure trait. This study investigated the suitability of NUE as a selection trait in future breeding programs. The relationships to classical growth performance and feed efficiency traits were analysed as well as the relationship to BUN to infer the role of BUN as an indicator trait to improve NUE via breeding. The analyzes were based on a Landrace F1 cross population consisting of 502 individuals who descended from 20 Piétrain sires. All animals were genotyped for 48,525 SNPs. They were phenotyped in two different fattening phases, i.e., FP1 and FP2, during the experiment. Uni- and bivariate analyses were run to estimate variance components and to determine the genetic correlation between different traits or between the same trait measured at different time points. Moderate heritabilities were estimated for all traits, whereby the heritability for NUE was h2 = 0.293 in FP1 and h2 = 0.163 in FP2 and BUN had the by far highest heritability (h2 = 0.415 in FP1 and h2 = 0.460 in FP2). The significant genetic correlation between NUE and BUN showed the potential of BUN to be considered an indicator trait for NUE. This was particularly pronounced when NUE was measured in FP1 (genetic correlations