一种常见的调控单倍型可使牛奶中的乳铁蛋白浓度增加一倍

IF 3.6 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Thomas J. Lopdell, Alexander J. Trevarton, Janelle Moody, Claire Prowse-Wilkins, Sarah Knowles, Kathryn Tiplady, Amanda J. Chamberlain, Michael E. Goddard, Richard J. Spelman, Klaus Lehnert, Russell G. Snell, Stephen R. Davis, Mathew D. Littlejohn
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引用次数: 0

摘要

牛乳铁蛋白(Lf)是一种具有抗菌、抗病毒和抗真菌活性的铁吸收乳清蛋白。乳铁蛋白具有很高的经济价值,其在牛奶中的浓度变化很大,部分原因是受挤奶频率、内陷或乳腺炎等环境因素的影响。以前也曾观察到遗传因素对牛奶中乳铁蛋白含量的重要影响。在此,我们结合 RNA-seq、ChIP-seq 和 ATAC-seq 数据对乳铁蛋白浓度进行了遗传图谱分析,以确定调节牛奶中乳铁蛋白浓度的候选致病变异。我们发现了一个高度显著的乳铁蛋白定量性状基因座(pQTL),以及一个映射到LTF基因座的顺式乳转铁蛋白(LTF)表达QTL(顺式-eQTL)。利用代表哺乳期乳腺组织样本的 ChIP-seq 和 ATAC-seq 数据集,我们还报告了染色质开放性受遗传影响的一些区域。其中一些区域还显示出高度显著的 QTL,其遗传特征与 pQTL 和 eQTL 分析所强调的特征相似。通过对这些 QTL 进行相关性分析,我们在 LTF 的推测启动子区域发现了一个 ATAC-seq 峰,该峰突出显示了一组 115 个高频变异,这些变异可能是造成这些效应的原因。这 115 个变异中的一个(rs110000337)映射在 ATAC-seq 峰上,据预测,它将改变已知参与泌乳相关通路的转录因子的结合位点。在此,我们报告了对牛奶乳铁蛋白浓度有显著影响的 115 个变异的调控单倍型。这些发现有助于为高产专业畜群选择动物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A common regulatory haplotype doubles lactoferrin concentration in milk
Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is economically valuable and has an extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence has also been previously observed to regulate lactoferrin content in milk. Here, we conducted genetic mapping of lactoferrin protein concentration in conjunction with RNA-seq, ChIP-seq, and ATAC-seq data to pinpoint candidate causative variants that regulate lactoferrin concentrations in milk. We identified a highly-significant lactoferrin protein quantitative trait locus (pQTL), as well as a cis lactotransferrin (LTF) expression QTL (cis-eQTL) mapping to the LTF locus. Using ChIP-seq and ATAC-seq datasets representing lactating mammary tissue samples, we also report a number of regions where the openness of chromatin is under genetic influence. Several of these also show highly significant QTL with genetic signatures similar to those highlighted through pQTL and eQTL analysis. By performing correlation analysis between these QTL, we revealed an ATAC-seq peak in the putative promotor region of LTF, that highlights a set of 115 high-frequency variants that are potentially responsible for these effects. One of the 115 variants (rs110000337), which maps within the ATAC-seq peak, was predicted to alter binding sites of transcription factors known to be involved in lactation-related pathways. Here, we report a regulatory haplotype of 115 variants with conspicuously large impacts on milk lactoferrin concentration. These findings could enable the selection of animals for high-producing specialist herds.
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来源期刊
Genetics Selection Evolution
Genetics Selection Evolution 生物-奶制品与动物科学
CiteScore
6.50
自引率
9.80%
发文量
74
审稿时长
1 months
期刊介绍: Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.
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