Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly.
Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly.
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DOI：
10.1111/age.12548
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发表时间：
2017-08
期刊：
影响因子：
2.4
通讯作者：
Griffin DK
中科院分区：
文献类型：
--
作者：
O'Connor RE;Fonseka G;Frodsham R;Archibald AL;Lawrie M;Walling GA;Griffin DK
平衡的染色体畸变已被证明会影响大多数研究物种的生育能力，常常导致猪等家畜的繁殖力低下（产仔数减少）。随着现代粮食生产越来越强调使用少量优质雄性进行人工授精，公猪、公牛、公羊等低繁殖力的潜在经济和环境成本是相当大的。因此，需要新的工具来促进快速、经济有效的染色体易位筛查。这以前是通过标准核型分析实现的；然而，这种方法依赖于大量的专业知识，并且识别微妙、神秘的易位的能力有限。为了解决这个问题，我们开发了一种使用亚端粒探针和荧光原位杂交进行易位筛选的新型设备和方案。使用来自每条猪染色体的短臂（p臂）和长臂（q臂）的亚端粒区域的BAC（细菌人工染色体）设计探针。在应用“多探针”装置之前，它们直接用 FITC 或德克萨斯红（分别为 p 臂和 q 臂）标记，从而能够在单张载玻片上同时检测每个单独的猪染色体。最初设计用于在亚端粒区域分离 BAC 的实验导致在猪基因组组装中发现了一系列错误定位的区域（在总共 82 个 BAC 中，只有 45 个 BAC 正确定位）。因此，我们的工作强调了对新测序的基因组进行准确的物理绘图的重要性。本文描述的系统允许对猪核型进行稳健和全面的分析，这是经典细胞遗传学的辅助手段，为加快高效、具有成本效益的食品生产提供了有价值的工具。
Balanced chromosomal aberrations have been shown to affect fertility in most species studied, often leading to hypoprolificacy (reduced litter size) in domestic animals such as pigs. With an increasing emphasis in modern food production on the use of a small population of high quality males for artificial insemination, the potential economic and environmental costs of hypoprolific boars, bulls, rams etc. are considerable. There is therefore a need for novel tools to facilitate rapid, cost‐effective chromosome translocation screening. This has previously been achieved by standard karyotype analysis; however, this approach relies on a significant level of expertise and is limited in its ability to identify subtle, cryptic translocations. To address this problem, we developed a novel device and protocol for translocation screening using subtelomeric probes and fluorescence in situ hybridisation. Probes were designed using BACs (bacterial artificial chromosomes) from the subtelomeric region of the short (p‐arm) and long (q‐arm) of each porcine chromosome. They were directly labelled with FITC or Texas Red (p‐arm and q‐arm respectively) prior to application of a ‘Multiprobe’ device, thereby enabling simultaneous detection of each individual porcine chromosome on a single slide. Initial experiments designed to isolate BACs in subtelomeric regions led to the discovery of a series of incorrectly mapped regions in the porcine genome assembly (from a total of 82 BACs, only 45 BACs mapped correctly). Our work therefore highlights the importance of accurate physical mapping of newly sequenced genomes. The system herein described allows for robust and comprehensive analysis of the porcine karyotype, an adjunct to classical cytogenetics that provides a valuable tool to expedite efficient, cost effective food production.
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