The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.

中文翻译：

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GenoTypeMapper：在遗传和基于序列的图谱上进行图形基因分型。


大型基因组（例如面包和硬粒小麦、大麦）及其注释的不断增加的可用性为在物理尺度上以图形方式呈现亲本和后代的基因组组织奠定了基础。遗传图谱对于育种者来说是非常重要的工具，但通常代表实际染色体的扭曲模型，例如着丝粒和端粒区域。这种有偏见的情况可能会导致对遗传区域的大小和复杂性以及选择合适的分子标记以将性状纳入育种群体或近等基因系（NIL）的不精确假设和估计。一些软件包允许基因型数据的图形说明，但据我们所知，目前还没有能够在物理和遗传尺度上比较基因型数据的合适软件包。我们开发了一个名为 GenoTypeMapper (GTM) 的简单基于 Java 的软件，用于比较遗传图谱和物理图谱上的基因型数据，并测试了它对两个 NIL 数据的有效性，这两个 NIL 携带 2BS 和 7AS 染色体上野生二粒小麦耐旱胁迫 QTL 区域。两种 NIL 都比其轮回亲本更能耐受干旱胁迫，但表现出额外的不良性状，例如抽穗时间延迟。在本文中，我们说明该软件可以轻松地允许用户显示和识别源自野生二粒小麦亲本的两个 NIL 中的其他染色体渗入。检测和减少联动阻力的能力对于预育种目的特别重要，而开发的软件在这方面是一个非常合适的工具。该软件基于杂交方案的后代和亲本之间的简单等位基因匹配算法。 尽管方法很简单，但 GTM 似乎是唯一允许我们分析、说明和比较不同杂交方案与两个不同图谱中最多四个亲本的后代的基因型数据的软件。到目前为止，该软件最多可以检查 500 个人以及最多 50,000 个标记。阻碍软件性能的主要限制是并行检查的标记数量。由于必须单独分析每个个体，目前一次运行最多可以显示 10 个个体。在配备第 8 代 Intel 5 处理器的计算机上，GTM 可以在不到五秒的时间内可靠地分析具有多达 12,000 个标记的单个个体或具有多达 3,600 个标记的 10 个个体。未来的工作旨在提高软件的性能，以便可以分析具有更多亲本和更多标记的更复杂的杂交方案。