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DNA标记生成器：利用二代测序短读长重测序数据简化扩增不应变突变系统（ARMS）和酶切扩增多态性序列（CAPS）标记开发

DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.

作者信息

Segawa Tenta, Saiga Sorachi, Takata Marina, Kumazawa Riki, Hara Makishi, Yamakawa Hiromoto, Takagi Hiroki

机构信息

Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.

Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.

出版信息

Breed Sci. 2024 Apr;74(2):73-82. doi: 10.1270/jsbbs.23048. Epub 2024 Feb 29.

DOI:10.1270/jsbbs.23048
PMID:39355627
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11442104/
Abstract

DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between cultivars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker's applicability by developing DNA markers for rice, potato, and turnip-each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breeding and genetic analysis in various crops.

摘要

DNA标记是育种选择和遗传分析的重要工具。然而，由于需要鉴定品种/品系之间的多态性并设计合适的引物，开发DNA标记可能既耗时又费力。为应对这些挑战，我们开发了DNAMarkMaker，这是一种利用重测序数据自动进行扩增不应性突变系统（ARMS）和酶切扩增多态性序列（CAPS）标记引物设计的工具。DNAMarkMaker的一个关键特性是其用户友好的图形用户界面（GUI），即使对于不太熟悉生物信息学的研究人员来说，也能确保其可访问性和易用性。我们通过为水稻、马铃薯和芜菁开发DNA标记（分别代表不同的基因组结构：纯合二倍体、杂合同源四倍体和杂合二倍体）来证实DNAMarkMaker的适用性。DNAMarkMaker将有助于快速高效地开发DNA标记，加速各种作物的育种和遗传分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/5322763912c6/74_073-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/3b98b395d949/74_073-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/19dcb147ec7b/74_073-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/d7e7bcde5483/74_073-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/a7b95996ed8a/74_073-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/e4c855bf9a7b/74_073-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/5322763912c6/74_073-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/3b98b395d949/74_073-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/19dcb147ec7b/74_073-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/d7e7bcde5483/74_073-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/a7b95996ed8a/74_073-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/e4c855bf9a7b/74_073-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1226/11442104/5322763912c6/74_073-g006.jpg

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本文引用的文献

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Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes.分子标记辅助选择的最新进展及其在植物育种计划中的应用。
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