Development of a web-based high-throughput marker design program: CAPS (cleaved amplified polymorphic sequence) Maker.

IF 4.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Joo-Seok Park, Yoram Choi, Jin-Hyun Kim, Chaeyoung Lee, Min-Gyun Jeong, Yeong-Il Jeong, Yang Jae Kang, Young-Soo Chung, Hong-Kyu Choi
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引用次数: 0

Abstract

Background: Genetic markers are crucial for breeding crops with desired agronomic traits, and their development can be expedited using next-generation sequencing (NGS) and bioinformatics tools. Numerous tools have been developed to design molecular markers, enhancing the convenience, accuracy, and efficiency of molecular breeding. However, these tools primarily focus on genetic variants within short user-input sequences, despite the availability of extensive omics data for genomic variants. To design molecular markers encompassing a vast number of genetic variants at the genome-wide scale in soybean, an automatic system capable of handling NGS-based big data is necessary.

Results: In this study, we developed a robust digital platform, the CAPS Maker, for designing cleaved amplified polymorphic sequence (CAPS)/derived CAPS (dCAPS) markers in soybeans. This platform simplifies the systematic design of genomic markers with a user-friendly graphical interface, featuring a 'SNP Browser' and 'Primer Table', along with internal programs (e.g., the eHT-PCR module) to design unique primer pairs for highly duplicated genomes like soybean.

Conclusions: The CAPS Maker's efficiency and reliability were experimentally verified by comparing its marker predictions with actual experimental results. Consequently, breeders can easily design CAPS/dCAPS markers using the CAPS Maker platform to develop new soybean cultivars with beneficial agronomic traits. This platform is freely accessible at https://tgil.donga.ac.kr/CAPSMaker .

开发基于网络的高通量标记设计程序:CAPS (cleaved amplified polymorphic sequence) Maker。
背景:遗传标记对于培育具有理想农艺性状的作物至关重要,利用下一代测序(NGS)和生物信息学工具可以加快遗传标记的开发。许多工具被开发用于设计分子标记,提高了分子育种的方便性、准确性和效率。然而,这些工具主要集中在短用户输入序列中的遗传变异,尽管基因组变异的广泛组学数据是可用的。为了在大豆全基因组范围内设计包含大量遗传变异的分子标记,需要一个能够处理基于ngs的大数据的自动系统。结果:在本研究中,我们开发了一个强大的数字平台CAPS Maker,用于设计大豆的cleaved amplified polymorphic sequence (CAPS)/derived CAPS (dCAPS)标记。该平台通过用户友好的图形界面简化了基因组标记的系统设计,具有“SNP浏览器”和“引物表”,以及内部程序(例如ept - pcr模块),可以为大豆等高度重复的基因组设计独特的引物对。结论:通过与实际实验结果的比较,验证了CAPS Maker的有效性和可靠性。因此,育种者可以利用CAPS Maker平台轻松设计CAPS/dCAPS标记,开发具有有益农艺性状的大豆新品种。该平台可在https://tgil.donga.ac.kr/CAPSMaker免费访问。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Plant Methods
Plant Methods 生物-植物科学
CiteScore
9.20
自引率
3.90%
发文量
121
审稿时长
2 months
期刊介绍: Plant Methods is an open access, peer-reviewed, online journal for the plant research community that encompasses all aspects of technological innovation in the plant sciences. There is no doubt that we have entered an exciting new era in plant biology. The completion of the Arabidopsis genome sequence, and the rapid progress being made in other plant genomics projects are providing unparalleled opportunities for progress in all areas of plant science. Nevertheless, enormous challenges lie ahead if we are to understand the function of every gene in the genome, and how the individual parts work together to make the whole organism. Achieving these goals will require an unprecedented collaborative effort, combining high-throughput, system-wide technologies with more focused approaches that integrate traditional disciplines such as cell biology, biochemistry and molecular genetics. Technological innovation is probably the most important catalyst for progress in any scientific discipline. Plant Methods’ goal is to stimulate the development and adoption of new and improved techniques and research tools and, where appropriate, to promote consistency of methodologies for better integration of data from different laboratories.
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