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

IF 2 4区农林科学 Q2 AGRONOMY

Breeding Science Pub Date : 2024-04-01 Epub Date: 2024-02-29 DOI:10.1270/jsbbs.23048

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

{"title":"DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.","authors":"Tenta Segawa, Sorachi Saiga, Marina Takata, Riki Kumazawa, Makishi Hara, Hiromoto Yamakawa, Hiroki Takagi","doi":"10.1270/jsbbs.23048","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":null,"pages":null},"PeriodicalIF":2.0000,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442104/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Breeding Science","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1270/jsbbs.23048","RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/2/29 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"AGRONOMY","Score":null,"Total":0}

引用次数: 0

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.

查看原文本刊更多论文

DNAMarkMaker：利用 NGS 短读数从重测序数据中简化 ARMS 和 CAPS 标记的开发。

DNA 标记是育种选育和遗传分析的重要工具。然而，由于需要识别不同栽培品种/品系之间的多态性并设计合适的引物，DNA 标记的开发耗时耗力。为了应对这些挑战，我们开发了 DNAMarkMaker，这是一种利用重测序数据为难扩增突变系统（ARMS）和裂解扩增多态性序列（CAPS）标记自动设计引物的工具。DNAMarkMaker 的一个主要特点是其友好的图形用户界面 (GUI)，确保即使是不精通生物信息学的研究人员也能轻松使用。我们为水稻、马铃薯和萝卜开发了DNA标记，证实了DNAMarkMaker的适用性，这些标记分别代表不同的基因组结构：同卵二倍体、异卵自四倍体和异卵二倍体。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。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Breeding Science 农林科学-农艺学

CiteScore

4.90

自引率

4.20%

发文量

审稿时长

1.5 months

期刊介绍： Breeding Science is published by the Japanese Society of Breeding. Breeding Science publishes research papers, notes and reviews related to breeding. Research Papers are standard original articles. Notes report new cultivars, breeding lines, germplasms, genetic stocks, mapping populations, database, software, and techniques significant and useful for breeding. Reviews summarize recent and historical events related breeding. Manuscripts should be submitted by corresponding author. Corresponding author must have obtained permission from all authors prior to submission. Correspondence, proofs, and charges of excess page and color figures should be handled by the corresponding author.