Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping

Author:

Sekine Daisuke1,Oku Satoshi2,Nunome Tsukasa1,Hirakawa Hideki3,Tsujimura Mai45,Terachi Toru5,Toyoda Atsushi6,Shigyo Masayoshi7,Sato Shusei8ORCID,Tsukazaki Hikaru2

Affiliation:

1. Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan

2. Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan

3. Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan

4. Department of Plant Life Science, Faculty of Agriculture, Ryukoku University , Otsu, Shiga 520-2194, Japan

5. Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan

6. Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan

7. Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University , Yamaguchi City, Yamaguchi 753-8515, Japan

8. Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan

Abstract

Abstract Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,General Medicine

Cited by 3 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3