- 著者
- Satoshi Natsume Kaori Oikawa Chihiro Nomura Kazue Ito Hiroe Utsushi Motoki Shimizu Ryohei Terauchi Akira Abe
- 出版者
- Japanese Society of Breeding
- 雑誌
- Breeding Science (ISSN:13447610)
- 巻号頁・発行日
- vol.73, no.4, pp.415-420, 2023 (Released:2023-10-03)
- 参考文献数
- 19
DNA markers are indispensable tools in genetics and genomics research as well as in crop breeding, particularly for marker-assisted selection. Recent advances in next-generation sequencing technology have made it easier to obtain genome sequences for various crop species, enabling the large-scale identification of DNA polymorphisms among varieties, which in turn has made DNA marker design more accessible. However, existing primer design software is not suitable for designing many types of genome-wide DNA markers from next-generation sequencing data. Here, we describe the development of V-primer, high-throughput software for designing insertion/deletion, cleaved amplified polymorphic sequence, and single-nucleotide polymorphism (SNP) markers. We validated the applicability of these markers in different crops. In addition, we performed multiplex PCR targeted amplicon sequencing using SNP markers designed with V-primer. Our results demonstrate that V-primer facilitates the efficient and accurate design of primers and is thus a useful tool for genetics, genomics, and crop breeding. V-primer is freely available at https://github.com/ncod3/vprimer.
- 著者
- Hideki INNAN Ryohei TERAUCHI Naohiko T. MIYASHITA Koichiro TSUNEWAKI
- 出版者
- The Genetics Society of Japan
- 雑誌
- 遺伝学雑誌 (ISSN:0021504X)
- 巻号頁・発行日
- vol.70, no.2, pp.185-196, 1995 (Released:2004-06-08)
- 参考文献数
- 22
- 被引用文献数
- 19 35
In order to investigate the intraspecific variation of Prunus yedoensis (Someiyoshino) and interspecific relationship among P. yedoensis, P. lannesiana (Oshimazakura) and P. pendula (Edohigan), DNA fingerprinting study was conducted by using two different kinds of probes, M13 repeat sequence and (GACA)4 synthetic oligonucleotide. In this study, 68 plants of P. yedoensis grown in 46 prefectures in Japan were investigated. All the P. yedoensis individuals investigated showed the completely same banding pattern, indicating their clonal origin from a single plant. On the other hand, each of P. lannesiana and P. pendula individuals investigated showed a unique banding pattern, suggesting a considerable amount of genetic variation in these two species. About 90% of bands in DNA fingerprints of P. yedoensis were detected in either P. lannesiana or P. pendula. This result supports the hypothesis that P. yedoensis is an interspecific hybrid between P. lannesiana and P. pendula. From those results, it is concluded that P. yedoensis was produced only once through hybridization between P. lannesiana and P. pendula, and that this particular hybrid plant has been spread vegetatively all over Japan.