- 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
- Yuichi Katayose Hiroyuki Kanamori Michihiko Shimomura Hajime Ohyanagi Hiroshi Ikawa Hiroshi Minami Michie Shibata Tomoko Ito Kanako Kurita Kazue Ito Yasutaka Tsubokura Akito Kaga Jianzhong Wu Takashi Matsumoto Kyuya Harada Takuji Sasaki
- 出版者
- Japanese Society of Breeding
- 雑誌
- Breeding Science (ISSN:13447610)
- 巻号頁・発行日
- vol.61, no.5, pp.661-664, 2012 (Released:2012-02-04)
- 参考文献数
- 10
- 被引用文献数
- 11 13 3
Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.