Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish Oplegnathus fasciatus
文献类型：期刊论文
| 作者 | Xiao, Yongshuang2,3,4; Xiao, Zhizhong2,3,4,5; Liu, Lin1; Ma, Yuting2,3,4; Zhao, Haixia2,3,4 ; Wu, Yanduo2,3,4; Huang, Jinwei2,3,4; Xu, Pingrui2,3,4; Liu, Jing2; Li, Jun2,3,4
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| 刊名 | GIGASCIENCE
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| 出版日期 | 2024-07-19 |
| 卷号 | 13页码:16 |
| 关键词 | large-segment insertion/deletion bulk primers design e-PCR technology Oplegnathus fasciatus high-throughput identification |
| ISSN号 | 2047-217X |
| DOI | 10.1093/gigascience/giae045 |
| 通讯作者 | Liu, Jing(jliu@qdio.ac.cn) ; Li, Jun(junli@qdio.ac.cn) |
| 英文摘要 | Background The use of sex-specific molecular markers has become a prominent method in enhancing fish production and economic value, as well as providing a foundation for understanding the complex molecular mechanisms involved in fish sex determination. Over the past decades, research on male and female sex identification has predominantly employed molecular biology methodologies such as restriction fragment length polymorphism, random amplification of polymorphic DNA, simple sequence repeat, and amplified fragment length polymorphism. The emergence of high-throughput sequencing technologies, particularly Illumina, has led to the utilization of single nucleotide polymorphism and insertion/deletion variants as significant molecular markers for investigating sex identification in fish. The advancement of sex-controlled breeding encounters numerous challenges, including the inefficiency of current methods, intricate experimental protocols, high costs of development, elevated rates of false positives, marker instability, and cumbersome field-testing procedures. Nevertheless, the emergence and swift progress of PacBio high-throughput sequencing technology, characterized by its long-read output capabilities, offers novel opportunities to overcome these obstacles. Findings Utilizing male/female assembled genome information in conjunction with short-read sequencing data survey and long-read PacBio sequencing data, a catalog of large-segment (>100 bp) insertion/deletion genetic variants was generated through a genome-wide variant site-scanning approach with bidirectional comparisons. The sequence tagging sites were ranked based on the long-read depth of the insertion/deletion site, with markers exhibiting lower long-read depth being considered more effective for large-segment deletion variants. Subsequently, a catalog of bulk primers and simulated PCR for the male/female variant loci was developed, incorporating primer design for the target region and electronic PCR (e-PCR) technology. The Japanese parrotfish (Oplegnathus fasciatus), belonging to the Oplegnathidae family within the Centrarchiformes order, holds significant economic value as a rocky reef fish indigenous to East Asia. The criteria for rapid identification of male and female differences in Japanese parrotfish were established through agarose gel electrophoresis, which revealed 2 amplified bands for males and 1 amplified band for females. A high-throughput identification catalog of sex-specific markers was then constructed using this method, resulting in the identification of 3,639 (2,786 INS/853 DEL, female as reference) and 3,672 (2,876 INS/833 DEL, male as reference) markers in conjunction with 1,021 and 894 high-quality genetic sex identification markers, respectively. Sixteen differential loci were randomly chosen from the catalog for validation, with 11 of them meeting the criteria for male/female distinctions. The implementation of cost-effective and efficient technological processes would facilitate the rapid advancement of genetic breeding through expediting the high-throughput development of sex genetic markers for various species. Conclusions Our study utilized assembled genome information from male and female individuals obtained from PacBio, in addition to data from short-read sequencing data survey and long-read PacBio sequencing data. We extensively employed genome-wide variant site scanning and identification, high-throughput primer design of target regions, and e-PCR batch amplification, along with statistical analysis and ranking of the long-read depth of the variant sites. Through this integrated approach, we successfully compiled a catalog of large insertion/deletion sites (>100 bp) in both male and female Japanese parrotfish. |
| WOS关键词 | PROVIDES INSIGHTS ; GENETIC DIFFERENTIATION ; STRUCTURAL VARIATION ; DNA MARKERS ; PCR-RFLP ; GENOME ; SEQUENCE ; IDENTIFICATION ; EVOLUTION ; MUTAGENESIS |
| 资助项目 | National Natural Science Foundation of China[42276107] ; National Natural Science Foundation of China[32270472] ; National Natural Science Foundation of China[CARS-47] ; National Natural Science Foundation of China[2022YFC3103600] ; National Key Research and Development Program[2023LZGCQY001] ; Shandong Province Key RD Program ; Key Deployment Projects of Center for Ocean Mega-Science[COMS2020Q05] ; Chinese Academy of Sciences |
| WOS研究方向 | Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics |
| 语种 | 英语 |
| WOS记录号 | WOS:001286727600003 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/196506]  |
| 专题 | 海洋研究所_实验海洋生物学重点实验室 |
| 通讯作者 | Liu, Jing; Li, Jun |
| 作者单位 | 1.Wuhan Frasergen Bioinformat Co Ltd, East Lake High Tech Zone, Wuhan 430073, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, Ctr Ocean Mega Sci, Key Lab Breeding Biotechnol & Sustainable Aquacult, Qingdao 266071, Peoples R China 3.Qingdao Marine Sci & Technol Ctr, Lab Marine Biol & Biotechnol, Qingdao 266071, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 5.Weihai Hao Huigan Marine Biotechnol Co, Weihai 26449, Peoples R China |
| 推荐引用方式 GB/T 7714 | Xiao, Yongshuang,Xiao, Zhizhong,Liu, Lin,et al. Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish Oplegnathus fasciatus[J]. GIGASCIENCE,2024,13:16. |
| APA | Xiao, Yongshuang.,Xiao, Zhizhong.,Liu, Lin.,Ma, Yuting.,Zhao, Haixia.,...&Li, Jun.(2024).Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish Oplegnathus fasciatus.GIGASCIENCE,13,16. |
| MLA | Xiao, Yongshuang,et al."Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish Oplegnathus fasciatus".GIGASCIENCE 13(2024):16. |
入库方式： OAI收割
来源：海洋研究所
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