1
|
Yang S, Tang X, Yan F, Yang H, Xu L, Jian Z, Deng H, He Q, Zhu G, Wang Q. A time-course transcriptome analysis revealing the potential molecular mechanism of early gonadal differentiation in the Chinese giant salamander. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101200. [PMID: 38320446 DOI: 10.1016/j.cbd.2024.101200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
The Chinese giant salamander (CGS) Andrias davidianus is the largest extant amphibian and has recently become an important species for aquaculture with high economic value. Meanwhile, its wild populations and diversity are in urgent need of protection. Exploring the mechanism of its early gonadal differentiation will contribute to the development of CGS aquaculture and the recovery of its wild population. In this study, transcriptomic and phenotypic research was conducted on the critical time points of early gonadal differentiation of CGS. The results indicate that around 210 days post-hatching (dph) is the critical window for female CGS's gonadal differentiation, while 270 dph is that of male CGS. Besides, the TRPM1 gene may be the crucial gene among many candidates determining the sex of CGS. More importantly, in our study, key genes involved in CGS's gonadal differentiation and development are identified and their potential pathways and regulatory models at early stage are outlined. This is an initial exploration of the molecular mechanisms of CGS's early gonadal differentiation at multiple time points, providing essential theoretical foundations for its captive breeding and offering unique insights into the conservation of genetic diversity in wild populations from the perspective of sex development.
Collapse
Affiliation(s)
- Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiong Tang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Fan Yan
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Han Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Lishan Xu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhijie Jian
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Huidan Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Qu He
- School of Foreign Languages, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| |
Collapse
|
3
|
Hu Q, Liu Y, Liao X, Tian H, Ji X, Zhu J, Xiao H. A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 2021; 22:230. [PMID: 33794798 PMCID: PMC8017863 DOI: 10.1186/s12864-021-07550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. RESULTS In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. CONCLUSION We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.
Collapse
Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China.
| | - Yang Liu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaolin Liao
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
| | - Xiangshan Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Jiajie Zhu
- Guangxi Academy of Fishery Sciences, Nanning, 530021, Guangxi Province, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
| |
Collapse
|
4
|
Zhang S, Zhang X, Chen X, Xu T, Wang M, Qin Q, Zhong L, Jiang H, Zhu X, Liu H, Shao J, Zhu Z, Shi Q, Bian W, You X. Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish ( Ictalurus punctatus). Front Genet 2019; 10:251. [PMID: 30984241 PMCID: PMC6448050 DOI: 10.3389/fgene.2019.00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
Collapse
Affiliation(s)
- Shiyong Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Qin Qin
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hucheng Jiang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaohua Zhu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Junjie Shao
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Zhifei Zhu
- BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| |
Collapse
|