Conservation Genetics Resources最新文献_第3页

Validation of a molecular sex marker in three sturgeons from eastern North America 北美东部三种鲟鱼分子性别标记的验证

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-01-27 DOI: 10.1007/s12686-024-01346-6

{"title":"Validation of a molecular sex marker in three sturgeons from eastern North America","authors":"","doi":"10.1007/s12686-024-01346-6","DOIUrl":"https://doi.org/10.1007/s12686-024-01346-6","url":null,"abstract":"<h3>Abstract</h3> Despite the importance of sex-specific information for sturgeon conservation and management, sex identification has been a major challenge outside of mature adults on spawning grounds. Recent work identified a sex-specific locus (AllWSex2) that appears to be broadly conserved across many Acipenserids, but the assay was not validated for all species within the family. We tested the AllWSex2 marker in three sturgeon taxa (shortnose sturgeon Acipenser brevirostrum, Gulf sturgeon A. oxyrhinchus desotoi, and Atlantic sturgeon A. oxyrhinchus oxyrhinchus) from the Atlantic and Gulf of Mexico Coasts of North America to validate its use for sex identification. Our results indicate AllWSex2 is conserved in all three taxa, presenting a new opportunity to derive sex-specific information from tissue samples, which are routinely collected from these taxa. We found high concordance (range: 97–100%) between genotypic and phenotypic/histological methods, suggesting the assay is broadly effective. However, the small amount of discordance between the methods (< 3%) suggests further refinement may be possible.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"59 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139580715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary stamps for adaptation traced in Cervus nippon genome using reduced representation sequencing 利用还原表示测序技术追踪海马基因组中的适应进化印记

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2024-01-27 DOI: 10.1007/s12686-023-01339-x

Nidhi Sukhija, Rangasai Chandra Goli, Mukul Sukhija, Pallavi Rathi, Komal Jaglan, Aishwarya Dash, P. B. Nandhini, K. K. Kanaka

{"title":"Evolutionary stamps for adaptation traced in Cervus nippon genome using reduced representation sequencing","authors":"Nidhi Sukhija, Rangasai Chandra Goli, Mukul Sukhija, Pallavi Rathi, Komal Jaglan, Aishwarya Dash, P. B. Nandhini, K. K. Kanaka","doi":"10.1007/s12686-023-01339-x","DOIUrl":"https://doi.org/10.1007/s12686-023-01339-x","url":null,"abstract":"Sika deer is indigenous to East Asia. Currently the species is extinct or are nearing the verge of extinction, in numerous places. Reduced population size is sensitive to climate change and has poor adaptation as a result of inbreeding. In this study genome-wide Single nucleotide polymorphisms (SNPs) were identified using double-digest restriction site associated digestion (ddRAD) approach and annotated further to identify genes related to fitness. A total 85,001 SNPs were retained following the quality control. Composite Likelihood Ratio (CLR) statistics found 13 stronger selective sweeps, identified sweeps overlapped with genes related to adaptation, reproduction, cellular functions. Average heterozygosity and nucleotide diversity were 0.27 and 0.29 respectively. Admixture analysis furnished a single cluster indicating no further sub-divergence of Sika deer. These findings would help fabricate appropriate genetic improvement programs by inclusion in the SNP chips, in order to get deeper insights into deer genetics, evolution, domestication and conservation.<h3 data-test=\"abstract-sub-heading\">Graphical Abstract</h3>Bioinformatic analysis for unravelling genomic variants and selective sweep regions in Cervus nippon\u0000","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"64 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139580787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in brown trout (Salmo trutta) 褐鳟（Salmo trutta）简单序列重复序列的全基因组鉴定和多态性 SSR 标记的开发

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-29 DOI: 10.1007/s12686-023-01341-3

Haibing Ma, Tianqing Huang, Wei Gu, Enhui Liu, Gaochao Wang, Bingqian Wang, Jianshe Zhou, Gefeng Xu

{"title":"Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in brown trout (Salmo trutta)","authors":"Haibing Ma, Tianqing Huang, Wei Gu, Enhui Liu, Gaochao Wang, Bingqian Wang, Jianshe Zhou, Gefeng Xu","doi":"10.1007/s12686-023-01341-3","DOIUrl":"https://doi.org/10.1007/s12686-023-01341-3","url":null,"abstract":"In China, the brown trout is a second-level key aquatic wildlife protection animal in the Tibet Autonomous Region. In order to protect the brown trout germplasm resources in the Tibet Autonomous Region, the Institute of Aquatic Sciences of the Academy of Agricultural and Animal Husbandry Sciences of the Tibet Autonomous Region and the Heilongjiang Institute of the Chinese Academy of Aquatic Sciences collaborated on research on the key technologies of brown trout family construction. A fast in silico simulation method was employed in this study to discover numerous polymorphic SSRs. A total of 1,115,563 SSR loci with two to six nucleotide repeat motifs were mined from 40 chromosomes of the brown trout reference genome by GMATA. The whole genome sequences (30×) of 30 brown trout samples were compared to the reference genome’s chromosome sequence. Then, the HipSTR program was employed to carry out in silico genotyping through comparisons and enumerations of repeat count variants on the motifs of the SSR loci among the samples. The loci with monomorphism and high deletion in the SSR genotype data were removed, and the loci with more than one non-reference allele were retained. The final set of polymorphic SSR loci screened was 106,194. Forty-three SSR markers were randomly selected for characteristic analysis. The range of alleles per locus was 3 to 9 (mean = 5). Observed heterozygosity was in the ranged from 0.167 to 1.000. Expected heterozygosity was in the ranged from 0.155 to 0.823. Twenty-three loci significantly deviated from Hardy-Weinberg equilibrium. These SSR markers will provide valuable information for assessing the genetic diversity of constructed brown trout families and for the genetic improvement of brown trout.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"23 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139062579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isolation and characterization of 55 SNP markers in Triplophysa (Hedinichthys) yarkandensis macroptera 叶尔羌三疣梭子蟹 55 个 SNP 标记的分离与鉴定

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-27 DOI: 10.1007/s12686-023-01345-z

引用次数: 0

Development of a multiplex real time-PCR assay to estimate the distribution of the genus Silurus in Lake Biwa using environmental DNA 利用环境 DNA 开发一种多重 real-time-PCR 检测方法，以估算琵琶湖中蚕蛾属的分布情况

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-19 DOI: 10.1007/s12686-023-01340-4

Tetsuro Inamoto, Yuu Kishimoto, Hisashi Okuyama, Ryoichi Tabata, Koichiro Nakano, Jun-ichi Takahashi

引用次数: 0

Development and validation of 98 SNP markers in Japanese anchovy, Engraulis japonicus 日本鳀鱼 98 个 SNP 标记的开发与验证

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-19 DOI: 10.1007/s12686-023-01342-2

Chenghui Song, Yang Liu, Congcong Wang

{"title":"Development and validation of 98 SNP markers in Japanese anchovy, Engraulis japonicus","authors":"Chenghui Song, Yang Liu, Congcong Wang","doi":"10.1007/s12686-023-01342-2","DOIUrl":"https://doi.org/10.1007/s12686-023-01342-2","url":null,"abstract":"The Japanese anchovy, Engraulis japonicus, is an important economic fish that is distributed in the northwest Pacific Ocean. The effective assessment and management of the Engraulis japonicus fishery requires reliable information regarding its population’s genetic structure. The recent development of double digest restriction-site associated DNA sequencing (ddRAD-Seq) methods may contribute to the discovery of SNPs and the assessment of genetic structure. In our study, 98 single nucleotide polymorphism (SNP) markers were developed using ddRAD-Seq. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.8000 and 0.2778 to 0.5000, respectively. The polymorphism information content (PIC) ranged from 0.239198 to 0.375. All loci have been substantiated to follow the Hardy–Weinberg equilibrium. These novel polymorphic SNP markers will play an important role in the genetic research of E.japonicus, which will be beneficial to the development and utilization of E.japonicus resources. This study aims to provide technical support for the research of genetic diversity of E. japonicus populations through the development of SNP markers.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"15 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138742185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An amplicon genotyping panel suitable for species identification and population genetics in sauger (Sander canadensis) and walleye (Sander vitreus) 适用于梭鱼（Sander canadensis）和马眼鱼（Sander vitreus）物种鉴定和种群遗传学的扩增子基因分型面板

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-19 DOI: 10.1007/s12686-023-01329-z

引用次数: 0

Genetic diversity assessment for reintroduced Przewalski’s horse (Equus ferus) based on newly developed SSR markers 基于新开发的 SSR 标记对重新引入的普氏马（Equus ferus）进行遗传多样性评估

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-18 DOI: 10.1007/s12686-023-01330-6

{"title":"Genetic diversity assessment for reintroduced Przewalski’s horse (Equus ferus) based on newly developed SSR markers","authors":"","doi":"10.1007/s12686-023-01330-6","DOIUrl":"https://doi.org/10.1007/s12686-023-01330-6","url":null,"abstract":"<h3>Abstract</h3> Przewalski’s horse (Equus ferus) is a national protected species in China. It first became extinct in the wild in 1976, and was reintroduced to the Kalamaili National Park (KNP) in Xinjiang, China in 2001. This study aimed to analyze the genetic diversity and structure of the reintroduced population of Przewalski’s horse in KNP. Here, we developed and designed microsatellite molecular markers using 48 feces samples and combined this with published genomic data from the species. A preliminary analysis of genetic diversity within the Przewalski’s horse population in the KNP was conducted using 16 pairs of simple sequence repeat (SSR) markers with high levels of polymorphism and high stability. A total of 199 alleles were amplified using 16 SSR primer pairs, averaging 12.438 at each locus. In the sample of 48 genomes, the average effective number of alleles detected was 2.695, the average expected heterozygosity was 0.577 and the inbreeding coefficient was 0.232. Twelve loci showed significant deviation from Hardy–Weinberg equilibrium following Bonferroni sequential corrections. Our research finds that the genetic diversity of the Przewalski’s horse population in the KNP remains high. This is the first research using newly developed SSR markers to describe the genetic diversity and structure of the reintroduced Przewalski’s horse population in KNP, China. As such, it can inform future reintroductions of the species and conservation measures.","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":"7 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138716969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization and cross-species amplification of 33 SNP markers for Liobagrus angullicauda (Teleostei, Siluriformes:Amblycipitidae) Liobagrus angullicauda (Teleostei, Siluriformes:Amblycipitidae) 33 个 SNP 标记的特征和跨物种扩增

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-08 DOI: 10.1007/s12686-023-01328-0

Xiang-Yang Jia, Wei Li, Jun Yan, Ling-Li Xia

引用次数: 0

Development of 60 SNP markers in Pelodiscus sinensis based on transcriptome sequencing 基于转录组测序的60个SNP标记的开发

IF 1.1 4区环境科学与生态学

Conservation Genetics Resources Pub Date : 2023-12-02 DOI: 10.1007/s12686-023-01335-1

Mingsong Xiao, Bing Gong, Huimin Xu, Dandan Ju

引用次数: 0