Pub Date : 2023-12-19DOI: 10.1007/s12686-023-01329-z
Abstract
Sauger (Sander canadensis) and walleye (Sander vitreus) are closely related North American fish species that are often managed by fishery agencies throughout their ranges. However, genotyping resources for sauger are presently limited to a small set of microsatellite loci. We evaluated whether primers in an existing walleye genotyping-in-thousands panel could amplify single nucleotide polymorphism loci (SNPs) in sauger. We identified 71 primer pairs that amplify 118 SNPs in both species. Allele frequency differences were large enough to confidently distinguish the species and identify hybrids. Additionally, we identified 41 loci with observed heterozygosity > 0.1 in sauger; these markers may be useful for simple population genetic analyses and parentage analysis when few contributors are present and for differentiating highly structured populations.
{"title":"An amplicon genotyping panel suitable for species identification and population genetics in sauger (Sander canadensis) and walleye (Sander vitreus)","authors":"","doi":"10.1007/s12686-023-01329-z","DOIUrl":"https://doi.org/10.1007/s12686-023-01329-z","url":null,"abstract":"<h3>Abstract</h3> <p>Sauger (<em>Sander canadensis</em>) and walleye (<em>Sander vitreus</em>) are closely related North American fish species that are often managed by fishery agencies throughout their ranges. However, genotyping resources for sauger are presently limited to a small set of microsatellite loci. We evaluated whether primers in an existing walleye genotyping-in-thousands panel could amplify single nucleotide polymorphism loci (SNPs) in sauger. We identified 71 primer pairs that amplify 118 SNPs in both species. Allele frequency differences were large enough to confidently distinguish the species and identify hybrids. Additionally, we identified 41 loci with observed heterozygosity > 0.1 in sauger; these markers may be useful for simple population genetic analyses and parentage analysis when few contributors are present and for differentiating highly structured populations.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138741783","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}
Pub Date : 2023-12-18DOI: 10.1007/s12686-023-01330-6
Abstract
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.
{"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> <p>Przewalski’s horse (<em>Equus ferus</em>) 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.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"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}
Pub Date : 2023-12-08DOI: 10.1007/s12686-023-01328-0
Xiang-Yang Jia, Wei Li, Jun Yan, Ling-Li Xia
Liobagrus angullicauda is an endemic species to streams along the southeast coast in China. Due to over fishing and habitat destruction, the natural population of L. angullicauda has decreased dramatically in recent years. Insufficient molecular markers have limited the effective conservation and management of this species. In the present study, we reported the isolation and characterization of 33 SNP markers in L. angullicauda. The minor allele frequency ranged from 0.083 to 0.507, and the observed and expected heterozygosities ranged from 0.177 to 0.624 and 0.290 to 0.712, respectively. Polymorphic information content ranged from 0.118 to 0.408. Among these SNPs, only four loci showed significant departures from the Hardy–Weinberg equilibrium (P < 0.05). Cross-amplification was tested in related species Liobagrus nigricauda, Liobagrus marginalus and Liobagrus marginatoides. The novel polymorphic SNPs should be helpful for the future study on genetic management and population conservation for this species.
{"title":"Characterization and cross-species amplification of 33 SNP markers for Liobagrus angullicauda (Teleostei, Siluriformes:Amblycipitidae)","authors":"Xiang-Yang Jia, Wei Li, Jun Yan, Ling-Li Xia","doi":"10.1007/s12686-023-01328-0","DOIUrl":"https://doi.org/10.1007/s12686-023-01328-0","url":null,"abstract":"<p><i>Liobagrus angullicauda</i> is an endemic species to streams along the southeast coast in China. Due to over fishing and habitat destruction, the natural population of <i>L. angullicauda</i> has decreased dramatically in recent years. Insufficient molecular markers have limited the effective conservation and management of this species. In the present study, we reported the isolation and characterization of 33 SNP markers in <i>L. angullicauda</i>. The minor allele frequency ranged from 0.083 to 0.507, and the observed and expected heterozygosities ranged from 0.177 to 0.624 and 0.290 to 0.712, respectively. Polymorphic information content ranged from 0.118 to 0.408. Among these SNPs, only four loci showed significant departures from the Hardy–Weinberg equilibrium (P < 0.05). Cross-amplification was tested in related species <i>Liobagrus nigricauda, Liobagrus marginalus</i> and <i>Liobagrus marginatoides.</i> The novel polymorphic SNPs should be helpful for the future study on genetic management and population conservation for this species.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138558367","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}
Pub Date : 2023-12-02DOI: 10.1007/s12686-023-01335-1
Mingsong Xiao, Bing Gong, Huimin Xu, Dandan Ju
The Chinese softshell turtle (Pelodiscus sinensis) is a kind of subaquatic reptile with high nutritional value, medicinal value and economic value. However, the number of wild turtles has dropped dramatically due to excessive fishing and habitat destruction. Artificial breeding of the turtle is facing the dilemma of germplasm degradation and lack of seedlings, which seriously hinders the sustainable development of the turtle industry. In the present study, 60 novel single nucleotide polymorphism (SNP) markers were developed based on high-throughput sequencing. Genetic diversity analysis revealed that the values of observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.0312 to 0.7500 and from 0.0312 to 0.4841, respectively, and the minor allele frequency ranged from 0.3333 to 0.5000. Only four loci showed significant deviation from Hardy–Weinberg equilibrium. The present study will provide a valuable tool for population study and resource conservation.
{"title":"Development of 60 SNP markers in Pelodiscus sinensis based on transcriptome sequencing","authors":"Mingsong Xiao, Bing Gong, Huimin Xu, Dandan Ju","doi":"10.1007/s12686-023-01335-1","DOIUrl":"https://doi.org/10.1007/s12686-023-01335-1","url":null,"abstract":"<p>The Chinese softshell turtle (<i>Pelodiscus sinensis</i>) is a kind of subaquatic reptile with high nutritional value, medicinal value and economic value. However, the number of wild turtles has dropped dramatically due to excessive fishing and habitat destruction. Artificial breeding of the turtle is facing the dilemma of germplasm degradation and lack of seedlings, which seriously hinders the sustainable development of the turtle industry. In the present study, 60 novel single nucleotide polymorphism (SNP) markers were developed based on high-throughput sequencing. Genetic diversity analysis revealed that the values of observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.0312 to 0.7500 and from 0.0312 to 0.4841, respectively, and the minor allele frequency ranged from 0.3333 to 0.5000. Only four loci showed significant deviation from Hardy–Weinberg equilibrium. The present study will provide a valuable tool for population study and resource conservation.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138513205","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}
Pub Date : 2023-12-02DOI: 10.1007/s12686-023-01333-3
Jack Rojahn, Alejandro Trujillo-González, Dianne Gleeson, Nathan Cutter, Elise M. Furlan
Environmental DNA (eDNA) surveys have gained popularity as a highly sensitive detection tool that generally outperform traditional detection techniques. eDNA surveys can provide a cost-effective means to identify species’ distributions and recent incursions, informing the control or containment of invasive species. The red-eared slider turtle, Trachemys scripta elegans, is one of the world’s most invasive species and is listed as a priority pest species for management in Australia. In this study, we validate two eDNA assays to detect this invasive turtle in Australia. We demonstrate high sensitivity in a laboratory setting and perfect detection rates in mesocosms for one of these eDNA assays but show that this does not translate to high detection rates in urban waterbodies at sites of known occupancy. In fact, our results suggest eDNA surveys provide sub-optimal performance compared to traditional detection methods for T.s. elegans. We suggest the capacity for eDNA surveys to provide a highly sensitive detection tool must be evaluated in natural environments on a species-by-species basis to understand any limitations and to avoid high error rates from eDNA surveys leading to wasted resources or inappropriate management decisions. For management of T.s. elegans in Australia, clearly defining the utility of certain eDNA based approaches to detect T.s. elegans and their incursions is vital for effective management of this pest species.
环境DNA (eDNA)调查作为一种高灵敏度的检测工具已经越来越受欢迎,通常优于传统的检测技术。eDNA调查可以提供一种经济有效的方法来确定物种的分布和最近的入侵,为控制或遏制入侵物种提供信息。红耳滑龟(Trachemys scripta elegans)是世界上最具入侵性的物种之一,在澳大利亚被列为优先管理的害虫物种。在这项研究中,我们验证了两种eDNA检测方法来检测澳大利亚的这种入侵龟。我们在实验室环境中展示了高灵敏度,并在中游环境中对这些eDNA分析中的一种进行了完美的检出率,但表明这并不能转化为在已知占用地点的城市水体中的高检出率。事实上,我们的研究结果表明,与传统的秀丽隐杆线虫检测方法相比,eDNA调查提供了次优的性能。我们建议,eDNA调查提供高灵敏度检测工具的能力必须在自然环境中以物种为基础进行评估,以了解任何局限性,并避免eDNA调查的高错误率导致资源浪费或不适当的管理决策。对于澳大利亚秀丽隐杆线虫的管理,明确定义某些基于eDNA的方法检测秀丽隐杆线虫及其入侵的效用对于有效管理该害虫物种至关重要。
{"title":"Does mesocosm validation of environmental DNA methods translate to natural environment monitoring applications? A case study detecting a high-profile invader; the red eared slider turtle, Trachemys scripta elegans, in Australia","authors":"Jack Rojahn, Alejandro Trujillo-González, Dianne Gleeson, Nathan Cutter, Elise M. Furlan","doi":"10.1007/s12686-023-01333-3","DOIUrl":"https://doi.org/10.1007/s12686-023-01333-3","url":null,"abstract":"<p>Environmental DNA (eDNA) surveys have gained popularity as a highly sensitive detection tool that generally outperform traditional detection techniques. eDNA surveys can provide a cost-effective means to identify species’ distributions and recent incursions, informing the control or containment of invasive species. The red-eared slider turtle, <i>Trachemys scripta elegans</i>, is one of the world’s most invasive species and is listed as a priority pest species for management in Australia. In this study, we validate two eDNA assays to detect this invasive turtle in Australia. We demonstrate high sensitivity in a laboratory setting and perfect detection rates in mesocosms for one of these eDNA assays but show that this does not translate to high detection rates in urban waterbodies at sites of known occupancy. In fact, our results suggest eDNA surveys provide sub-optimal performance compared to traditional detection methods for <i>T.s. elegans</i>. We suggest the capacity for eDNA surveys to provide a highly sensitive detection tool must be evaluated in natural environments on a species-by-species basis to understand any limitations and to avoid high error rates from eDNA surveys leading to wasted resources or inappropriate management decisions. For management of <i>T.s. elegans</i> in Australia, clearly defining the utility of certain eDNA based approaches to detect <i>T.s. elegans</i> and their incursions is vital for effective management of this pest species.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138513211","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}
The sleepy cod Oxyeleotris lineolata is native to northern Australia. At present, there is little information on the genome information of the sleepy cod. In this study, a total of 48 novel single nucleotide polymorphism (SNP) markers were developed based on whole-genome resequencing. The analysis of the 48 SNP genotypes in 58 fish showed that the observed heterozygosity and expected heterozygosity ranged from 0.3030 to 0.6667 and 0.2133 to 0.8541, respectively. The minor allele frequency ranged from 0.1211 to 0.4899, and the polymorphism information content ranged from 0.1902 to 0.3749. Among these SNPs, seven SNPs were found to deviate from Hardy–Weinberg equilibrium significantly (P < 0.05). These SNP markers could find application in genetic linkage maps and association analysis with growth traits of sleepy cod.
{"title":"Isolation and characterization of 48 SNP markers of sleepy cod, Oxyeleotris lineolata by whole-genome resequencing","authors":"Jiajia Fan, Dongmei Ma, Huaping Zhu, Minghui Lin, Huanhuan Su, Zaixuan Zhong","doi":"10.1007/s12686-023-01334-2","DOIUrl":"https://doi.org/10.1007/s12686-023-01334-2","url":null,"abstract":"<p>The sleepy cod <i>Oxyeleotris lineolata</i> is native to northern Australia. At present, there is little information on the genome information of the sleepy cod. In this study, a total of 48 novel single nucleotide polymorphism (SNP) markers were developed based on whole-genome resequencing. The analysis of the 48 SNP genotypes in 58 fish showed that the observed heterozygosity and expected heterozygosity ranged from 0.3030 to 0.6667 and 0.2133 to 0.8541, respectively. The minor allele frequency ranged from 0.1211 to 0.4899, and the polymorphism information content ranged from 0.1902 to 0.3749. Among these SNPs, seven SNPs were found to deviate from Hardy–Weinberg equilibrium significantly (<i>P</i> < 0.05). These SNP markers could find application in genetic linkage maps and association analysis with growth traits of sleepy cod.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138525370","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}
Pub Date : 2023-11-22DOI: 10.1007/s12686-023-01325-3
Kelley Leung
Sampling the DNA of rare animal species should have minimal impacts on individual health. This can be accomplished through non-lethal/non-invasive sampling. Few of these methods have been developed for invertebrates, including the Mollusca, which are in global decline. Tissue clipping the foot is a common non-lethal method for gastropods. However, it causes permanent damage and is inappropriate for smaller snails. This study used Flinders Technology Associates (FTA) cards to sample DNA from snail mucus for species of different sizes and habitat types, and across evolutionarily distant lineages. In a survival assay, the death rate of individuals sampled with FTA cards (12.1%) was greater than in the controls (3.7%), but the difference was not significant. Of 224 individuals representing 27 snail species (17 Hawaiian native, ten non-native) sampled using both FTA cards and tissue clipping, 80.4% of FTA samples and 91.6% of tissue samples amplified for COI, a significant difference. COI sequencing success did not differ significantly between the two methods. For individuals that failed to produce a COI sequence, an attempt was made to sequence 16S. For 16S, amplification and sequencing rates did not differ significantly between FTA and tissue samples. Habitat type and shell size did not affect FTA sampling success. Phylogenetically basal taxa exhibited lower success rates, but this may have been because of difficulty in sampling operculate taxa, and not because of identity. These results indicate that the FTA sampling is a viable non-lethal alternative to tissue clipping and can be used for diverse gastropods.
{"title":"A size and taxonomic assessment of non-lethal DNA sampling of gastropods using Flinders Technology Associates (FTA) cards","authors":"Kelley Leung","doi":"10.1007/s12686-023-01325-3","DOIUrl":"https://doi.org/10.1007/s12686-023-01325-3","url":null,"abstract":"<p>Sampling the DNA of rare animal species should have minimal impacts on individual health. This can be accomplished through non-lethal/non-invasive sampling. Few of these methods have been developed for invertebrates, including the Mollusca, which are in global decline. Tissue clipping the foot is a common non-lethal method for gastropods. However, it causes permanent damage and is inappropriate for smaller snails. This study used Flinders Technology Associates (FTA) cards to sample DNA from snail mucus for species of different sizes and habitat types, and across evolutionarily distant lineages. In a survival assay, the death rate of individuals sampled with FTA cards (12.1%) was greater than in the controls (3.7%), but the difference was not significant. Of 224 individuals representing 27 snail species (17 Hawaiian native, ten non-native) sampled using both FTA cards and tissue clipping, 80.4% of FTA samples and 91.6% of tissue samples amplified for COI, a significant difference. COI sequencing success did not differ significantly between the two methods. For individuals that failed to produce a COI sequence, an attempt was made to sequence 16S. For 16S, amplification and sequencing rates did not differ significantly between FTA and tissue samples. Habitat type and shell size did not affect FTA sampling success. Phylogenetically basal taxa exhibited lower success rates, but this may have been because of difficulty in sampling operculate taxa, and not because of identity. These results indicate that the FTA sampling is a viable non-lethal alternative to tissue clipping and can be used for diverse gastropods.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138525369","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}
Pub Date : 2023-11-21DOI: 10.1007/s12686-023-01332-4
Deokjea Cha, Jin-Young Kim, Kang-San Kim, Young-Joong Kim
Koreanohadra koreana (K. koreana) is an endemic species in South Korea that is listed as endangered. While the ecology and phylogenetics of K. koreana have been studied, its morphological similarity to the related species Koreanohadra kurodana (K. kurodana), can make species identification difficult. Furthermore, this has led to confusion when determining essential habitat information for the conservation of K. koreana. To bypass this issue, we have developed a non-invasive species identification method that can genetically differentiate between them. While there are already various non-invasive genomic DNA (gDNA) extraction methods that utilize the mucus from mollusks, they are limited as they require the target species to be physically located. To address this, in this investigation a method of extracting gDNA from the feces of snails was developed. The method utilized a primer set to amplify a cytochrome b fragment from K. koreana but not K. kurodana or other terrestrial snails. The feces of terrestrial snails could thus be used to obtain gDNA to a genetically usable level if collected within 5 days of excretion. This non-invasive species identification method using feces will help to facilitate genetic research without harming the endangered species and if the target species is not physically in the habitat. Moreover, K. koreana and K. kurodana could perhaps be further distinguished, using their habitat information to help facilitate essential conservation measures.
韩国野鸭(Koreanohadra koreana)是被列为濒危物种的韩国特有物种。虽然对韩国金龟的生态学和系统发育进行了研究,但其与近缘种Koreanohadra kurodana (K. kurodana)在形态上的相似性给物种鉴定带来了困难。此外,这也导致了在确定保护韩国虎的基本栖息地信息时的混乱。为了绕过这个问题,我们开发了一种非侵入性的物种识别方法,可以从基因上区分它们。虽然已经有各种利用软体动物黏液的非侵入性基因组DNA (gDNA)提取方法,但由于需要对目标物种进行物理定位,这些方法受到限制。为了解决这一问题,本研究建立了一种从蜗牛粪便中提取基因dna的方法。该方法利用一组引物扩增了韩国田螺的细胞色素b片段,但没有扩增黑田螺或其他陆地蜗牛的细胞色素b片段。因此,如果在排泄后5天内收集陆生蜗牛的粪便,可用于获得基因可用水平的gDNA。这种利用粪便的非侵入性物种识别方法将有助于促进基因研究,而不会伤害濒危物种,如果目标物种不在栖息地。此外,利用它们的栖息地信息来帮助采取必要的保护措施,或许可以进一步区分韩国黑田鼠和韩国黑田鼠。
{"title":"Species identification method by a new non-invasive technique in Korean endangered terrestrial snail, Koreanohadra Koreana (Gastropoda: Mollusca)","authors":"Deokjea Cha, Jin-Young Kim, Kang-San Kim, Young-Joong Kim","doi":"10.1007/s12686-023-01332-4","DOIUrl":"https://doi.org/10.1007/s12686-023-01332-4","url":null,"abstract":"<p><i>Koreanohadra koreana</i> (<i>K. koreana</i>) is an endemic species in South Korea that is listed as endangered. While the ecology and phylogenetics of <i>K. koreana</i> have been studied, its morphological similarity to the related species <i>Koreanohadra kurodana</i> (<i>K. kurodana</i>), can make species identification difficult. Furthermore, this has led to confusion when determining essential habitat information for the conservation of <i>K. koreana</i>. To bypass this issue, we have developed a non-invasive species identification method that can genetically differentiate between them. While there are already various non-invasive genomic DNA (gDNA) extraction methods that utilize the mucus from mollusks, they are limited as they require the target species to be physically located. To address this, in this investigation a method of extracting gDNA from the feces of snails was developed. The method utilized a primer set to amplify a cytochrome <i>b</i> fragment from <i>K. koreana</i> but not <i>K. kurodana</i> or other terrestrial snails. The feces of terrestrial snails could thus be used to obtain gDNA to a genetically usable level if collected within 5 days of excretion. This non-invasive species identification method using feces will help to facilitate genetic research without harming the endangered species and if the target species is not physically in the habitat. Moreover, <i>K. koreana</i> and <i>K. kurodana</i> could perhaps be further distinguished, using their habitat information to help facilitate essential conservation measures.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138525475","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}
Pub Date : 2023-11-21DOI: 10.1007/s12686-023-01337-z
Jeong Gyu Kim, Seung Hyun Yoo, Yong Bae Seo, Jong-Oh Kim, Gun-Do Kim
Red sea bream is a commercially valuable fish that is used as ingredients in the food industry. To prevent a decrease in fishing yield, farmed red sea bream is released. However, this may cause a decrease in the genetic diversity of wild populations, so systematic resource management is required. In this study, 68 single nucleotide polymorphism (SNP) markers were developed using a genotyping-by-sequencing (GBS) analysis. The minor allele frequency (MAF) ranged from 0.1802 to 0.5000, the observed heterozygosity (Ho) ranged from 0.0864 to 0.5000, expected heterozygosity (He) ranged from 0.2955 to 0.5000, and the polymorphism information content (PIC) ranged from 0.2518 to 0.3750. Of these SNPs, 25 loci significantly deviated from the Hardy–Weinberg equilibrium after a Bonferroni correction (p < 0.00074). These SNP markers will be useful for the further genetic analysis of the red sea bream population.
{"title":"Development and characterization of 68 SNP markers in red sea bream, Pagrus major","authors":"Jeong Gyu Kim, Seung Hyun Yoo, Yong Bae Seo, Jong-Oh Kim, Gun-Do Kim","doi":"10.1007/s12686-023-01337-z","DOIUrl":"https://doi.org/10.1007/s12686-023-01337-z","url":null,"abstract":"<p>Red sea bream is a commercially valuable fish that is used as ingredients in the food industry. To prevent a decrease in fishing yield, farmed red sea bream is released. However, this may cause a decrease in the genetic diversity of wild populations, so systematic resource management is required. In this study, 68 single nucleotide polymorphism (SNP) markers were developed using a genotyping-by-sequencing (GBS) analysis. The minor allele frequency (MAF) ranged from 0.1802 to 0.5000, the observed heterozygosity (H<sub>o</sub>) ranged from 0.0864 to 0.5000, expected heterozygosity (H<sub>e</sub>) ranged from 0.2955 to 0.5000, and the polymorphism information content (PIC) ranged from 0.2518 to 0.3750. Of these SNPs, 25 loci significantly deviated from the Hardy–Weinberg equilibrium after a Bonferroni correction (<i>p</i> < 0.00074). These SNP markers will be useful for the further genetic analysis of the red sea bream population.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138542888","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}
Pub Date : 2023-11-21DOI: 10.1007/s12686-023-01326-2
Wei Xu, Daxing Xie, Jie Kou, Xiuyue Zhang, Yan Li, Ye Wang, Liang Zhang, Hong Liu, Jiawen Liu, Juan Wang, Li Luo, Xiaolan Wang, Kongju Wu, Fujun Shen
A non-invasive, fast, and reliable method for sex identification of the giant panda (Ailuropoda melanoleuca) was developed by genotyping five SNPs located at the sex chromosome amelogenin (AMEL) paralogs. The giant panda’s sex can be accurately distinguished by the homozygous or heterozygous SNP genotypes. Mass spectrometry assay and Sanger sequencing both successfully genotyped tissue and fresh fecal samples collected from known-sex giant pandas. Additionally, we simulated the conditions of wild fecal samples, which were naturally degraded for up to two weeks, and successfully genotyped these samples by mass spectrometry assay in parallel. These results suggest that this is a powerful method for sex determination in highly degraded and lower concentrated DNA samples.
{"title":"Development of SNP markers to identify the sex of the giant panda from naturally degraded fecal samples","authors":"Wei Xu, Daxing Xie, Jie Kou, Xiuyue Zhang, Yan Li, Ye Wang, Liang Zhang, Hong Liu, Jiawen Liu, Juan Wang, Li Luo, Xiaolan Wang, Kongju Wu, Fujun Shen","doi":"10.1007/s12686-023-01326-2","DOIUrl":"https://doi.org/10.1007/s12686-023-01326-2","url":null,"abstract":"<p>A non-invasive, fast, and reliable method for sex identification of the giant panda (<i>Ailuropoda melanoleuca</i>) was developed by genotyping five SNPs located at the sex chromosome amelogenin (<i>AMEL</i>) paralogs. The giant panda’s sex can be accurately distinguished by the homozygous or heterozygous SNP genotypes. Mass spectrometry assay and Sanger sequencing both successfully genotyped tissue and fresh fecal samples collected from known-sex giant pandas. Additionally, we simulated the conditions of wild fecal samples, which were naturally degraded for up to two weeks, and successfully genotyped these samples by mass spectrometry assay in parallel. These results suggest that this is a powerful method for sex determination in highly degraded and lower concentrated DNA samples.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138525376","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}