Article
Genetics & Heredity
Miriam Ruocco, Marlene Jahnke, Joao Silva, Gabriele Procaccini, Emanuela Dattolo
Summary: Plant populations of seagrass Cymodocea nodosa along a latitudinal gradient show patterns of clinal variation in genotype and phenotype, influenced by differences in photoperiod and temperature cues. The study identified potential outlier loci related to adaptive differentiation across latitudes, with some SNPs associated to specific protein-coding genes and biological processes enriched in regulation of transcription and signalling. The results suggest the importance of gene-regulatory networks and epigenetic regulation for enabling adaptation of seagrass populations along environmental gradients.
FRONTIERS IN GENETICS
(2022)
Article
Environmental Sciences
Zhaozhao Xue, Yangchun Han, Bingli Liu, Yujuan Gu, Wen Tian, Nathan Whiting-Wagner, Hong Zhao, Wei Zhang
Summary: The study used a 2b-RAD approach to investigate bacterial diversity in ballast water and sediments, identifying a large number of bacteria species including 13 pathogens of concern in marine environments and aquaculture. Although there were differences in species composition, sediments shared most of the concerned pathogens with ballast water, highlighting the importance of sediment management in ballast water management. The 2b-RAD sequencing method shows promise for future ballast water management.
MARINE POLLUTION BULLETIN
(2021)
Article
Food Science & Technology
Carmen E. Vargas-Peralta, Cristian Araneda, Clara E. Galindo-Sanchez, M. Angelica Larrain, Miguel A. Del Rio-Portilla, Fabiola Lafarga-De La Cruz
Summary: This study analyzed the genetic data of five abalone species using RAD-seq and developed markers for traceability and specimen identification, providing a basis for fishery management measures in abalone trade.
Article
Fisheries
Chuankun Zhu, Haiyang Liu, Lei Cheng, Zhengjun Pan, Guoliang Chang, Nan Wu, Hui Wang, Huaiyu Ding, Ying Fang, Long Wang
Summary: Sex-specific markers and sequences are essential tools for analyzing sex-determination mechanisms and sex-control breeding in fishes. In this study, using 2b-RAD sequencing, potential male-specific tags were identified in Pseudobagrus ussuriensis, a valuable aquaculture fish. The results included 14 sex-specific sequences, three male-specific markers, and seven male-specific sequences, as well as the identification of candidate genes related to sex determination. These findings may contribute to further research on the sex determination mechanism and all-male breeding in P. ussuriensis.
Article
Biology
Shuangmeng Zhang, Zisheng Xu, Lifei Luo, Shuxin Gu, Zhen Hu, Shiming Wan, Zexia Gao
Summary: Coilia nasus, a migratory fish species, has high nutritional and economic value. However, its germplasm resources have sharply declined due to habitat deterioration and overfishing. Artificial farming has become important for protecting and utilizing the germplasm resources, but improper breeding strategies put the resources and genetic diversity at risk. This study analyzed the genetic diversity and structure of natural and farmed populations to provide insights for germplasm conservation and breeding strategy optimization.
Article
Biodiversity Conservation
Andre Lasalle, Pablo Caceres, Tamara Montenegro, Cristian Araneda, Jose Yanez, Denise Vizziano-Cantonnet
Summary: Researchers have generated a high-quality SNP panel from female and male sturgeons through high-depth RAD-seq, which can facilitate genetic studies and improve caviar production.
CONSERVATION GENETICS RESOURCES
(2022)
Article
Biotechnology & Applied Microbiology
Shahril Ab Razak, Mohd Norfaizal Ghazalli, Nor Helwa Ezzah Nor Azman, Alny Marlynni Abd Majid, Siti Norhayati Ismail
Summary: The study utilized NGS and RAD-seq to identify and develop microsatellite markers for taro, resulting in 14 polymorphic SSR markers, with two being monomorphic. These SSR markers serve as a molecular identification tool and provide important information for future genetic resource management of taro.
BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT
(2021)
Article
Horticulture
Manikanda Boopathi Narayanan, Shobhana V. Gnanapanditha Mohan, Praneetha Subramanyam, Rajasree Venkatachalam, Kesavan Markkandan
Summary: This study identified novel SNPs and InDels in the genes related to gynoecy and found two important functional markers, including a SNP in gene CsaV3_6G037780 encoding ACS1 enzyme and an InDel in gene CsaV3_6G304050 encoding histone lysine N-methyl transferase. These markers have significant implications for the development of gynoecious hybrids in global cucumber breeding programs.
Article
Evolutionary Biology
Roberto Biello, Mauro Zampiglia, Silvia Fuselli, Giulia Fabbri, Roberta Bisconti, Andrea Chiocchio, Stefano Mazzotti, Emiliano Trucchi, Daniele Canestrelli, Giorgio Bertorelle
Summary: Assigning individuals to their source populations is crucial for conservation research. This study developed a panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. The results showed that these SNPs can accurately determine the geographical origin of the tortoises, providing important information for management and conservation efforts.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Genetics & Heredity
Tullia Terraneo, Roberto Arrigoni, Fabio Marchese, Giovanni Chimienti, Ameer Abdulla Eweida, Mattie Rodrigue, Francesca Benzoni
Summary: In this study, we reconstructed the complete mitochondrial genome of Dendrophyllia minuscula from mesophotic depths in the Red Sea NEOM area. The mitochondrial genome consisted of 19,054 bp, organized in a typical Scleractinia mitogenome organization. This contributes to a better understanding of mesophotic and deep-water coral diversity and evolutionary history.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Fisheries
Haiyang Liu, Weiwei Xia, Bingjie Li, Lan Liu, Yakun Wang, Qing Luo, Mi Ou, Xinping Zhu, Kunci Chen, Jian Zhao
Summary: This study identified sex-specific markers in mud carp using 2b-RAD and genome sequencing. A male mud carp's genome was sequenced, and 12 male-specific scaffolds were isolated. Primers were designed based on these scaffolds, and five male-specific markers successfully discriminated males from females with 100% accuracy. Additionally, five male-specific SNPs were identified and verified, confirming a male-heterogametic XX/XY sex-determination system in mud carp. These findings provide valuable insights for understanding the genetic basis of sex determination and improving breeding efficiency in mud carp.
Article
Medicine, Legal
Thassia Mayra Telles Carratto, Leticia Marcorin, Guilherme do Valle-Silva, Maria Luiza Guimaraes de Oliveira, Eduardo Antonio Donadi, Aguinaldo Luiz Simoes, Erick C. Castelli, Celso Teixeira Mendes-Junior
Summary: Human pigmentation is a complex trait involving over 100 genes, and predicting phenotypes using SNPs from these genes is important for forensic purposes. The HIrisPlex tool was developed for eye and hair color prediction in Europeans, achieving high accuracy; however, its performance in admixed populations is limited due to higher rates of intermediate phenotypes.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Evolutionary Biology
Brenda Larison, Alec R. Lindsay, Christen Bossu, Michael D. Sorenson, Joseph D. Kaplan, David C. Evers, James Paruk, Jeffrey M. DaCosta, Thomas B. Smith, Kristen Ruegg
Summary: The study demonstrates the use of SNP panels to identify the breeding origins of carcasses collected during the nonbreeding season can improve our understanding of population-specific impacts of mortality from disease and anthropogenic stressors, ultimately allowing more effective management.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Genetics & Heredity
Megan M. Foley, Fabio Oldoni
Summary: The research and usage of next-generation systems are shaping the future of forensic DNA testing. Despite the slow adoption of NGS in casework, researchers have extensive knowledge on this technology. Currently, NGS is primarily used for SNP analysis and mitochondrial DNA analysis, and future applications will include testing of STR and SNP for general casework.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Oncology
Anqi Chen, Lei Xiong, Yiling Qu, Shihan Xi, Ruiyang Tao, Chengtao Li, Suhua Zhang
Summary: Personal identification using tumor DNA is important in tissue management and forensic identification. Traditional methods face challenges due to loss of heterozygosity in tumor tissues, but next-generation sequencing (NGS) offers promise. The study found that NGS-STR system can better detect germline-originated alleles and a scoring system based on NGS-STR allows for tumor source identification.
FRONTIERS IN ONCOLOGY
(2022)
Article
Fisheries
Oscar Aramburu, Andres Blanco, Carmen Bouza, Paulino Martinez
Summary: Disease resilience is crucial for turbot aquaculture. Researchers have compiled genomic information to construct an atlas of candidate genes and genomic regions involved in pathogen resistance. This information can help develop effective breeding strategies to enhance turbot's resistance against pathogens.
Article
Agronomy
Carmen Bouza, Iria Lorenzo, Manuel A. Rodriguez-Guitian, Adrian Casanova, Carlos Real, Rosa Romero, Manuel Vera
Summary: The present study analyzed the genetic diversity and population structure of Arnica montana L. in the northern Iberian Peninsula using nuclear and plastid DNA markers. Two distinct plastid DNA groups were identified and their distribution was found to be wider than previously described. The microsatellite analysis confirmed high genetic diversity and significant population differentiation, indicating the presence of five distinct genetic units. No relationship was found between genetic and geographical distances, suggesting a significant impact of genetic drift. Management actions for the conservation of A. montana resources are provided.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Roberto de la Herran, Miguel Hermida, Juan Andres Rubiolo, Jessica Gomez-Garrido, Fernando Cruz, Francisca Robles, Rafael Navajas-Perez, Andres Blanco, Paula Rodriguez Villamayor, Dorinda Torres, Pablo Sanchez-Quinteiro, Daniel Ramirez, Maria Esther Rodriguez, Alberto Arias-Perez, Ismael Cross, Neil Duncan, Teresa Martinez-Pena, Ana Riaza, Adrian Millan, M. Cristina De Rosa, Davide Pirolli, Marta Gut, Carmen Bouza, Diego Robledo, Laureana Rebordinos, Tyler Alioto, Carmelo Ruiz-Rejon, Paulino Martinez
Summary: This study reports a novel molecular sexing tool, which identified 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) gene through whole genome resequencing of six males and six females, and validated the sex association. The study also found differential expression of the fshr gene between male and female gonads at an early stage of gonadal differentiation, suggesting a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Alessia Lunetta, Marina Albentosa, Elisabet Nebot-Colomer, Belen G. Pardo, Paulino Martinez, Antonio Villalba, Gemma Donato, Makanjuola Akinyemi, Maite Vazquez-Luis
Summary: The Mar Menor, a hypersaline coastal lagoon in Southeastern Spain, has suffered from severe eutrophication due to environmental events. A study assessed oyster recruitment, taxonomic allocation, and functionality in the lagoon. Oyster recruits were collected using spat collectors, and genetic analysis identified two species, Ostrea edulis and O. stentina. The majority of recruits (95%) were O. stentina. Laboratory experiments explored the growth rate and clearance measurements of oysters for potential bioremediation purposes.
REGIONAL STUDIES IN MARINE SCIENCE
(2023)
Article
Environmental Sciences
Manuel Vera, Enric Aparicio, Sandra Heras, Alba Abras, Adrian Casanova, Maria-Ines Roldan, Jose-Luis Garcia-Marin
Summary: The European brown trout species has been relatively unaffected in the IUCN Red List, but anthropic impacts and introgressive hybridization from non-native Atlantic stocks have greatly damaged native populations in Mediterranean rivers. Climate change is expected to worsen this situation. This study investigates the effects of hatchery releases and climatic variables on introgression in brown trout populations in a Pyrenean river. Overall, introgressive hybridization was observed in all studied sites, with larger divergence among populations at tributaries compared to the main stem. It is recommended to involve regional social groups in citizen science programs to monitor the spread of non-native phenotypes and aid in the preservation and recovery of native populations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
M. Pampin, A. Casanova, C. Fernandez, A. Blanco, M. Hermida, M. Vera, B. G. Pardo, R. M. Coimbra, A. Cao, D. Iglesias, M. J. Carballal, A. Villalba, P. Martinez
Summary: In this study, SNP markers associated with resilience to marteiliosis were identified using a population genomics approach. These markers can be used for obtaining cockle strains resilient to marteiliosis and restoring affected cockle beds. The selected SNPs were closely related to immune response, defense, and stress functions.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Fisheries
David Iglesias, Asuncion Cao, Maria J. Carballal, Antonio Villalba
Summary: A mass mortality of cockles in Galicia caused by Marteilia cochillia led to the collapse of the cockle fishery in 2012. However, since 2016, wild cockle populations have shown increased resistance to the parasite, potentially due to natural selection and a decrease in parasite abundance and/or virulence.
DISEASES OF AQUATIC ORGANISMS
(2023)
Article
Evolutionary Biology
Antonio Villalba, Raquel M. Coimbra, Marina Pampin, David Iglesias, Damian Costas, Carlos Marino, Andres Blanco, Manuel Vera, Marta Dominguez, Eva Cacabelos, Emilio Abella, Monica Incera, Rosa Fernandez Otero, Paulino Martinez
Summary: The common cockle in the Atlantic European coasts has developed resilience to the parasite Marteilia cochillia through natural selection after consecutive outbreaks. Researchers identified markers associated with this resilience and confirmed their role through experiments.
EVOLUTIONARY APPLICATIONS
(2023)
Review
Agriculture, Dairy & Animal Science
Luis A. Quintela, Juan J. Becerra, Ana I. Pena, Uxia Yanez, Paula R. Villamayor, Pablo Sanchez-Quinteiro, Paulino Martinez, Pedro G. Herradon
Summary: The commercial use of AI in rabbit farming is relatively recent and has been evolving. This review article highlights two important milestones: the introduction of biostimulation and the addition of GnRH analogues to induce ovulation. Biostimulation practically eliminates the use of hormones to synchronize heat with AI, while the vaginal administration of GnRH offers advantages in terms of health, animal welfare, and workforce. It has been approved by the EMA and might become the most widely used method.
WORLD RABBIT SCIENCE
(2023)
Article
Oncology
Alicia L. Bruzos, Martin Santamarina, Daniel Garcia-Souto, Seila Diaz, Sara Rocha, Jorge Zamora, Yunah Lee, Alejandro Vina-Feas, Michael A. Quail, Iago Otero, Ana Pequeno-Valtierra, Javier Temes, Jorge Rodriguez-Castro, Leyre Aramburu, Andre Vidal-Capon, Antonio Villanueva, Damian Costas, Rosana Rodriguez, Tamara Prieto, Laura Tomas, Pilar Alvarino, Juana Alonso, Asuncion Cao, David Iglesias, Maria J. Carballal, Ana M. Amaral, Pablo Balseiro, Ricardo Calado, Bouchra El Khalfi, Urtzi Izagirre, Xavier de Montaudouin, Nicolas G. Pade, Ian Probert, Fernando Ricardo, Pamela Ruiz, Maria Skazina, Katarzyna Smolarz, Juan J. Pasantes, Antonio Villalba, Zemin Ning, Young Seok Ju, David Posada, Jonas Demeulemeester, Adrian Baez-Ortega, Jose M. C. Tubio
Summary: This study investigates the evolution of bivalve transmissible neoplasia in cockles and reveals the origins and factors influencing this disease. The study identifies two lineages of the disease with potential links to mitochondrial capture and host co-infection. The study also uncovers genomic instability and likely drivers of the disease, such as whole-genome duplication, oncogene amplification, and alkylation-repair suppression.
Article
Fisheries
Pauline Kamermans, Ainhoa Blanco, Pim van Dalen, Marc Engelsma, Nienke Bakker, Pascalle Jacobs, Marco Dubbeldam, Ines M. Sambade, Manuel Vera, Paulino Martinez
Summary: This study collected infected flat oysters (Ostrea edulis) with the pathogenic parasite Bonamia ostreae in the Dutch Delta area and successfully selected individuals with Bonamia resistance to produce Bonamia-free larvae. The results showed that it is possible to screen for individuals with resistance to Bonamia during the hatchery production of flat oysters. Evaluation: 8 points.
AQUATIC LIVING RESOURCES
(2023)
Article
Multidisciplinary Sciences
Thaissa D. Serrano, Diego H. M. D. Vieira, Larissa S. Pelegrini, Lucia V. V. Fragoso, Beatriz N. Agostinho, Manuel Vera, Fabio Porto-Foresti, Rodney K. De Azevedo, Vanessa D. Abdallah
Summary: This study aimed to characterize the L3 larval types of Hysterothylacium collected in Pomatomus saltatrix and Pagrus pagrus from the Brazilian coast. Hysterothylacium type V and type X larvae were found in P. saltatrix, while P. pagrus was only parasitized by type V larvae. Genetic analysis showed close relationships between Hysterothylacium types V and other related species. This study expands the knowledge of hosts and localities for Hysterothylacium.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2023)
Article
Zoology
David Iglesias, Antonio Villalba, Carlos Marino, Edgar No, Maria J. Carballal
Summary: Despite the growing impact of marine disease outbreaks, the drivers behind them are poorly understood. A unique case study on cockles in Galician rias revealed that the introduction of the protistan Marteilia cochillia led to fishery collapse in 2012. However, intensive surveys over eight years showed evidence of increasing resistance to marteiliosis in the cockle population, possibly due to natural selection. Factors triggering marteiliosis outbreaks were analyzed, but no clear relationships were found. The findings have potential implications for managing diseased populations, but continued research is needed.
JOURNAL OF INVERTEBRATE PATHOLOGY
(2023)