Article
Agriculture, Dairy & Animal Science
Rie Saito, Natsuko Ito Kondo, Yui Nemoto, Reiko Kumada, Nobuyoshi Nakajima, Masanori Tamaoki
Summary: After the Fukushima nuclear incident, the number of wild boars in the DRZ area increased significantly, raising concerns about the spread of highly contaminated boars to other areas. This study used MIG-seq analysis to uncover the dispersal and gene flow of wild boar population in Fukushima and found significant genetic differences between the eastern and western groups, divided by the Abukuma River. The study suggests that the river and urbanization along it may affect the migration of wild boars.
Article
Biodiversity Conservation
Meile Sun, Xiangrong Ren, Ya Liu, Jing Yang, Jingtao Hui, Yukun Zhang, Yanhua Cui, Jun Zhang, Guocang Lin, Yan Li
Summary: In this study, the genetic structure of 57 rose cultivars and one wild species with different scents was evaluated through whole genome re-sequencing. The study revealed that the genetic background of roses is complex and can be divided into three main clusters. Genes related to fatty acid derivatives, terpenoids, and benzenoids/phenylpropanoids showed positive selection in rose cultivars with strong fragrance.
Article
Biochemistry & Molecular Biology
Huashui Ai, Mingpeng Zhang, Bin Yang, Amy Goldberg, Wanbo Li, Junwu Ma, Debora Brandt, Zhiyan Zhang, Rasmus Nielsen, Lusheng Huang
Summary: Research on Eurasian pig populations revealed significant genetic haplotype differences and hybridization history. By analyzing Y chromosome data, the study uncovered three distinct waves of European gene introgression into Asian pig populations in the last 200 years, as well as the presence and distribution of European Y chromosomes in Chinese pig breeds. The European Y haplotype in Chinese pigs is associated with lean meat production, suggesting artificial selection as a driving force for its increased frequency.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Limei Zhong, Youlin Zhu, Kenneth M. Olsen
Summary: This study used genome scans to uncover selection marks of hard and soft sweeps in domesticated soybeans, revealing that hard sweeps are mainly present in domesticated soybeans, while soft sweeps are more common in wild ancestors. The results contribute to a better understanding of genetic characteristics of domestication traits in soybeans.
Article
Plant Sciences
Xi-ou Xiao, Ning Zhang, Hui Jin, Huaijun Si
Summary: This study evaluated the genetic diversity and population structure of 135 autotetraploid potatoes using SLAF-seq methods. Analysis of 3,397,137 high-quality SNPs revealed that the classification of these potatoes based on SNP profiles did not correlate with their geographical origins. Furthermore, 71 PARMS-SNP markers were successfully used to analyze 190 autotetraploid potato varieties. Overall, these novel SNP markers provide a solid foundation for potato genetic diversity analysis, DUS testing, and plant variety protection.
Article
Biotechnology & Applied Microbiology
Yan Jing, Weili Teng, Lijuan Qiu, Hongkun Zheng, Wenbin Li, Yingpeng Han, Xue Zhao
Summary: The study of 185 representative soybean accessions revealed partial resistance related to SSR disease, and potential candidate genes were identified through sequencing and association analysis.
Article
Clinical Neurology
Mathew J. Koretsky, Chelsea Alvarado, Mary B. Makarious, Dan Vitale, Kristin Levine, Sara Bandres-Ciga, Anant Dadu, Sonja W. Scholz, Lana Sargent, Faraz Faghri, Hirotaka Iwaki, Cornelis Blauwendraat, Andrew Singleton, Mike Nalls, Hampton Leonard
Summary: Koretsky et al. used genome-wide data to cluster patients based on their genetic status across known risk variants for five neurodegenerative disorders. The results suggest that neurodegenerative diseases have more overlapping genetic aetiology than previously assumed and that neurodegeneration should be viewed as a spectrum of symptomatology.
Article
Plant Sciences
Melinda R. Grosser, Samantha K. Sites, Mayara M. Murata, Yolanda Lopez, Karen C. Chamusco, Kyra Love Harriage, Jude W. Grosser, James H. Graham, Fred G. Gmitter, Christine D. Chase
Summary: Plant genomes contain nuclear, plastid, and mitochondrial components which have different inheritance and evolutionary patterns. Genetic markers from these three genomes can be used to study inheritance, genetic relationships, and phenotypic contributions. Developing mitochondrial markers is challenging due to their high variability in size, gene order, and non-coding sequences, as well as their conservation in protein-coding sequences. PCR amplification of introns using conserved flanking exons is an effective method for developing polymorphic nuclear genome markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Justyna Basak, Danuta Piotrzkowska, Ireneusz Majsterek, Ewa Kucharska
Summary: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system with no cure and unclear etiology. This study aimed to identify SNPs associated with an increased risk of developing MS. The findings suggest that the GG AGO1 rs636832 and AA GEMIN4 rs7813 genotypes are associated with an increased risk of MS.
Article
Environmental Sciences
Ruirui Zhao, Shanshan Cai, Dingfang Lu, Pengfei Li, Shengyong Xu, Yuan Li
Summary: This study compared the genomes of wild and domesticated white-spotted bamboo sharks using resequencing data, revealing that the domesticated sample had a larger genome size and higher heterozygosity. Through the identification of microsatellite markers and SNPs, genetic differences between wild and domesticated populations were uncovered.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Catalina Molina, Natalia Cristina Aguirre, Pablo Alfredo Vera, Carla Valeria Filippi, Andrea Fabiana Puebla, Susana Noemi Marcucci Poltri, Norma Beatriz Paniego, Alberto Acevedo
Summary: The study optimized the identification of SNPs in sugarcane and recommended the use of long read size and paired-end reads, medium sequencing coverage, and Illumina NovaSeq6000 platform. Functional analysis showed that most of the SNPs landed within regulatory regions. The protocol demonstrated robustness in analyzing replicated genotypes.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Magdalena Niedzialkowska, Ewa Tarnowska, Joanna Ligmanowska, Bogumila Jedrzejewska, Tomasz Podgorski, Anna Radziszewska, Iwona Ratajczyk, Szilvia Kusza, Aleksei N. Bunevich, Gabriel Danila, Maryna Shkvyria, Tomasz Grzybowski, Marcin Wozniak
Summary: The study of genetic diversity and structure of wild boar populations in Central and Eastern Europe revealed five distinct phylogenetic clades with different contributions from various regions.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Wen Feng, Lei Zhou, Pengju Zhao, Heng Du, Chenguang Diao, Yu Zhang, Zhen Liu, Wenjiao Jin, Jian Yu, Jianlin Han, Edward Okoth, Raphael Mrode, Jian-Feng Liu
Summary: This study aimed to fill the gaps in understanding the evolution and genetic basis of African Suidae, particularly in relation to warthog resistance against African swine fever (ASF). The analysis of warthog and Kenyan domestic pig genomes revealed the adaptation of warthogs to the African environment and identified lactate dehydrogenase B (LDHB) as a potential tolerance gene to ASF. This study provides valuable resources and data support for future evolutionary research on African pigs and sheds light on the resistance mechanisms of warthogs against ASF.
Article
Plant Sciences
Zoe Andrijanic, Nelson Nazzicari, Hrvoje Sarcevic, Aleksandra Sudaric, Paolo Annicchiarico, Ivan Pejic
Summary: This study investigates the genetic diversity and structure of European soybean cultivars and American introductions registered in Europe, supporting optimal exploitation of genetic resources. Results show that the European soybean gene pool still has sufficient diversity due to differences in historical breeding practices and relatively short breeding period in Europe.
Article
Plant Sciences
Mbali Thembi Gumede, Abe Shegro Gerrano, Assefa Beyene Amelework, Albert Thembinkosi Modi
Summary: This study assessed the genetic diversity and population structure of 90 cowpea accessions using SNP markers. The results showed that cowpea has high tolerance to heat and drought stresses, making it important for improving crop production resilience. The study also revealed low genetic diversity and high homozygosity among cowpea accessions.
Article
Agriculture, Dairy & Animal Science
Samuele Bovo, Giuseppina Schiavo, Luca Fontanesi
Summary: This study investigated genetic variability in cattle to identify variants that might confer susceptibility or resistance to coronavirus diseases. The results highlight the importance of considering host genetic variability in designing One Health strategies for coronavirus prevention and control.
Article
Agriculture, Dairy & Animal Science
Mohamad Ballan, Giuseppina Schiavo, Samuele Bovo, Michele Schiavitto, Riccardo Negrini, Andrea Frabetti, Daniela Fornasini, Luca Fontanesi
Summary: In this study, SNP chip datasets were used to analyze Runs of Homozygosity (ROH) in different rabbit breeds. It was found that fancy breeds had a higher level of genomic inbreeding indicated by ROH and several ROH islands contained genes related to various traits.
Article
Multidisciplinary Sciences
Samuele Bovo, Valerio Joe Utzeri, Anisa Ribani, Valeria Taurisano, Giuseppina Schiavo, Luca Fontanesi
Summary: This study developed and tested a genotyping method using environmental DNA from honey to accurately identify the subspecies of honey bees and the entomological origin of honey.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Samuele Bovo, Anisa Ribani, Valerio Joe Utzeri, Valeria Taurisano, Gianmaria Bertarini, Luca Fontanesi
Summary: In this study, whole genome sequencing data from five canary lines or populations were analyzed to identify candidate genes associated with pigmentation variability in canary breeds and varieties. The study revealed genes involved in carotenoid-derived pigmentation variants and melanogenesis-related genes, with putative causative mutations identified in the MLPH gene. Additionally, other signatures of selection were found that may explain phenotypic differences between canary populations.
Letter
Food Science & Technology
Luca Fontanesi, Valeria Taurisano, Anisa Ribani, Valerio Joe Utzeri
Article
Genetics & Heredity
Francesca Bertolini, Anisa Ribani, Fabrizio Capoccioni, Luca Buttazzoni, Samuele Bovo, Giuseppina Schiavo, Massimo Caggiano, Max F. Rothschild, Luca Fontanesi
Summary: A genomic strategy was developed in this study to identify selective markers and highly differentiated genomic regions in gilthead seabream populations. The results highlighted the importance of controlling the genetic effect of breeding programs to avoid reducing genetic variability and increasing inbreeding levels.
Review
Agriculture, Dairy & Animal Science
Martina Zappaterra, Luigi Faucitano, Leonardo Nanni Costa
Summary: A large body of literature has focused on the welfare effects of transport-related factors on adult pigs, while less attention has been given to weaned piglets. However, it is crucial to understand how to safely transport weaned piglets, as they face unique challenges and risks. Despite the lack of scientific research on this topic, transporting piglets immediately after weaning is a common practice, leading to potential negative impacts on their health and welfare. This review discusses the main factors affecting the welfare of weaned piglets during transport and emphasizes the need for further research to provide scientific evidence for existing recommendations and regulations.
Article
Agriculture, Dairy & Animal Science
Anisa Ribani, Valeria Taurisano, Despoina Karatosidi, Giuseppina Schiavo, Samuele Bovo, Francesca Bertolini, Luca Fontanesi
Summary: The Greek Black Pig is the only indigenous pig breed in Greece with a solid black coat. This study found evidence of introgression from wild boars and admixture from other pig breeds in the past, enriching the genetic pool of the Greek Black Pig. A new MC1R allele with two missense mutations was identified, providing insights into the production of melanin pigments. This study highlights the importance of local genetic resources in uncovering unexpected genetic variants.
Article
Agriculture, Dairy & Animal Science
Mohamad Ballan, Samuele Bovo, Francesca Bertolini, Giuseppina Schiavo, Michele Schiavitto, Riccardo Negrini, Luca Fontanesi
Summary: In this study, genotyping and analysis revealed the genetic relationship between exterior traits and rabbit breeds. It was found that breeds with similar phenotypic traits shared common ancestries and specific genes associated with coat color and body size were identified. This study provides insights into the genetic events that led to the formation of rabbit breeds and the genetic mechanisms behind their phenotypic variability.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Veterinary Sciences
Anisa Ribani, Valeria Taurisano, Valerio Joe Utzeri, Luca Fontanesi
Summary: This study detected the DNA of small hive beetle and greater wax moth in 82 honey samples from Italy using PCR. Only one sample was positive for small hive beetle DNA, while about 66% of samples were positively amplified for greater wax moth DNA. The use of honey eDNA is important for controlling the spread of these pests.
VETERINARY SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Adrian Lopez-Catalina, Valentin Costes, Ramon Peiro-Pastor, Helene Kiefer, Oscar Gonzalez-Recio
Summary: Epigenetic marks can explain part of the phenotypic variance in animal breeding models. Nanopore sequencing shows high correlation with bisulphite sequencing in identifying DNA methylation marks. Different sequencing methods highlight differentially methylated genes and positions of economic interest in animal breeding.
