Article
Biochemistry & Molecular Biology
Daronja Trense, Thomas L. Schmidt, Qiong Yang, Jessica Chung, Ary A. Hoffmann, Klaus Fischer
Summary: This study investigated gene flow and genetic structure of the Sooty Copper butterfly in the Alpine otz valley system in Austria. High gene flow levels were found, influenced by anthropogenic as well as natural structures, particularly ravines, forests, and roads. Additionally, loci potentially under thermal selection were detected.
Article
Psychiatry
Ming-Chen Tsai, Chia-Lin Tsai, Chih-Sung Liang, Yu-Kai Lin, Guan-Yu Lin, Chia-Kuang Tsai, Po-Kuan Yeh, Yi Liu, Kuo-Sheng Hung, Fu-Chi Yang
Summary: This study investigates the genetic association between depression and migraine in the Han Chinese population in Taiwan. The results suggest that variants in the CDH4 intron region, NTRK3-AS1 downstream region, and between LINC01918 and GPR45 are associated with depression. Additionally, 20 susceptibility loci are found within different migraine subtypes. These findings provide genetic candidates for further research on the comorbidity of depression and migraine.
FRONTIERS IN PSYCHIATRY
(2023)
Article
Biotechnology & Applied Microbiology
Nicholas P. Howard, Michela Troggio, Charles-Eric Durel, Helene Muranty, Caroline Denance, Luca Bianco, John Tillman, Eric van de Weg
Summary: This study assessed the concordance and accuracy of Illumina Infinium and Affymetrix Axiom SNP array data in apple genomes. The majority of the data was found to be compatible, although intense data filtering and curation were required for data integration. This in-depth analysis may provide valuable insights for future work on SNP array data integration and interpretation, as well as for probe/platform development.
Article
Biochemistry & Molecular Biology
Maria Radanova, Mariya Levkova, Galya Mihaylova, Rostislav Manev, Margarita Maneva, Rossen Hadgiev, Nikolay Conev, Ivan Donev
Summary: There is a growing interest in studying single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, as they may be associated with susceptibility, prognosis, and treatment response in colorectal cancer (CRC). These miRNA-SNPs could serve as non-invasive biomarkers for early detection of CRC. However, contradictory findings have been reported when different research groups investigated the same SNP in a gene for a specific miRNA, highlighting the need for more case-control studies involving participants from different ethnic backgrounds. According to our review, three miRNA-SNPs - miR-146a rs2910164, miR-27a rs895819, and miR-608 rs4919510 - appear to be promising prognostic, diagnostic, and predictive biomarkers for CRC.
Article
Plant Sciences
Julio Cesar F. Elias, Maria Celeste Goncalves-Vidigal, Andrea Ariani, Giseli Valentini, Maria da Conceicao Martiniano-Souza, Mariana Vaz Bisneta, Paul Gepts
Summary: Abiotic stress is a limiting factor for common bean production globally. Based on genotyping-by-sequencing analysis, associations between SNPs and bioclimatic indexes were discovered on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, Pv09, Pv10, and Pv11 of common bean. Candidate genes related to temperature and precipitation were identified, suggesting the potential for developing drought-tolerant cultivars through marker-assisted selection.
Article
Agriculture, Dairy & Animal Science
Peng Wang, Wentao Li, Ziyi Liu, Xiaoyun He, Rong Lan, Yufang Liu, Mingxing Chu
Summary: This study analyzed the association between PPP2R5C and SLC39A5 gene polymorphisms and litter size in Yunshang black goats. The results showed that the polymorphisms PPP2R5C g.65977743C>T and SLC39A5 g.50676693T>C were significantly associated with the litter size of the third parity in Yunshang black goats. Further experiments confirmed that individuals with CC genotype of PPP2R5C and TT genotype of SLC39A5 had higher expression of these genes in goat ovarian tissues. These findings provide new insights into candidate gene selection for marker-assisted selection in goats.
Article
Agronomy
Rahele Panhabadi, Asadollah Ahmadikhah, Naser Farrokhi, Nadali Bagheri
Summary: This study conducted a genome-wide association study (GWAS) to identify genetic regions and candidate genes associated with seed germination and post-germination related seedling traits in rice. The results revealed several significant quantitative trait loci (QTLs) and candidate genes that play a role in regulating these traits.
Article
Biotechnology & Applied Microbiology
L. D. Bertola, M. Vermaat, F. Lesilau, M. Chege, P. N. Tumenta, E. A. Sogbohossou, O. D. Schaap, H. Bauer, B. D. Patterson, P. A. White, H. H. de Iongh, J. F. J. Laros, K. Vrieling
Summary: This study used low-depth whole genome sequencing to analyze ten lions sampled across their geographic range, resulting in the discovery of over 150,000 single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed the split between northern and southern populations, as well as four population clusters on a local scale. A SNP panel was designed and tested on over 200 lions, allowing individuals to be assigned to one of the four major clades and providing detailed delineation of these clades.
Article
Plant Sciences
Xujiang Wu, Junchan Wang, Di Wu, Wei Jiang, Zhifu Gao, Dongsheng Li, Rongling Wu, Derong Gao, Yong Zhang
Summary: A genome-wide association study of sharp eyespot resistance in 262 wheat varieties from all China wheat regions identified two QTLs and 5 significantly related SNP loci. Results showed that only 6.5% of the varieties were resistant to sharp eyespot, with varieties from the middle and lower Yangtze River exhibiting higher resistance than those from Huanghuai wheat zone.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Giuseppe Silvestri, Carla Canedo-Ribeiro, Maria Serrano-Albal, Remi Labrecque, Patrick Blondin, Steven G. Larmer, Gabriele Marras, Desmond A. R. Tutt, Alan H. Handyside, Marta Farre, Kevin D. Sinclair, Darren K. Griffin
Summary: The study demonstrated that screening for aneuploid embryos using PGT-A can significantly improve pregnancy and live birth rates in cattle IVP programs. Analyzing 1713 cattle embryos revealed that aneuploid embryos have lower chances of establishing pregnancies and giving rise to live births compared to euploid embryos.
Article
Biochemistry & Molecular Biology
Hui-Jeong An, Sung-Hwan Cho, Han-Sung Park, Ji-Hyang Kim, Young-Ran Kim, Woo-Sik Lee, Jung-Ryeol Lee, Seong-Soo Joo, Eun-Hee Ahn, Nam-Keun Kim
Summary: This study investigated the genetic association between recurrent pregnancy loss (RPL) and microRNA (miRNA) polymorphisms in miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G in Korean women. The study identified specific genotypes of miR-10a and miR-499 that are associated with increased RPL risk.
Article
Nutrition & Dietetics
Yu-Min Huang, Weu Wang, Po-Pin Hsieh, Hsin-Hung Chen
Summary: The genetic effect of obesity plays a significant role in the development of an obesogenic environment. Genes rs712221 and rs2016520 are associated with obesity and show a synergistic effect, increasing the risk of obesity.
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
Agronomy
Mohammad Wali Salari, Patrick Obia Ongom, Rima Thapa, Henry T. Nguyen, Tri D. Vuong, Katy Martin Rainey
Summary: This study investigated the genetic control of sucrose, raffinose, and stachyose in soybeans, identifying several quantitative trait loci (QTLs) on chromosomes 1, 3, and 6. These QTLs explain variance in the levels of these carbohydrates, with potential candidate genes involved in seed development and plant growth.
Article
Biochemistry & Molecular Biology
Jinhan Zhao, Xiaoyi Xu, Xinhuan Wei, Shuang Zhang, Hangfei Xu, Xiaodie Wei, Yang Zhang, Jing Zhang
Summary: This study identified a significant correlation between SAMM50 genetic polymorphism and NAFLD in the elderly, contributing to a better understanding of the impact of age and genetics on this condition. Additionally, it provides a potential predictive model for early clinical warning of NAFLD.
Article
Biotechnology & Applied Microbiology
Nga T. T. Vu, Kyall R. Zenger, Jarrod L. Guppy, Melony J. Sellars, Catarina N. S. Silva, Shannon R. Kjeldsen, Dean R. Jerry
Article
Fisheries
Monal M. Lal, Salote S. Waqairatu, Kyall R. Zenger, Maria G. Nayfa, Timothy D. Pickering, Avinash Singh, Paul C. Southgate
Summary: Genetic analysis of the GIFT strain of Nile tilapia in Fiji revealed mild declines in genetic diversity, with some ponds showing signs of reduced effective population size and allelic diversity. Management practices and potential wild interbreeding were identified as factors influencing genetic structure and relatedness within the broodstock nucleus. Regular genetic monitoring and evaluation of performance are recommended to preserve valuable genetic diversity in the long term.
Correction
Biotechnology & Applied Microbiology
Nga T. T. Vu, Kyall R. Zenger, Jarrod L. Guppy, Melony J. Sellars, Catarina N. S. Silva, Shannon R. Kjeldsen, Dean R. Jerry
Article
Evolutionary Biology
Nga T. T. Vu, Kyall R. Zenger, Catarina N. S. Silva, Jarrod L. Guppy, Dean R. Jerry
Summary: The giant black tiger shrimp (Penaeus monodon) exhibits strong genetic structure among populations in the Indo-Pacific, with varying levels of genetic diversity and migration events. Putatively adaptive single nucleotide polymorphisms were identified, suggesting potential roles in cellular processes, pigmentation, and immune response. This study provides insights with direct implications for aquaculture and fishery management practices related to P. monodon.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Environmental Sciences
Shelby R. Marhoefer, Kyall R. Zenger, Jan M. Strugnell, Murray Logan, Madeleine J. H. van Oppen, Carly D. Kenkel, Line K. Bay
Summary: This study conducted in the southern Great Barrier Reef, Australia, investigated the phenotypic variation of the common brooding coral Pocillopora damicornis between depth habitats, revealing strong population-by-habitat interactions and potential genetic basis for adaptation and acclimatization. The results suggest that local adaptation and acclimatization may contribute to the survival and response of corals to changing environmental conditions, highlighting the importance of environmental factors and symbiont composition in determining the adaptive potential of corals.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Fisheries
C. Massault, D. B. Jones, K. R. Zenger, J. M. Strugnell, R. Barnard, D. R. Jerry
Summary: A genetic tool for resolving pedigree relationships in the silver-lipped pearl oyster, Pinctada maxima, has been developed and shown to accurately assign progeny to parents with a 95% confidence using a panel of 50 or more SNPs.
AQUACULTURE REPORTS
(2021)
Article
Fisheries
Dean R. Jerry, David B. Jones, Marie Lillehammer, Cecile Massault, Shannon Loughnan, Holly S. Cate, Paul J. Harrison, Jan M. Strugnell, Kyall R. Zenger, Nicholas A. Robinson
Summary: The article discusses the breeding programs for barramundi based on genomic selection and pedigree-based selection, finding that genomic selection yields better results in terms of genetic gains. Through experiments with various breeding strategies, it was discovered that genomic-based breeding programs can achieve higher genetic gains in different environments compared to pedigree-based programs.
Review
Ecology
Tiffany A. Kosch, Anthony W. Waddle, Caitlin A. Cooper, Kyall R. Zenger, Dorian J. Garrick, Lee Berger, Lee F. Skerratt
Summary: The rate of global wildlife extinctions is increasing, and conservation breeding programs are needed to preserve many species. However, preserving the genetic diversity of founder populations may also preserve characteristics that make them vulnerable to extinction. Targeted genetic intervention (TGI) is introduced as an alternative approach to promote traits that enable species to persist in the face of threats by changing the incidence of alleles that impact fitness.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Genetics & Heredity
Roger Huerlimann, Jeff A. Cowley, Nicholas M. Wade, Yinan Wang, Naga Kasinadhuni, Chon-Kit Kenneth Chan, Jafar Jabbari, Kirby Siemering, Lavinia Gordon, Matthew Tinning, Juan D. Montenegro, Gregory E. Maes, Melony J. Sellars, Greg J. Coman, Sean McWilliam, Kyall R. Zenger, Mehar S. Khatkar, Herman W. Raadsma, Dallas Donovan, Gopala Krishna, Dean R. Jerry
Summary: This study presents the draft genome assembly of an Australian black tiger shrimp, revealing the presence of endogenous viral elements. The discovery of these elements has implications for disease detection and the understanding of shrimp immune mechanisms.
G3-GENES GENOMES GENETICS
(2022)
Article
Fisheries
Cecile Massault, Cara Jeffrey, David B. Jones, Roger Barnard, Jan M. Strugnell, Kyall R. Zenger, Dean R. Jerry
Summary: This study validated the efficiency of using the swab technique to collect DNA for breeding programs of pearl oysters, and demonstrated that this method reliably collects sufficient quantity and quality of DNA for accurate pedigree reconstruction.
Correction
Multidisciplinary Sciences
Roger Huerlimann, Nicholas M. Wade, Lavinia Gordon, Juan D. Montenegro, Jake Goodall, Sean McWilliam, Matthew Tinning, Kirby Siemering, Erika Giardina, Dallas Donovan, Melony J. Sellars, Jeff A. Cowley, Kelly Condon, Greg J. Coman, Mehar S. Khatkar, Herman W. Raadsma, Gregory E. Maes, Kyall R. Zenger, Dean R. Jerry
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Donald T. McKnight, Roger Huerlimann, Deborah S. Bower, Lin Schwarzkopf, Ross A. Alford, Kyall R. Zenger
Summary: The bacterial and fungal microbiomes of four Australian frog species were examined to understand their role in infection dynamics. Both microbial communities were correlated, suggesting mutual influences. There was mixed evidence of associations between richness and the fungal disease, with high richness potentially providing protection.
Article
Fisheries
Nga T. T. Vu, Dean R. Jerry, Richard C. Edmunds, David B. Jones, Kyall R. Zenger
Summary: This study introduces five low-density SNP panels for the giant black tiger shrimp, which can improve aquaculture practices and fishery management strategies by enhancing diversity, provenance, and pedigree determination.
Article
Biodiversity Conservation
Brooke L. L. Whitelaw, David B. B. Jones, Jarrod Guppy, Peter Morse, Jan M. M. Strugnell, Ira R. R. Cooke, Kyall Zenger
Summary: The study presents the first linkage map of a cephalopod species, H. maculosa, providing valuable insights into the evolution of cephalopod genomes.