Article
Biology
Rongrong Ding, Rodrigo Savegnago, Jinding Liu, Nanye Long, Cheng Tan, Gengyuan Cai, Zhanwei Zhuang, Jie Wu, Ming Yang, Yibin Qiu, Donglin Ruan, Jianping Quan, Enqin Zheng, Huaqiang Yang, Zicong Li, Suxu Tan, Mohammed Bedhane, Robert Schnabel, Juan Steibel, Cedric Gondro, Jie Yang, Wen Huang, Zhenfang Wu
Summary: The SWine IMputation (SWIM) haplotype reference panel and web server provide a valuable resource for improving imputation and genetic discoveries in pigs. By developing a reference haplotype panel based on 2259 whole genome-sequenced animals representing 44 pig breeds, this study overcomes the limitation of low density genotyped variant sites, resulting in improved genetic mapping resolution. The use of this resource for genotype imputation demonstrates significant improvements in genetic mapping resolution.
COMMUNICATIONS BIOLOGY
(2023)
Article
Plant Sciences
Naihui Guo, Yakun Wang, Wei Chen, Shengjia Tang, Ruihu An, Xiangjin Wei, Shikai Hu, Shaoqing Tang, Gaoneng Shao, Guiai Jiao, Lihong Xie, Ling Wang, Zhonghua Sheng, Peisong Hu
Summary: By constructing a near-isogenic line and conducting genetic analysis, this study identified LOC_Os04g43910 as a potential target gene for the quantitative trait locus (QTL) qSE4, which controls the stigma exsertion rate (SER) in rice. Knocking out LOC_Os04g43910 resulted in significantly lower SER and altered hormone synthesis and signaling pathways. These findings contribute to a better understanding of the molecular mechanisms of SER and have implications for improving hybrid seed production.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Si Fengfeng, Fan Fengfeng, Wei Xiao, He Shihao, Li Xianlong, Peng Xiaojue, Li Shaoqing
Summary: This study explored the QTL for photosynthetic rate and biomass in wild rice through the analysis of backcross inbred lines and identified several novel QTL that are associated with these traits. Some of these QTL significantly improve photosynthetic rate, while others affect both photosynthetic rate and biomass. These findings provide new insights into the exploration of new genes and resources for yield potential in rice.
Article
Multidisciplinary Sciences
Liang Tong, Ying Zhou, Yixing Guo, Hui Ding, Donghai Ji
Summary: This study proposes a new QTL mapping strategy that can more accurately map QTLs of multiple traits while considering genotype errors. Simulation and real data analysis show that this method can improve the accuracy of parameter estimation.
Article
Fisheries
Jiamin Guo, Anqi Wang, Siqi Mao, Xiaoyan Xu, Jiale Li, Yubang Shen
Summary: This study constructed the first high-density genetic linkage map of black carp and identified QTL related to growth traits. The map provides valuable genomic resources for understanding economically important traits in black carp and can be used for comparative genomics and evolutionary studies.
Article
Plant Sciences
Zigang Liu, Xiaoyun Dong, Xiaodong Cao, Chunmei Xu, Jiaping Wei, Guoqiang Zhen, Jinxiong Wang, Hui Li, Xinlin Fang, Yin Wang, Hai Yan, Chao Mi, Caixia Zhao, Wenbo Mi
Summary: This study identified the genetic mechanism underlying the cold tolerance of winter rapeseed (Brassica napus) and discovered QTLs and candidate genes related to winter survival. These results are important for improving the cold tolerance and overwintering success of winter oilseed rape.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Plant Sciences
Xuejun Zhang, Yueming Ling, Wenli Yang, Minghua Wei, Zhenzhu Wang, Meihua Li, Yong Yang, Bin Liu, Hongping Yi, Yang-Dong Guo, Qiusheng Kong
Summary: This study constructed two F-2 populations using the DM-resistant accession PI 442177 and mapped QTLs conferring DM resistance. A high-density genetic map was generated and a major QTL DM9.1 was consistently detected at different growth stages. QTL-seq analysis validated the presence of DM9.1 and a KASP marker co-segregating with DM9.1 was successfully developed, providing valuable information for DM-resistant gene cloning and melon DM-resistant breeding programs.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Wenjing Yin, Tianqi Lu, Zhengai Chen, Tao Lu, Hanfei Ye, Yijian Mao, Yiting Luo, Mei Lu, Xudong Zhu, Xi Yuan, Yuchun Rao, Yuexing Wang
Summary: This study generated 120 recombinant inbred line populations to investigate salt tolerance in rice. By measuring germination under high salt conditions and mapping quantitative trait loci (QTL), a candidate gene LOC_Os12g25200 was found. It was narrowed down to a 192 kb region on chromosome 12 using a map-based cloning strategy, suggesting that LOC_Os12g25200 might negatively regulate salt tolerance in rice.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Horticulture
Wenbing Gong, Kefang Liu, Xinru Li, Lin Zhang, Nan Shen, Yinbing Bian, Yang Xiao
Summary: Mycelial growth is crucial for substrate colonization in mushrooms. This study identified a gene called LeHD1 that regulates mycelial growth in Lentinula edodes and demonstrated its functional role through overexpression and interference experiments.
SCIENTIA HORTICULTURAE
(2022)
Article
Plant Sciences
Carmen Santos, Davide Coelho Martins, Maria Jose Gonzalez-Bernal, Diego Rubiales, Maria Carlota Vaz Patto
Summary: In this study, a combination of phenotyping, gene expression, and linkage mapping was used to prioritize four candidate genes relevant for disease-resistance precision breeding in Lathyrus cicera. These genes are involved in adaptation to biotic stress, cellular and organelle homeostasis, and proteins directly involved in plant defense.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Fisheries
Lina Wu, Yang Yang, Xi Wang, Zhuoying Weng, Sijie Hua, Duo Li, Junhong Xia, Xiaochun Liu, Zining Meng
Summary: In this study, a high-density genetic linkage map was constructed for the giant grouper, and QTL mapping was performed for growth traits. Six growth-associated QTLs were identified, and candidate genes were validated. Additionally, RNA-seq analysis revealed differentially expressed genes that may play important roles in cell growth, signal transduction, metabolic pathways, and skeletal development.
Article
Biochemistry & Molecular Biology
Hongzheng Sun, Zeke Yuan, Fuhao Li, Qianqian Zhang, Ting Peng, Junzhou Li, Yanxiu Du
Summary: This study aimed to map the QTLs controlling grain chalkiness in japonica rice by crossing two cultivars and performing QTL-seq analysis. A QTL controlling grain chalkiness, qChalk1, was detected in both F-2 and BC1F2 segregating populations, and it was located in a 1.1 Mb genomic region on chromosome 1.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Fisheries
Jiamin Guo, Meng Zhang, Shentong Wang, Xiaoyan Xu, Yubang Shen, Jiale Li
Summary: In this study, a high-density linkage map was constructed for grass carp, which was used for mapping QTL of growth-related traits. Comparative genomic analysis revealed high synteny between grass carp and zebrafish.
Article
Genetics & Heredity
Shakti Prakash Mohanty, Deepak Kumar Nayak, Priyadarsini Sanghamitra, Saumya Ranjan Barik, Elssa Pandit, Abhisarika Behera, Dipti Ranjan Pani, Shibani Mohapatra, K. R. Reshmi Raj, Kartik Chandra Pradhan, Chita Ranjan Sahoo, Mihir Ranjan Mohanty, Chinmayee Behera, Alok Kumar Panda, Binod Kumar Jena, Lambodar Behera, Prasanta K. K. Dash, Sharat Kumar Pradhan
Summary: Seed vigor, an important performance parameter of seed quality, was studied in this research. A panel of genotypes representing different seedling growth parameters was created from 278 germplasm lines and showed a wide variation in traits. The panel was categorized into four genetic structure groups, showing the presence of linkage disequilibrium in the population. Using 143 SSR markers, a moderate to high level of diversity parameters was observed. Analysis methods such as principal component analysis, coordinate analysis, neighbor-joining tree, and cluster analysis showed correspondences between subpopulations and growth parameters. Marker-trait association analysis identified eight novel QTLs that can improve seed vigor in rice.
Article
Agriculture, Multidisciplinary
Harun Bektas
Summary: Root system architecture has gained attention due to climate change and abiotic stress on crops. The study investigated the genetic of seedling root system architecture and identified major loci on different chromosomes. The correlations between seedling and mature root traits and the newly identified QTL may be promising for unraveling the genetic structure of root traits and marker-assisted selection.
TURKISH JOURNAL OF AGRICULTURE AND FORESTRY
(2021)
Article
Genetics & Heredity
Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan L. Archibald, David A. Hume, Emily L. Clark
G3-GENES GENOMES GENETICS
(2019)
Article
Genetics & Heredity
Oswald Matika, Diego Robledo, Ricardo Pong-Wong, Stephen C. Bishop, Valentina Riggio, Heather Finlayson, Natalie R. Lowe, Annabelle E. Hoste, Grant A. Walling, Jorge del Pozo, Alan L. Archibald, John A. Woolliams, Ross D. Houston
Article
Genetics & Heredity
Kim M. Summers, Stephen J. Bush, Chunlei Wu, Andrew I. Su, Charity Muriuki, Emily L. Clark, Heather A. Finlayson, Lel Eory, Lindsey A. Waddell, Richard Talbot, Alan L. Archibald, David A. Hume
FRONTIERS IN GENETICS
(2020)
Article
Genetics & Heredity
Rebecca J. Bengtsson, Bryan A. Wee, Gonzalo Yebra, Rodrigo Bacigalupe, Eleanor Watson, Roberto M. C. Guedes, Magdalena Jacobson, Tomasz Stadejek, Alan L. Archibald, J. Ross Fitzgerald, Tahar Ait-Ali
MICROBIAL GENOMICS
(2020)
Correction
Virology
Christine Burkard, Tanja Opriessnig, Alan J. Mileham, Tomasz Stadejek, Tahar Ait-Ali, Simon G. Lillico, C. Bruce A. Whitelaw, Alan L. Archibald
JOURNAL OF VIROLOGY
(2020)
Article
Biology
Amanda Warr, Nabeel Affara, Bronwen Aken, Hamid Beiki, Derek M. Bickhart, Konstantinos Billis, William Chow, Lel Eory, Heather A. Finlayson, Paul Flicek, Carlos G. Giron, Darren K. Griffin, Richard Hall, Greg Hannum, Thibaut Hourlier, Kerstin Howe, David A. Hume, Osagie Izuogu, Kristi Kim, Sergey Koren, Haibou Liu, Nancy Manchanda, Fergal J. Martin, Dan J. Nonneman, Rebecca E. O'Connor, Adam M. Phillippy, Gary A. Rohrer, Benjamin D. Rosen, Laurie A. Rund, Carole A. Sargent, Lawrence B. Schook, Steven G. Schroeder, Ariel S. Schwartz, Ben M. Skinner, Richard Talbot, Elizabeth Tseng, Christopher K. Tuggle, Mick Watson, Timothy P. L. Smith, Alan L. Archibald
Article
Multidisciplinary Sciences
Prasun Dutta, Andrea Talenti, Rachel Young, Siddharth Jayaraman, Rebecca Callaby, Santosh Kumar Jadhav, Velu Dhanikachalam, Mayakannan Manikandan, Bhim B. Biswa, Wai Y. Low, John L. Williams, Elizabeth Cook, Phil Toye, Eileen Wall, Appolinaire Djikeng, Karen Marshall, Alan L. Archibald, Suresh Gokhale, Satish Kumar, David A. Hume, James G. D. Prendergast
NATURE COMMUNICATIONS
(2020)
Article
Genetics & Heredity
Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gazova, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan L. Archibald, Shannon M. Clarke, Brenda M. Murdoch, Emily L. Clark
FRONTIERS IN GENETICS
(2020)
Article
Biology
Carolina Penaloza, Alejandro P. Gutierrez, Lel Eory, Shan Wang, Ximing Guo, Alan L. Archibald, Tim P. Bean, Ross D. Houston
Summary: A chromosome-level assembly for the Pacific oyster (C. gigas) was created and annotated, providing a valuable resource for genetics and genomics studies, as well as selective breeding in aquaculture.
Article
Biology
Stephen Meek, Tom Watson, Lel Eory, Gus McFarlane, Felicity J. Wynne, Stephen McCleary, Laura E. M. Dunn, Emily M. Charlton, Chloe Craig, Barbara Shih, Tim Regan, Ryan Taylor, Linda Sutherland, Anton Gossner, Cosmin Chintoan-Uta, Sarah Fletcher, Philippa M. Beard, Musa A. Hassan, Finn Grey, Jayne C. Hope, Mark P. Stevens, Monika Nowak-Imialek, Heiner Niemann, Pablo J. Ross, Christine Tait-Burkard, Sarah M. Brown, Lucas Lefevre, Gerard Thomson, Barry W. McColl, Alistair B. Lawrence, Alan L. Archibald, Falko Steinbach, Helen R. Crooke, Xuefei Gao, Pentao Liu, Tom Burdon
Summary: This study investigates the potential of porcine pluripotent stem cells to provide a limitless source of macrophages, demonstrating their molecular and functional characteristics, as well as their susceptibility to infection by pig pathogens. The study also shows the successful application of CRISPR/Cas9 gene editing in these cells, presenting new opportunities for researching host-pathogen interactions in pigs.
Article
Veterinary Sciences
Hamish A. Salvesen, Fiona A. Sargison, Alan L. Archibald, Tahar Ait-Ali
Summary: Research suggests that Lawsonia intracellularis disrupts host autophagy response in the ileum, potentially aiding in bacterial propagation and pathogenesis by disturbing the normal intestinal homeostasis.
VETERINARY RESEARCH COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Mazdak Salavati, Shernae A. Woolley, Yennifer Cortes Araya, Michelle M. Halstead, Claire Stenhouse, Martin Johnsson, Cheryl J. Ashworth, Alan L. Archibald, Francesc X. Donadeu, Musa A. Hassan, Emily L. Clark
Summary: This research identified regulatory sequences in the pig genome through Omni-ATAC-Seq analysis of semitendinosus muscle from 24 male piglets. Over 50% of the open chromatin regions were found near known transcription start sites. Differential analysis revealed genomic regions with significantly different chromatin accessibility across developmental time points.
G3-GENES GENOMES GENETICS
(2022)
Review
Biotechnology & Applied Microbiology
Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kuhn, Sigbjorn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle, Elisabetta Giuffra
Article
Biotechnology & Applied Microbiology
Richard I. Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald, David W. Burt
Correction
Agriculture, Dairy & Animal Science
Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P. M. A. Crooijmans, Natalia Zinovieva, Lawrence B. Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodalia Dias, Peter Dovc, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A. M. Groenen, Lusheng Huang, Hendrik-Jan Megens
GENETICS SELECTION EVOLUTION
(2020)