Article
Agronomy
Gabriele Magris, Serena Foria, Silvano Ciani, Dipak K. Santra, Ombretta Polenghi, Virna Cerne, Michele Morgante, Gabriele Di Gaspero
Summary: This study used a genome sequencing technique to investigate the genome composition of broomcorn millet, and found that registered varieties have incomplete genetic purification and lack genetic diversity.
Review
Plant Sciences
Jagesh Kumar Tiwari, Suresh Reddy Yerasu, Nagendra Rai, Dhananjaya P. Singh, Achuit K. Singh, Suhas G. Karkute, Prabhakar M. Singh, Tusar K. Behera
Summary: Tomatoes are important vegetable crops, and genomics-assisted breeding shows great potential in this field. With the rapid development and cost reduction of sequencing technologies, as well as the use of high-throughput genotyping platforms and bioinformatics tools, the tomato genome has been decoded and extensively studied, providing valuable information for breeding programs. Genomics-assisted breeding has made progress in identifying genes and SNP markers associated with agronomic traits, and the genomic selection method is expected to improve breeding efficiency and genetic gain.
CRITICAL REVIEWS IN PLANT SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jae-Eun Oh, Ji-Eun Kim, Jangmi Kim, Myoung-Hee Lee, Keunpyo Lee, Tae-Ho Kim, Sung-Hwan Jo, Jeong-Hee Lee
Summary: This study developed a genome-wide set of KASP markers for marker-assisted recurrent selection in the tetraploid minor crop perilla. By using genotyping-by-sequencing to construct high-resolution linkage maps of two F2 populations, 96 genome-wide markers were selected for MARS. The accuracy of markers was confirmed using a high-throughput Fluidigm system, providing a foundation for marker-assisted backcrossing and the development of new varieties of perilla.
MOLECULAR GENETICS AND GENOMICS
(2023)
Review
Plant Sciences
Federico Scossa, Saleh Alseekh, Alisdair R. Fernie
Summary: Our agricultural systems are facing the urgent challenge of feeding a growing global population, requiring a better understanding of plant genetic and phenotypic diversity. Recent advances in plant genomics, combined with molecular profiling approaches such as genomics, transcriptomics, and metabolomics, offer insights into the complex architecture of agricultural traits and guide crop breeding strategies.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Review
Genetics & Heredity
Faheem Shehzad Baloch, Muhammad Tanveer Altaf, Waqas Liaqat, Mehmet Bedir, Muhammad Azhar Nadeem, Gonul Comertpay, Nergiz Coban, Ephrem Habyarimana, Celaleddin Barutcular, Ibrahim Cerit, Ndomelele Ludidi, Tolga Karakoy, Muhammad Aasim, Yong Suk Chung, Muhammad Amjad Nawaz, Rustu Hatipoglu, Kagan Kokten, Hyeon-Jin Sun
Summary: Marker-assisted breeding has greatly improved the development of high-yield, disease-resistant, and climate-resilient crops, contributing to agricultural productivity.
FRONTIERS IN GENETICS
(2023)
Article
Agronomy
Goro Ishikawa, Hiroaki Sakai, Nobuyuki Mizuno, Elena Solovieva, Tsuyoshi Tanaka, Kazuki Matsubara
Summary: This study developed core marker sets for wheat and barley, which can efficiently capture polymorphisms across the entire genome and accelerate breeding processes in a cost-effective manner.
Article
Oncology
Sydney R. Grant, Spencer R. Rosario, Andrew D. Patentreger, Nico Shary, Megan E. Fitzgerald, Prashant K. Singh, Barbara A. Foster, Wendy J. Huss, Lei Wei, Gyorgy Paragh
Summary: Mutations in healthy skin occur in specific areas of the genome known as mutation hotspots, and these mutations accumulate over time, potentially leading to skin cancer. To study these mutations, we have developed an algorithm that formats mutation data into targetable genomic segments for sequencing experiments. Our algorithm significantly improves the efficiency of mutation capture compared to traditional methods. Our web application, hotSPOT, provides a valuable resource for researchers to design custom panels and study mutations in healthy tissues and cancer.
Article
Agronomy
Juan Li, Rui Han, Ruonan Li, Qiang Xu, Mingzhu Li, Yue Tang, Jixiang Li, Xi Wang, Zhao Li, Qing Li, Zaiwen Feng, Lin Li
Summary: This study presents a new multiplex targeted genotyping and epigenotyping system called iBP-seq, which allows efficient detection of genotypes and methylation levels. It can be used for building linkage maps, fine mapping of quantitative-trait loci, and detecting genome editing mutations at a low cost. An automated bioinformatics pipeline is developed for primer design, genotyping and epigenotyping analysis, and result visualization.
Article
Biotechnology & Applied Microbiology
Alexandra Carrier, Julien Prunier, William Poisson, Mallorie Trottier-Lavoie, Isabelle Gilbert, Maria Cavedon, Kisun Pokharel, Juha Kantanen, Marco Musiani, Steeve D. Cote, Vicky Albert, Joelle Taillon, Vincent Bourret, Arnaud Droit, Claude Robert
Summary: This study reports the development of a SNP-array for the endangered Rangifer tarandus using a multi-platform sequencing approach. A total of 63,336 SNPs were selected from a comprehensive catalog of SNPs detected in diverse populations. This SNP-array design allows for the assessment of genetic metrics related to population structure, inbreeding, and sex determination, and is of great importance for conservation planning.
Review
Agronomy
Congwei Sun, Huiting Hu, Yongzhen Cheng, Xi Yang, Qi Qiao, Canguan Wang, Leilei Zhang, Daiying Chen, Simin Zhao, Zhongdong Dong, Feng Chen
Summary: Common wheat contributes to 20% of the total calorie intake in human diet. Recent advances in whole-genome sequencing have provided new opportunities for uncovering genetic variations in wheat traits and accelerating breeding strategies with the assistance of genomics. Combining traditional breeding, marker-assisted selection, and genomic selection with high-density SNP markers can enhance the breeding process and increase genetic gain. Genomics-assisted breeding is becoming the preferred strategy for developing superior wheat cultivars with traits such as high yield, nutritional quality, and climate resilience.
Article
Biodiversity Conservation
Stefan Gavriliuc, Salman Reza, Chanwoori Jeong, Fitsum Getachew, Philip D. McLoughlin, Jocelyn Poissant
Summary: The development of high-throughput sequencing has led to a shift in wildlife genetics towards using single nucleotide polymorphisms (SNPs) instead of microsatellites. However, genotyping large numbers of SNPs from non-invasive samples remains challenging due to the requirement for relatively large amounts of DNA. In this study, the efficacy of a target enrichment method called Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data from feral horses using DNA isolated from fecal swabs was assessed. The results show that ATG is suitable for non-invasive targeted SNP genotyping and has the potential to facilitate further research in equids and related species.
CONSERVATION GENETICS RESOURCES
(2022)
Article
Plant Sciences
Vincent P. Reyes, Rosalyn B. Angeles-Shim, Merlyn S. Mendioro, Ma Carmina C. Manuel, Ruby S. Lapis, Junghyun Shim, Hidehiko Sunohara, Shunsaku Nishiuchi, Mayumi Kikuta, Daigo Makihara, Kshirod K. Jena, Motoyuki Ashikari, Kazuyuki Doi
Summary: This study successfully introgressed and stacked major yield QTLs Gn1a and WFP into selected NERICA cultivars using marker-assisted backcross breeding, leading to improvements in rice yield traits. The combination of marker-assisted selection and phenotypic evaluation at BC3F4 and BC3F5 generations effectively selected lines with target alleles and traits. Genotyping-by-sequencing validated the introgression and demonstrated the potential of utilizing yield QTLs and marker-assisted selection to improve rice cultivars.
Review
Plant Sciences
Mahendar Thudi, Ramesh Palakurthi, James C. Schnable, Annapurna Chitikineni, Susanne Dreisigacker, Emma Mace, Rakesh K. Srivastava, C. Tara Satyavathi, Damaris Odeny, Vijay K. Tiwari, Hon-Ming Lam, Yan Bin Hong, Vikas K. Singh, Guowei Li, Yunbi Xu, Xiaoping Chen, Sanjay Kaila, Henry Nguyen, Sobhana Sivasankar, Scott A. Jackson, Timothy J. Close, Wan Shubo, Rajeev K. Varshney
Summary: Climate change has had a serious impact on agriculture in the past 40 years, and there is a need to use genomic breeding methods to accelerate the development of crops with climate resilience and high nutritional value.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Article
Genetics & Heredity
Malachy T. Campbell, Haixiao Hu, Trevor H. Yeats, Lauren J. Brzozowski, Melanie Caffe-Treml, Lucia Gutierrez, Kevin P. Smith, Mark E. Sorrells, Michael A. Gore, Jean-Luc Jannink
Summary: The study evaluated the use of TGRMs to accommodate information on intermediate molecular phenotypes and predict total lipid content in oat seed. The MK-TGRM-BLUP approach significantly outperformed MT-gBLUP, highlighting the utility of TGRMs to accommodate information on endophenotypes and improve genomic prediction for a conventional agronomic trait.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Michael Schneider, Federico Casale, Benjamin Stich
Summary: This new method estimates recombination rate by using allele frequency differences and physical distance of neighboring polymorphisms, which significantly reduces cost compared to traditional mapping. Simulations and experiments on barley populations showed high correlations between this new pool genetic mapping approach and conventional mapping. Therefore, this method provides reliable genetic map positions and recombination rate estimations.
Article
Agronomy
Frederick G. Sunstrum, Wubishet A. Bekele, Charlene P. Wight, Weikai Yan, Yuanhong Chen, Nicholas A. Tinker
Article
Biology
Peter J. Maughan, Rebekah Lee, Rachel Walstead, Robert J. Vickerstaff, Melissa C. Fogarty, Cory R. Brouwer, Robert R. Reid, Jeremy J. Jay, Wubishet A. Bekele, Eric W. Jackson, Nicholas A. Tinker, Tim Langdon, Jessica A. Schlueter, Eric N. Jellen
Article
Agronomy
Aida Z. Kebede, Belayneh Admassu-Yimer, Wubishet A. Bekele, Tyler Gordon, J. Michael Bonman, Ebrahiem Babiker, Yue Jin, Sam Gale, Charlene P. Wight, Nicholas A. Tinker, Jim G. Menzies, Aaron D. Beattie, Jennifer Mitchell Fetch, Thomas G. Fetch, Kathy Esvelt Klos, Curt A. McCartney
THEORETICAL AND APPLIED GENETICS
(2020)
Article
Multidisciplinary Sciences
Robert G. Latta, Wubishet A. Bekele, Charlene P. Wight, Nicholas A. Tinker
SCIENTIFIC REPORTS
(2019)
Article
Plant Sciences
Jun Zhao, Aida Z. Kebede, Wubishet A. Bekele, Jim G. Menzies, James Chong, Jennifer W. Mitchell Fetch, Nicholas A. Tinker, Aaron D. Beattie, Yuan-Ying Peng, Curt A. McCartney
Article
Plant Sciences
Greg Mellers, Ian Mackay, Sandy Cowan, Irene Griffiths, Pilar Martinez-Martin, Jesse A. Poland, Wubishet Bekele, Nicholas A. Tinker, Alison R. Bentley, Catherine J. Howarth
Article
Plant Sciences
Aida Z. Kebede, Wubishet A. Bekele, Jennifer W. Mitchell Fetch, Aaron D. Beattie, Shiaoman Chao, Nicholas A. Tinker, Thomas G. Fetch, Curt A. McCartney
Article
Agronomy
Honghai Yan, Pingping Zhou, Yun Peng, Wubishet A. Bekele, Changzhong Ren, Nicholas A. Tinker, Yuanying Peng
THEORETICAL AND APPLIED GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Xianran Li, Tingting Guo, Jinyu Wang, Wubishet A. Bekele, Sivakumar Sukumaran, Adam E. Vanous, James P. McNellie, Laura E. Tibbs-Cortes, Marta S. Lopes, Kendall R. Lamkey, Mark E. Westgate, John K. Mckay, Sotirios V. Archontoulis, Matthew P. Reynolds, Nicholas A. Tinker, Patrick S. Schnable, Jianming Yu
Summary: The article discusses the mechanisms involved in gene-environment interplay and phenotypic plasticity, emphasizing the importance of establishing an integrated framework with environmental dimension and using an environmental index for genome-wide association studies and performance prediction in crop breeding.
Article
Agronomy
F. J. Canales, G. Montilla-Bascon, W. A. Bekele, C. J. Howarth, T. Langdon, N. Rispail, N. A. Tinker, E. Prats
Summary: Genomic analysis of Mediterranean oats reveals high genetic diversity and adaptation loci; an interactive map resource combining genetic and phenotypic data was created; distinct genetic differences and adaptation loci were identified in red and white oat types from the Mediterranean region.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Food Science & Technology
Kathy Esvelt Klos, Belayneh A. Yimer, Catherine J. Howarth, Michael S. McMullen, Mark E. Sorrells, Nicholas A. Tinker, Weikai Yan, Aaron D. Beattie
Summary: This study aimed to characterize the genetic architecture of traits related to milling quality by identifying quantitative trait loci contributing to variation among a diverse collection of elite and foundational spring oat lines important to North American oat breeding programs. Fifty-seven QTL influencing one or more of the milling quality related traits were identified, with fourteen QTL mapped influencing mean and variance across location years. The most prominent QTL was identified on chromosome 4D at approximately 212 cM, influencing the mean levels of all traits.
Article
Genetics & Heredity
Mohannad Mahmoud, Zhou Zhou, Rajvinder Kaur, Wubishet Bekele, Nicholas A. Tinker, Jaswinder Singh
Summary: Oat is an important cereal, but its genetic and genomic studies have been limited due to its large and complex genomes. In this study, transposons were introduced into the oat genome to develop a gene tagging system. Stable transgenic events were obtained, and Ds-tagged sites in the oat genome were identified. This gene tagging system can facilitate functional genomic studies in oat.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2022)
Article
Biology
Nicholas A. Tinker, Charlene P. Wight, Wubishet A. Bekele, Weikai Yan, Eric N. Jellen, Nikos Tsardakas Renhuldt, Nick Sirijovski, Thomas Lux, Manuel Spannagl, Martin Mascher
Summary: This study utilized a newly sequenced and annotated oat reference genome to locate and characterize QTLs affecting agronomic and grain-quality traits in oat populations. The results revealed significant associations between the positions of candidate genes and QTLs for various traits. Additionally, the study identified common chromosome rearrangements in oat that affect the segregation and localization of QTLs in breeding programs.
COMMUNICATIONS BIOLOGY
(2022)
Article
Mathematical & Computational Biology
Victoria C. Blake, Margaret R. Woodhouse, Gerard R. Lazo, Sarah G. Odell, Charlene P. Wight, Nicholas A. Tinker, Yi Wang, Yong Q. Gu, Clay L. Birkett, Jean-Luc Jannink, Dave E. Matthews, David L. Hane, Steve L. Michel, Eric Yao, Taner Z. Sen
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2019)