Article
Plant Sciences
Catja Selga, Alexander Koc, Aakash Chawade, Rodomiro Ortiz
Summary: The study introduces a pipeline to reduce genotyping costs by decreasing the number of SNPs and individuals, as well as pruning for linkage disequilibrium. Both GWAS and GS analyses can be performed without loss of information, making them applicable to large potato breeding populations.
Article
Clinical Neurology
Gie Ken-Dror, Ioana Cotlarciuc, Ida Martinelli, Elvira Grandone, Sini Hiltunen, Erik Lindgren, Maurizio Margaglione, Veronique Le Cam Duchez, Aude Bagan Triquenot, Marialuisa Zedde, Michelangelo Mancuso, Ynte M. Ruigrok, Thomas Marjot, Brad Worrall, Jennifer J. Majersik, Tiina M. Metso, Jukka Putaala, Elena Haapaniemi, Susanna M. Zuurbier, Matthijs C. Brouwer, Serena M. Passamonti, Maria Abbattista, Paolo Bucciarelli, Braxton D. Mitchell, Steven J. Kittner, Robin Lemmens, Christina Jern, Emanuela Pappalardo, Paolo Costa, Marina Colombi, Diana Aguiar de Sousa, Sofia Rodrigues, Patricia Canhao, Aleksander Tkach, Rosa Santacroce, Giovanni Favuzzi, Antonio Arauz, Donatella Colaizzo, Kostas Spengos, Amanda Hodge, Reina Ditta, Alessandro Pezzini, Stephanie Debette, Jonathan M. Coutinho, Vincent Thijs, Katarina Jood, Guillaume Pare, Turgut Tatlisumak, Jose M. Ferro, Pankaj Sharma
Summary: A genome-wide association study identified new genetic variants influencing susceptibility to CVT, with the discovery validated in an independent European cohort. These findings provide important new insights into the pathophysiology of CVT.
ANNALS OF NEUROLOGY
(2021)
Article
Fisheries
Antoine Jourdan, Romain Morvezen, Florian Enez, Pierrick Haffray, Adeline Lange, Emilie Vetois, Francois Allal, Florence Phocas, Jerome Bugeon, Lionel Degremont, Pierre Boudry
Summary: Selective breeding programs have been initiated for the Pacific oyster Crassostrea gigas, using genomic tools to improve growth and disease resistance. The study evaluated the potential of genomic selection (GS) for growth-related and shell color traits in commercially selected populations. The results showed a high correlation between growth-related traits and low correlation with color traits. The accuracy of prediction was higher with the genomic model compared to the classical model, indicating the potential of GS in mixed-family breeding programs for C. gigas.
Article
Genetics & Heredity
Shirin Rahimmadar, Mokhtar Ghaffari, Mahdi Mokhber, John L. Williams
Summary: The assessment of LD structure and Ne in different water buffalo breeds revealed potential for the use of Affymetrix Axiom 90 K SNP genomic array in GWAS and GS. Studying the persistency of LD phase and population genetic diversity highlighted the necessity for breeding plans to safeguard these buffalo populations.
FRONTIERS IN GENETICS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: This paper quantifies the genome-wide consequences of natural selection and addresses the effects of indirect selection due to the correlation of genetic regions. The critiques on the paper do not substantially affect the findings of the study.
Article
Plant Sciences
Wenchong Chen, Weiwu Yu, Ang Dong, Yanru Zeng, Huwei Yuan, Bingsong Zheng, Rongling Wu
Summary: This study utilizes advanced genotyping technologies to investigate the genetic structure of Torreya grandis, a species with high economic and ornamental values. A high-density linkage map is constructed, and the results suggest that the identified QTLs are relatively young and can be better utilized through clonal propagation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Siyi Liu, Tianxiong Yao, Dong Chen, Shijun Xiao, Liqing Chen, Zhiyan Zhang
Summary: This study explores the potential application of genomic selection of purebred (PB) animals using genotypes of commercial crossbred (CB) animals with extreme phenotypes as the reference population. The results show that using CB animals with extreme phenotypes as the reference population, in combination with the Bayesian sparse linear mixed model (BSLMM) prediction model, significantly improves selection response for CB performance. For high-heritability traits, the predictive performance of a reference population of extreme CB phenotypes is comparable to that of PB phenotypes and can even exceed it if the reference population size is large enough. The use of extreme CB phenotypes outperforms the use of PB phenotypes for selecting first and terminal sires in a three-way crossbreeding system.
GENETICS SELECTION EVOLUTION
(2023)
Article
Plant Sciences
Chiming Gu, Wei Huang, Yue Li, Yinshui Li, Changbin Yu, Jing Dai, Wenshi Hu, Xiaoyong Li, Margot Brooks, Lihua Xie, Xing Liao, Lu Qin
Summary: Research has shown that intercropping with green manure during the oilseed rape season can significantly reduce nitrogen fertilizer application, increase rapeseed yield, and improve nitrogen fertilizer efficiency. Additionally, incorporating green manure can increase soil organic matter content and soil-available nitrogen, reducing reliance on chemical nitrogen fertilizers and enhancing soil quality for increased crop production.
Article
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: Understanding the impact of selection on the genome is crucial in biology. Indirect selection can affect functionally neutral genetic regions through statistical associations with genes under direct selection, leading to widespread genetic loci being impacted across the genome. This process, including unknown causal variants and genetic associations, makes aspects of evolution more predictable and has implications for evolutionary principles in both basic and applied science.
Review
Plant Sciences
Pusarla Susmitha, Pawan Kumar, Pankaj Yadav, Smrutishree Sahoo, Gurleen Kaur, Manish K. Pandey, Varsha Singh, Te Ming Tseng, Sunil S. Gangurde
Summary: Legumes are valuable due to their high protein content and other nutritional components. Climate change poses challenges to maintaining the quantity and quality of these nutritional compounds. Genome-wide association studies (GWAS) and machine learning methods have promising applications in addressing these challenges in agricultural genetics.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Michael A. Hardigan, Anne Lorant, Dominique D. A. Pincot, Mitchell J. Feldmann, Randi A. Famula, Charlotte B. Acharya, Seonghee Lee, Sujeet Verma, Vance M. Whitaker, Nahla Bassil, Jason Zurn, Glenn S. Cole, Kevin Bird, Patrick P. Edger, Steven J. Knapp
Summary: The cultivated strawberry, originating from early 18th-century Europe, has undergone significant genomic changes over 300 years of breeding history, leading to global expansion in production. Research shows increased heterozygosity in interspecific hybrids, selective sweeps across the genome, and substantial allelic diversity in octoploid species. Despite genetic gains in modern cultivars, nucleotide diversity and heterozygosity are lower, suggesting potential trade-offs in agricultural selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Habtamu Ayalew, Joshua D. Anderson, Nick Krom, Yuhong Tang, Twain J. Butler, Nidhi Rawat, Vijay Tiwari, Xue-Feng Ma
Summary: Triticale, a hybrid species between wheat and rye, has a limited genomic resource due to its large and complex genome. This study used genotyping-by-sequencing to generate dense marker data and identified a large number of single nucleotide polymorphism markers. Genetic diversity and population structure analysis provided insights into the genetic background and population composition of triticale. Additionally, genomic selection models were used to estimate the accuracy of improving forage yield in triticale, showing the potential of genomic selection in triticale breeding.
G3-GENES GENOMES GENETICS
(2022)
Article
Ecology
Zachary L. Nikolakis, Drew R. Schield, Aundrea K. Westfall, Blair W. Perry, Kathleen N. Ivey, Richard W. Orton, Nicole R. Hales, Richard H. Adams, Jesse M. Meik, Joshua M. Parker, Cara F. Smith, Zachariah Gompert, Stephen P. Mackessy, Todd A. Castoe
Summary: Hybrid zones provide valuable insights into the genetic mechanisms of speciation. This study investigates introgression in a hybrid zone of two rattlesnake species, finding a large number of excess ancestry loci associated with higher recombination rates. The study also identifies correlated allele frequencies across physically unlinked genomic regions in hybrids. These findings highlight the impact of multilocus evolutionary processes on hybrid fitness in this system.
Editorial Material
Biochemistry & Molecular Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: This article addresses recent claims regarding the importance of indirect selection, arguing that it is not a new or poorly studied phenomenon and that alternative explanations exist for the patterns described by the authors.
Article
Green & Sustainable Science & Technology
Arifa Jannat, Yuki Ishikawa-Ishiwata, Jun Furuya
Summary: According to the World Bank, non-cereal crops such as vegetable oils will surpass cereals in demand by 2050. This study examined the influence of temperature and rainfall patterns on rapeseed production, as well as the impact of rapeseed prices in major trading countries on production and consumption patterns in developing nations. The findings showed that temperature changes have the most significant effect on rapeseed yield, positively impacting the growing season but negatively affecting the maturity stages. It is projected that rapeseed exports from Canada will increase by 2040, while China and the US will see simultaneous increases in imports. The relative demand for rapeseed oil is also expected to continue rising in the coming decades.
Article
Biochemical Research Methods
Charlotte Rambla, Sarah Van der Meer, Kai P. Voss-Fels, Manar Makhoul, Christian Obermeier, Rod Snowdon, Eric S. Ober, Michelle Watt, Samir Alahmad, Lee T. Hickey
Summary: This study presents a useful framework for rapidly modifying root traits in elite germplasm, using a wheat exemplar. The approach combines phenotypic selection, marker-assisted selection, and speed breeding to accelerate the process. The results demonstrate the potential of this approach in rapidly shifting root angle and developing wheat lines with diverse root configurations. This method has significant implications for improving yield stability in different environments and soil types.
Article
Plant Sciences
Stjepan Vukasovic, Samir Alahmad, Jack Christopher, Rod J. Snowdon, Andreas Stahl, Lee T. Hickey
Summary: Given the increasing climate change and drought frequency, identifying and developing traits that can adapt to low rainfall drought-prone regions and improve crop yield stability is of great importance. This study investigated early vigour in bread wheat populations using multi-reference nested association mapping and found markers associated with vegetation index and projected leaf area.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Maria L. Federico, Augusto L. Diniz, Glaucia M. Souza, Rod Snowdon, Luis Erazzu
Summary: In this study, researchers used sorghum as a reference crop to identify regions associated with bioenergy production in the sugarcane genome. Comparative genomics revealed highly conserved chromosome blocks between sorghum and sugarcane. A targeted candidate search identified genes involved in sugar and cell wall metabolism, providing insights for genomics-assisted breeding in sugarcane.
Article
Plant Sciences
Yaping Wang, Antje Habekuss, Murukarthick Jayakodi, Martin Mascher, Rod J. Snowdon, Andreas Stahl, Janina Fuss, Frank Ordon, Dragan Perovic
Summary: In this study, 423 F-4 segmental recombinant inbred lines were developed from crosses of Chikurin Ibaraki 1 with two BaMMV-susceptible cultivars, Igri and Uschi. Using a set of 32 KASP assays, the target locus was narrowed down and several candidate genes were identified for further functional analysis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Subhadra Chakrabarty, Raphael Mufumbo, Steffen Windpassinger, David Jordan, Emma Mace, Rod J. Snowdon, Adrian Hathorn
Summary: This study characterized the germplasm collection of sorghum in Uganda and identified five subgroups within the population. Samples from the southwestern highlands were found to be genetically distinct. The study also identified genetic markers associated with cold tolerance in the sorghum accessions. The findings highlight the potential of genebank genomics for utilizing untapped germplasm collections for trait evaluation and allele mining.
Article
Plant Sciences
Manar Makhoul, Harmeet S. Chawla, Benjamin Wittkop, Andreas Stahl, Kai Peter Voss-Fels, Holger Zetzsche, Rod J. Snowdon, Christian Obermeier
Summary: In this study, single-molecule long-amplicon sequencing was used to detect sequence variations in multiple VRN1 genes in wheat, revealing novel haplotypes and alleles associated with economically important traits. Wheat cultivars carrying structural variations within VRN1 genes showed reduced grain yield and biomass, while those carrying specific haplotypes with a high number of SNPs exhibited improved yield and spike traits. Additionally, a new SNP polymorphism within the promoter of vrn-A1 was found to be associated with root depth in winter wheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
R. Mufumbo, S. Chakrabarty, M. Nyine, S. M. Windpassinger, J. W. Mulumba, Y. Baguma, L. T. Odong, M. Frisch, R. J. Snowdon
Summary: The Uganda National GeneBank serves as an important reservoir of genetic diversity for sorghum, and a core collection has been selected to capture maximum genetic and phenotypic diversity, enabling cost-effective evaluation.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
Article
Plant Sciences
Samson Ugwuanyi, Obi Sergius Udengwu, Rod J. Snowdon, Christian Obermeier
Summary: Common bean, known for its rich protein and micronutrients content, is an important crop for providing cheap food and protein sources worldwide. This study identified 62 quantitative trait loci (QTL) associated with 16 agronomically important traits in common bean, as well as candidate gene models for 10 traits including flowering, yield, and seed quality. Additionally, the study found 6 QTL related to pod shattering, with 3 of them potentially useful for breeding.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Mauricio Orantes-Bonilla, Manar Makhoul, HueyTyng Lee, Harmeet Singh Chawla, Paul Vollrath, Anna Langstroff, Fritz J. Sedlazeck, Jun Zou, Rod J. Snowdon
Summary: Novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring, leading to unexpected phenotypic variation. Natural genome restructuring can have a more drastic impact on genetic diversity in agricultural ecosystems than precise biotechnological genome modifications.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Mauricio Orantes-Bonilla, Hao Wang, Huey Tyng Lee, Agnieszka A. A. Golicz, Dandan Hu, Wenwen Li, Jun Zou, Rod J. J. Snowdon
Summary: Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development in oilseed rape revealed the dominance levels of expression and methylation, which have implications on early stage heterosis.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Plant Sciences
Goezde Yildiz, Silvia F. Zanini, Nazanin P. Afsharyan, Christian Obermeier, Rod J. Snowdon, Agnieszka A. Golicz
Summary: Structural variations (SVs) have a strong impact on agronomical traits and play an important role in environmental adaptation. The development of long-read sequencing technologies allows for comprehensive SV discovery and characterization. However, most SV discovery pipeline benchmarks do not include complex plant genome datasets. In this study, we benchmarked SV detection tools for crop plant genomes and provided a useful guide for designing SV discovery pipelines for crop plants.
Article
Plant Sciences
Khadija Sabir, Till Rose, Benjamin Wittkop, Andreas Stahl, Rod J. Snowdon, Agim Ballvora, Wolfgang Friedt, Henning Kage, Jens Leon, Frank Ordon, Hartmut Stuetzel, Holger Zetzsche, Tsu-Wei Chen
Summary: Environmental fluctuations affect physiological processes in different developmental phases of cereal crops, and these effects are associated with the cultivar-specific phenology. Studies on different cultivars can yield contradictory results regarding key phases impacting yield performance. By investigating 220 cultivars of winter wheat and analyzing their sensitivities to global radiation, temperature, and precipitation in 81 time-windows, this study reveals stage-specific genotype-by-environment interactions during spike and kernel development. It also provides new information on the positive impact of global radiation on kernel weight during canopy senescence.
Article
Computer Science, Artificial Intelligence
Iulian Gabur, Danut Petru Simioniuc, Rod J. Snowdon, Dan Cristea
Summary: This study utilizes machine learning methods to analyze plant breeding datasets and improve understanding of nonlinear interactions through feature selection and linear or nonlinear predictors. Experimental results demonstrate that machine learning methods outperform traditional approaches, increasing prediction accuracy, reducing computing time, and improving the detection of important alleles.
FRONTIERS IN ARTIFICIAL INTELLIGENCE
(2022)
Article
Biotechnology & Applied Microbiology
Zengdong Tan, Yan Peng, Yao Xiong, Feng Xiong, Yuting Zhang, Ning Guo, Zhuo Tu, Zhanxiang Zong, Xiaokun Wu, Jiang Ye, Chunjiao Xia, Tao Zhu, Yinmeng Liu, Hongxiang Lou, Dongxu Liu, Shaoping Lu, Xuan Yao, Kede Liu, Rod J. Snowdon, Agnieszka A. Golicz, Weibo Xie, Liang Guo, Hu Zhao
Summary: This study comprehensively characterizes the gene regulatory features in Brassica napus seeds and reveals the gene networks regulating the seed oil content.
Article
Plant Sciences
Hanmei Du, Harsh Raman, Akitomo Kawasaki, Geetha Perera, Simon Diffey, Rod Snowdon, Rosy Raman, Peter R. Ryan
Summary: This study identified quantitative trait loci that affect acid tolerance in canola through genome-wide association study, and identified related genes. These findings provide new genetic resources and markers to enhance aluminum resistance in canola germplasm through genomic and marker-assisted selection.
FUNCTIONAL PLANT BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xue-Mei Yang, Jing-Hao Zhao, Xiao-Yu Xiong, Zhang-Wei Hu, Ji-Fen Sun, Hao Su, Yan-Jing Liu, Ling Xiang, Yong Zhu, Jin-Lu Li, Sadam Hussain Bhutto, Guo-Bang Li, Shi-Xin Zhou, Chi Li, Mei Pu, He Wang, Zhi-Xue Zhao, Ji-Wei Zhang, Yan-Yan Huang, Jing Fan, Wen-Ming Wang, Yan Li
Summary: The Arabidopsis RPW8.1 gene enhances disease resistance but compromises plant growth. It has been found that RPW8.1 constitutively enhances the expression of WRKY51 transcription factor and activates salicylic acid and ethylene signaling pathways. WRKY51, in turn, suppresses RPW8.1 expression, forming a feedback regulation loop.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Hannes Claeys, Eveline Neyrinck, Lies Dumoulin, Anne Pharazyn, Arne Verstichele, Laurens Pauwels, Michael L. Nuccio, Frederic Van Ex
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Melanie Ormancey, Bruno Guillotin, Camille Ribeyre, Clemence Medina, Nathanael Jariais, Helene San Clemente, Patrice Thuleau, Serge Plaza, Martina Beck, Jean-Philippe Combier
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Edgar Perez-Matas, Diego Hidalgo-Martinez, Elisabeth Moyano, Javier Palazon, Mercedes Bonfill
Summary: In this study, the production of paclitaxel was enhanced by overexpressing the bottleneck genes BAPT and DBTNBT in Taxus baccata cells. The transgenic cells showed significantly higher expression of these genes and improved taxane production compared to the wild type. Transcriptional profiling revealed that the GGPPS, TXS, and DBAT genes were most responsive to DBTNBT overexpression and the dual elicitation treatment.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Biying Dong, Dong Meng, Zhihua Song, Hongyan Cao, Tingting Du, Meng Qi, Shengjie Wang, Jingyi Xue, Qing Yang, Yujie Fu
Summary: This study identified the involvement of the citrate transporter CcMATE35 and the long noncoding RNA CcLTCS in aluminum stress response in pigeon pea. These findings suggest that the modules CcNFYB3-CcMATE35 and CcLTCS-CcCS jointly regulate the efflux and synthesis of citrate to enhance the resistance of pigeon pea under aluminum stress.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Review
Biotechnology & Applied Microbiology
Tien V. Vu, Ngan Thi Nguyen, Jihae Kim, Jong Chan Hong, Jae-Yean Kim
Summary: Prime editing technology uses an extended guide RNA to direct a fusion peptide to a specific location in the genome, enabling precise gene editing. This groundbreaking tool has potential in improving crop varieties, but efficiency limitations exist in certain plants.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Yan Xu, Jinyi Tan, Junxing Lu, Yuelin Zhang, Xin Li
Summary: Sclerotinia sclerotiorum causes white mold in economically important plants, and the discovery of SsGAP1 and SsRAS1/SsRAS2 genes as essential regulators of fungal development and virulence provides potential targets for controlling the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Xiaoyang Chen, Chen Liu, Hailin Wang, Qi Liu, Yaping Yue, Yuhang Duan, Zhaoyun Wang, Lu Zheng, Xiaolin Chen, Yaohui Wang, Junbin Huang, Qiutao Xu, Yuemin Pan
Summary: This study identified a secreted protein, Uv1809, as a key virulence factor in Ustilaginoidea virens-rice interactions. Uv1809 inhibits rice immunity and promotes infection by targeting and enhancing rice histone deacetylase OsSRT2-mediated histone deacetylation. CRISPR-Cas9 edited ossrt2 mutants showed broad-spectrum resistance to rice pathogens, indicating its potential as a genetic resource for breeding disease resistance.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Weishuai Bi, Jing Liu, Yuanyuan Li, Ziwei He, Yongming Chen, Tingting Zhao, Xiangxiu Liang, Xiaodan Wang, Xiangzong Meng, Daolong Dou, Guangyuan Xu
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Shengjie You, Yu Wu, Wen Li, Xiaofeng Liu, Qinlan Tang, Fengkun Huang, Yan Li, Hsihua Wang, Mingchun Liu, Yang Zhang
Summary: In this study, a transcription factor called SlERF.G3-Like in tomato was found to play a role in regulating ethylene synthesis, cell wall degradation, and the flavonoid pathway. The researchers also discovered the interaction between SlERF.G3-Like and the master ripening regulator SlRIN, and increased the production of resveratrol derivatives through genetic manipulation. These findings provide insights into the coordination of fruit maturation and metabolic changes in tomatoes, and have implications for metabolic engineering.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Thomas R. Aalders, Mara de Sain, Fleur Gawehns, Nina Oudejans, Yoran D. Jak, Henk L. Dekker, Martijn Rep, Harrold A. van den Burg, Frank L. W. Takken
Summary: The TPL1 and TPL2 genes in tomato are closely associated with susceptibility to Fusarium wilt disease, and mutating these genes can enhance plant resistance to the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
