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
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)
Article
Biotechnology & Applied Microbiology
Norman Munyengwa, Vincent Le Guen, Hermine Ngalle Bille, Livia M. Souza, Andre Clement-Demange, Pierre Mournet, Aurelien Masson, Mouman Soumahoro, Daouda Kouassi, David Cros
Summary: The study compared the accuracy of genomic predictions using different imputation methods on GBS data. Results showed that using genetically mapped SNPs improved accuracy, with LinkImputeR, Beagle, and FImpute being the best imputation approaches.
Article
Biotechnology & Applied Microbiology
Ehsan Rabieyan, Mohammad Reza Bihamta, Mohsen Esmaeilzadeh Moghaddam, Valiollah Mohammadi, Hadi Alipour
Summary: The study focused on determining the population structure of Iranian wheat landraces and cultivars and detecting marker-trait associations for drought-tolerance breeding. Results revealed genetic differences among wheat accessions and showed that the gBLUP model is a suitable tool for genomic selection in wheat.
Article
Agronomy
Qing Yang, Jianan Zhang, Xiaolei Shi, Lei Chen, Jun Qin, Mengchen Zhang, Chunyan Yang, Qijian Song, Long Yan
Summary: A high-throughput genotyping platform with customized flexibility, high genotyping accuracy, and low cost was developed for marker-assisted selection and genetic mapping in soybean. The GBTS method using selected SNP panels accurately identified alleles and constructed linkage maps. The 10K panel successfully identified a genetic locus controlling 100-seed weight. Compared with other methods, the 40K, 20K, and 10K panels significantly reduced costs. These low-cost genotyping panels facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and genomic selection.
MOLECULAR BREEDING
(2023)
Article
Agriculture, Multidisciplinary
Xiangyu Zhao, Shouhui Pan, Zhongqiang Liu, Yanyun Han, Qi Zhang, Kaiyi Wang
Summary: This paper introduces the decision support tools of the golden seed breeding cloud platform, including graphical user interfaces, statistical tools, and intelligent decision support tools, which have significantly improved breeding efficiency, data management, and application capabilities.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(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.
Article
Agronomy
Muhammad Massub Tehseen, Yaojie Zheng, Nathan A. Wyatt, Melvin D. Bolton, Shengming Yang, Steven S. Xu, Xuehui Li, Chenggen Chu
Summary: A STARP marker system was developed to enable the allelic discrimination of SNPs in sugarbeet plants using both fluorescence signals and traditional gel electrophoresis. The system is particularly useful for crops with strong background signal noise during PCR reactions and has potential applications in other plant species.
Article
Biotechnology & Applied Microbiology
Miroslaw Tyrka, Monika Mokrzycka, Beata Bakera, Dorota Tyrka, Magdalena Szeliga, Stefan Stojalowski, Przemyslaw Matysik, Michal Rokicki, Monika Rakoczy-Trojanowska, Pawel Krajewski
Summary: This study evaluated the genetic structure of 509 wheat accessions using high-density genotyping-by-sequencing, revealing significant differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. Analyses also identified genomic regions targeted by breeding efforts.
Article
Agronomy
Xiaodong Li, Xumei Liu, Yonghai Fan, Shengting Li, Mengna Yu, Mingchao Qian, Yuling Chen, Hongqiao Chen, Xinchun Li, Bei Liu, Xinfu Xu, Cunmin Qu, Jiana Li, Kun Lu
Summary: In this study, a target capture sequencing SNP genotyping platform named BnaPan50T was developed for detecting genetic variation and constructing gene maps in rapeseed. The platform has a high density of SNPs and a high proportion of functional genes, promising wide application in genetic research and breeding of rapeseed.
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
Plant Sciences
Wei Zhang, Natasha T. Forester, Christina D. Moon, Paul H. Maclean, Milan Gagic, Sai Krishna Arojju, Stuart D. Card, Cory Matthew, Richard D. Johnson, Linda J. Johnson, Marty J. Faville, Christine R. Voisey
Summary: The study found that the upregulation of resistance genes in low-transmission hosts to the AR37 strain, along with differences in endophyte biomass and gene SNPs, may be the primary factors influencing the efficiency of endophyte seed transmission.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Erdem Kahveci, Zuebeyir Devran, Ercan oezkaynak, Yiguo Hong, David J. Studholme, Mahmut Toer
Summary: Cucumber vein yellowing virus (CVYV) causes economic losses in cucumber crops, with limited resistance sources and lack of tightly linked molecular markers hindering breeding progress. Genomic analysis and marker-assisted selection could aid in developing resistant lines against CVYV.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Nayyer Abdollahi Sisi, Nils Stein, Axel Himmelbach, Seyed Abolghasem Mohammadi
Summary: In this study, a high-density linkage map was constructed using genotyping-by-sequencing technology, revealing 85 QTLs associated with drought tolerance traits in wheat, including 20 novel QTLs. These findings are of great importance for improving wheat yield and drought resistance.
Article
Biochemistry & Molecular Biology
Alan Chambers, Angelica Cibrian-Jaramillo, Adam P. Karremans, David Moreno Martinez, Juan Hernandez-Hernandez, Maria Brym, Marcio F. R. Jr Jr Resende, Ruth Moloney, Sheryl N. Sierra, Tomas Hasing, Yasmin A. Alomia, Ying Hu
Summary: Genomics-based diversity analysis of natural vanilla populations is crucial for conservation efforts and genetic improvement through plant breeding. The commercial reliance on descendants of a few foundational clones has led to a heightened risk of catastrophic failure due to extremely narrow genetic diversity in the industry.
Article
Agronomy
P. S. Baenziger, K. A. Frels, J. Boehm, V. Belamkar, D. J. Rose, L. Xu, S. M. Finnie, S. N. Wegulo, T. Regassa, A. C. Easterly, C. F. Creech, D. K. Santra, R. N. Klein, Y. Jin, J. Kolmer, M. -S. Chen, R. L. Bowden, M. J. Guttieri, G. Bai, I. El-Basyoni Salah, S. D. Masterson, J. Poland
Summary: A new hard white winter wheat variety, NW13493, was developed for the Great Plains region. It has white kernels, good agronomic performance, disease resistance, and suitable quality for making bread. NW13493 was licensed to Bay State Milling Company and released in February 2021. It shows excellent winter survival, agronomic performance, disease resistance, and end-use quality for bread making.
JOURNAL OF PLANT REGISTRATIONS
(2023)
Article
Agronomy
P. S. Baenziger, S. D. Masterson, J. D. Boehm, V Belamkar, M. D. Barnett, D. J. Rose, L. Xu, S. N. Wegulo, T. Regassa, A. C. Easterly, C. F. Creech, D. K. Santra, G. R. Kruger, G. W. Hergert, R. N. Klein, Y. Jin, J. Kolmer, M. -S Chen, G. L. Hein, R. L. Bowden, M. J. Guttieri, G. Bai, I. El-Basyoni Salah, J. Poland
Summary: LCS Valiant is a wheat cultivar developed by the University of Nebraska-Lincoln and USDA-ARS, known for its early maturity, strong adaptability, disease resistance, and good quality for making bread.
JOURNAL OF PLANT REGISTRATIONS
(2023)
Article
Genetics & Heredity
Adam Schoen, Inderjit Yadav, Shuangye Wu, Jesse Poland, Nidhi Rawat, Vijay Tiwari
Summary: In this study, a novel tillering number gene was identified in wheat through the use of a mutagen and genetic mapping techniques. The gene was located on chromosome 2DS within a 2.1 Mb region, and 22 candidate genes were identified.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Genetics & Heredity
Guotai Yu, Oadi Matny, Spyridon Gourdoupis, Naganand Rayapuram, Fatimah R. Aljedaani, Yan L. Wang, Thorsten Nuernberger, Ryan Johnson, Emma E. Crean, Isabel M. -L. Saur, Catherine Gardener, Yajuan Yue, Ngonidzashe Kangara, Burkhard Steuernagel, Sadiye Hayta, Mark Smedley, Wendy Harwood, Mehran Patpour, Shuangye Wu, Jesse Poland, Jonathan D. G. Jones, T. Lynne Reuber, Moshe Ronen, Amir Sharon, Matthew N. Rouse, Steven Xu, Katerina Holusova, Jan Bartos, Istvan Molnar, Miroslava Karafiatova, Heribert Hirt, Ikram Blilou, Lukasz Jaremko, Jaroslav Dolezel, Brian J. Steffenson, Brande B. H. Wulff
Summary: To protect bread wheat from pests and diseases, breeders have introduced over 200 resistance genes, nearly doubling the number of designated resistance genes in its gene pool. One of these genes, Sr43, which was derived from the wild grass Thinopyrum elongatum, encodes a protein kinase fused to two unknown function domains. Transgenic expression of Sr43 in wheat provides high levels of resistance against various isolates of stem rust, indicating its potential in resistance breeding and engineering.
Article
Genetics & Heredity
Yajun Wang, Michael Abrouk, Spyridon Gourdoupis, Dal-Hoe Koo, Miroslava Karafiatova, Istvan Molnar, Katerina Holusova, Jaroslav Dolezel, Naveenkumar Athiyannan, Emile Cavalet-Giorsa, Lukasz Jaremko, Jesse Poland, Simon G. Krattinger
Summary: To enrich crop germplasm with disease-resistance genes, we successfully cloned the leaf rust resistance gene Lr9 through mutagenesis and transcriptome sequencing, and found that Lr9 encodes an unusual tandem kinase fusion protein. By utilizing long-read sequencing, we identified the Lr9 translocation of approximately 28.4-Mb and the translocation breakpoint in a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor. We also discovered a homologous gene Lr58 with the same coding sequence as Lr9, which was reportedly introgressed from Aegilops triuncialis, indicating a common translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.
Article
Multidisciplinary Sciences
Cherinet Alem Gesesse, Bogale Nigir, Kaue de Sousa, Luca Gianfranceschi, Guido Roberto Gallo, Jesse Poland, Yosef Gebrehawaryat Kidane, Ermias Abate Desta, Carlo Fadda, Mario Enrico Pe, Matteo Dell'Acqua
Summary: This study combines genomics with participatory research to tap into the traditional knowledge of smallholder farming systems in sub-Saharan Africa and highlights the importance of integrating such knowledge into breeding pipelines. The research demonstrates that farmer appreciation scores can be used to train a genomic selection model for better prediction accuracy in grain yield. Furthermore, forward genetics approaches were used to identify marker-trait associations for agronomic traits and farmer appreciation scores, contributing to the selection of best allelic combinations for local adaptation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Environmental Sciences
Lee R. DeHaan, James A. Anderson, Prabin Bajgain, Andrea Basche, Douglas J. Cattani, Jared Crain, Timothy E. Crews, Christophe David, Olivier Duchene, Jessica Gutknecht, Richard C. Hayes, Fengyi Hu, Jacob M. Jungers, Soren Knudsen, Wenqian Kong, Steve Larson, Per-Olof Lundquist, Guangbin Luo, Allison J. Miller, Pheonah Nabukalu, Matthew T. Newell, Lennart Olsson, Michael Palmgren, Andrew H. Paterson, Valentin D. Picasso, Jesse A. Poland, Erik J. Sacks, Shuwen Wang, Anna Westerbergh
Summary: Perennial grains have the potential to contribute to ecological intensification of food production by direct harvesting of human-edible crops, and studies show their ability to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, limited investment in genetic improvement of perennial grain candidates has hindered their development. Recent advancements in crop breeding and genetics, such as low-cost genotyping and genome editing, can address these concerns and allow for the development of new perennial grain crops with atmospheric greenhouse gas reductions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Agronomy
Anmol Kajla, Adam Schoen, Carl Paulson, Inderjit Singh Yadav, Kumari Neelam, Oscar Riera-Lizarazu, Jeff Leonard, Bikram S. S. Gill, Prakash Venglat, Raju Datla, Jesse Poland, Gary Coleman, Nidhi Rawat, Vijay Tiwari
Summary: This study provides an approach to precisely map wheat genes in the centromeric and pericentromeric regions using the example of the C-locus. Integration of radiation hybrid and high-resolution genetic mapping successfully located the C-locus on a specific arm of chromosome 2D. This study demonstrates the value of this integrated strategy in mapping dominant genes in low-recombination regions.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Plant Sciences
Sandesh Shrestha, Dal-Hoe Koo, Byron Evers, Shuangye Wu, Sean Walkowiak, Pierre Hucl, Curtis Pozniak, Allan Fritz, Jesse Poland
Summary: Double haploid (DH) populations are commonly used in crop breeding and genetic studies. However, the genome shock that occurs during DH induction can lead to chromosomal aberrations, impacting genome integrity and plant performance. We studied two wheat DH populations and found a high proportion of abnormal DH lines, which exhibited genetic instability and were observed in subsequent generations. These findings have important implications for the use of DH lines in genetics and breeding.
Article
Multidisciplinary Sciences
Hanin Ibrahim Ahmed, Matthias Heuberger, Adam Schoen, Dal-Hoe Koo, Jesus Quiroz-Chavez, Laxman Adhikari, John Raupp, Stephane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Gerard R. Lazo, Nagarajan Kathiresan, Parva K. Sharma, Ian Moot, Inderjit Singh Yadav, Lovepreet Singh, Gautam Saripalli, Nidhi Rawat, Raju Datla, Naveenkumar Athiyannan, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Vijay K. Tiwari, Michael Abrouk, Jesse Poland, Simon G. Krattinger
Summary: Genome sequencing of wild and domesticated wheat provides insights into its evolutionary history, genetic diversity, and its contribution to bread wheat. This research is valuable for improving both einkorn and bread wheat through genomics-assisted approaches.
Article
Genetics & Heredity
Sandeep Marla, Terry Felderhoff, Chad Hayes, Ramasamy Perumal, Xu Wang, Jesse Poland, Geoffrey P. Morris
Summary: In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, the chilling sensitivity of sorghum limits early planting, and conventional breeding has faced challenges in developing chilling tolerance while avoiding undesirable traits. This study used phenomics and genomics approaches to prebreed sorghum with early-season chilling tolerance. High-throughput phenotyping using unmanned aircraft systems (UAS) showed moderate correlation with manual phenotyping, and UAS data successfully identified chilling tolerance quantitative trait locus (QTL) that colocalized with manual phenotyping QTL. The use of second-generation molecular markers based on population genomics allowed for successful tracking of the chilling tolerance allele in diverse sorghum breeding lines. Marker-assisted breeding improved early-planted seedling performance in chilling-sensitive sorghum lines by up to 13-24%. These findings highlight the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Rae Page, Shuyi Huang, Moshe Ronen, Hanan Sela, Amir Sharon, Sandesh Shrestha, Jesse Poland, Brian J. Steffenson
Summary: New resistance loci for rust diseases have been identified in Ae. longissima, providing potential genetic resources for wheat breeding.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Gautam Saripalli, Laxman Adhikari, Cameron Amos, Ashraf Kibriya, Hanin Ibrahim Ahmed, Matthias Heuberger, John Raupp, Naveenkumar Athiyannan, Thomas Wicker, Michael Abrouk, Sydney Wallace, Seyedali Hosseinirad, Parveen Chhuneja, Janelle Livesay, Nidhi Rawat, Simon G. Krattinger, Jesse Poland, Vijay Tiwari
Summary: This study utilized genomic advancements to map agronomic traits in einkorn wheat, resulting in the identification of candidate genes and a domestication locus. This resource can be utilized to improve wheat cultivars and explore agronomically important traits.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Matteo Togninalli, Xu Wang, Tim Kucera, Sandesh Shrestha, Philomin Juliana, Suchismita Mondal, Francisco Pinto, Velu Govindan, Leonardo Crespo-Herrera, Julio Huerta-Espino, Ravi P. Singh, Karsten Borgwardt, Jesse Poland
Summary: Developing new crop varieties with superior performance is crucial for global food security, but the process is limited by long field cycles. This study proposes a machine learning model that combines genotype and phenotype measurements using data collected by unmanned aerial systems. The model significantly improves yield prediction accuracy, providing valuable insights for breeding programs and accelerating the delivery of improved varieties.
Article
Mathematical & Computational Biology
Parva Kumar Sharma, Hanin Ibrahim Ahmed, Matthias Heuberger, Dal-Hoe Koo, Jesus Quiroz-Chavez, Laxman Adhikari, John Raupp, Stephane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Inderjit Singh Yadav, Nagarajan Kathiresan, Naveenkumar Athiyannan, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Michael Abrouk, Yong Q. Gu, Jesse Poland, Simon G. Krattinger, Gerard R. Lazo, Vijay K. Tiwari
Summary: This study generated reference-level assemblies of two einkorn wheat accessions and developed a einkorn genome database. The database provides functions for comparative genomics, applied genetics, and breeding research, including querying annotated genes, conducting sequence alignments, and visualizing genome. This resource will significantly contribute to wheat research and breeding.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)