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The Plant Genome is a gold open access journal that provides the latest advances and breakthroughs in plant genomics research, with special attention to innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement.
SPECIAL SECTIONS: Call for papers! View the open calls for papers for upcoming issues of TPG.
Featured
Soybean genomics research community strategic plan: A vision for 2024-2028
The soybean genomics research community engages with an ever-changing landscape of challenges and opportunities related to the study, application, and utility of soybean research. A group of soybean researchers, including representatives from public institutions, industry, and funding entities across the United States, recently gathered to discuss these challenges and opportunities, with a focus on recent progress and future priorities for the research community. The resulting report provides a framework for the current state of the soybean genomics community and can be used by researchers and funding agencies to prioritize research objectives. Read more.
Browse Articles
Open access
Erratum to: Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative
Ambra Viviani, Jemanesh K. Haile, W. G. Dilantha Fernando, Carla Ceoloni, Ljiljana Kuzmanović, Dhondup Lhamo, Yong-Qiang Gu, Steven S. Xu, Xiwen Cai, Hermann Buerstmayr, Elias M. Elias, Alessia Confortini, Matteo Bozzoli, Gurcharn Singh Brar, Yuefeng Ruan, Samia Berraies, Walid Hamada, Safa Oufensou, Malini Jayawardana, Sean Walkowiak, Salim Bourras, Monika Dayarathne, Julio Isidro y Sánchez, Fiona Doohan, Agata Gadaleta, Ilaria Marcotuli, Xinyao He, Pawan K. Singh, Susanne Dreisigacker, Karim Ammar, Valentyna Klymiuk, Curtis J. Pozniak, Roberto Tuberosa, Marco Maccaferri, Barbara Steiner, Anna Maria Mastrangelo, Luigi Cattivelli,
- 20 January 2025
Open access
Issue Information
- 20 January 2025
Graphical Abstract
On the cover: The production of embryogenic callus and somatic embryos in tissue culture has been a critical component of crop genome engineering and editing systems. In many species, including maize (pictured), the ability to produce somatic embryo-forming (embryogenic) tissue cultures is highly genotype dependent, limiting the scope and efficiency of engineering and editing-based applications. Although some modern transformation and editing methods reduce genotype dependence, they are not yet completely genotype independent. A new review describes the history of research into somatic embryogenesis, embryogenic cultures, and plant transformation, with a focus on how these technologies were developed and applied to maize. Current research into genotype-flexible, morphogenic gene-based transformation and gene editing is also discussed. The evolution of plant tissue culture, transformation, and gene editing systems has fundamentally changed agriculture and accelerated functional genomics research and genetic enhancement of maize and other crops. See McFarland and Kaeppler (https://doi.org/10.1002/tpg2.20451). Photo credit: Richard Pratt.
Open access
Combined transcriptomic and metabolomic analyses reveal the pharmacognostic mechanism of the metabolism of flavonoids in different parts of Polygonum capitatum
- 14 January 2025
Core Ideas
- Flavonoids are differentially distributed in different medicinal parts of Polygonum capitatum.
- The leaves exhibited significant accumulation of these ingredients, such as gallic acid, quercetin, and quercitrin.
- Gallic acid, quercetin, and quercitrin are considered potential quality markers of P. capitatum.
- These quality markers are involved in the flavonoid and polyphenol biosynthesis pathways.
- The expression levels of genes encoding enzymes, including the shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), flavonoid 3′,5′-hydroxylase (CYP75A), flavones 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin reductase (LAR), trans-cinnamate 4-monooxygenase (CYP73A), and shikimate kinase (SK), were the lowest in the leaves.
Open access
Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley
Yi Hong, Hui Zhou, Mengna Zhang, Yuhang Zhang, Juan Zhu, Chao Lv, Baojian Guo, Feifei Wang, Qingliang Li, Jie Sun, Rugen Xu,
- 13 January 2025
Core Ideas
- A novel quantitative trait loci (QTL) (QRym.ZN1-7H) for barley yellow mosaic disease resistance was identified from bulbous barley.
- QRym.ZN1-7H was fine mapped to the 14- to 39-Mb interval on chromosome 7H.
- Transcriptome analysis identified nine differentially expressed genes both in roots and leaves (at QRym.ZN1-7H).
- QRym.ZN1-7H may be involved in signal transduction in plant innate immune response.
Open access
Within‐family genomic selection in strawberry: Optimization of marker density, trial design, and training set composition
- 9 January 2025
Core Ideas
- Genomic selection is effective for selecting seedlings within biparental families in strawberry.
- In strawberry, genomic selection is efficient with a low- to medium-density genotyping platform.
- Genomic selection is highly stable without clonal replication, substantially reducing the need for phenotyping.
Open access
Status and prospects of genome‐wide association studies in plants
- The Plant Genome
- 13 January 2021
Core Ideas
- GWAS dissect complex traits by testing genome-wide SNPs across an assembled population.
- Unified mixed-model GWAS control for both population structure and kinship.
- New GWAS methods build on this widely adopted mixed model foundation.
- Ongoing challenges call for the further development of GWAS methods and software.
Open access
What plant breeding may (and may not) look like in 2050?
- The Plant Genome
- 16 July 2023
Core Ideas
- A genomic revolution in plant breeding shall become a reality from parents selection to variety commercialization.
- Higher rates of genetic gain can be achieved via the deployment of the latest plant breeding methods.
- These higher genetic gain rates are costly and promise to put out of business those that cannot afford them.
- Providers of several services are due to enter the commercial space, changing forever the figure of a plant breeder.
Open access
Understanding role of roots in plant response to drought: Way forward to climate‐resilient crops
- The Plant Genome
- 18 October 2023
Core Ideas
- The root is the first plant organ to sense drought and responds through morphological, anatomical, and genetic changes.
- These changes explore and secure resources with minimal metabolic cost.
- Using high-throughput and advanced phenotyping, root system architecture (RSA) can be studied comprehensively.
- Such a study can pave the way for strategic modifications in RSA to develop resilient crops.
Open access
Maize and heat stress: Physiological, genetic, and molecular insights
Ivica Djalovic, Sayanta Kundu, Rajeev Nayan Bahuguna, Ashwani Pareek, Ali Raza, Sneh L. Singla-Pareek, P. V. Vara Prasad, Rajeev K. Varshney,
- The Plant Genome
- 16 August 2023
Core Ideas
- Maize is an important food, nutrition, and climate security crop around the world.
- Heat stress negatively impacts the growth, development, and yield of maize.
- Genotypes respond to heat stress at physiological, biochemical, and molecular levels.
- Current knowledge and advances in traits and genotypic responses are discussed.
Open access
Developing drought‐smart, ready‐to‐grow future crops
Ali Raza, Muhammad Salman Mubarik, Rahat Sharif, Madiha Habib, Warda Jabeen, Chong Zhang, Hua Chen, Zhong-Hua Chen, Kadambot H. M. Siddique, Weijian Zhuang, Rajeev K. Varshney,
- The Plant Genome
- 10 November 2022
Core Ideas
- Drought stress (DS) significantly affects plant growth and development.
- Plants respond and adapt to DS by modifying several physiological, biochemical, and molecular functions.
- Advances in different conventional, biochemical, biotechnological, and breeding techniques reveal plant drought tolerance mechanisms.
- Data from different approaches can be used with speed breeding for drought-smart, ready-to-grow future crops.
ORIGINAL RESEARCH
Open access
Introgression of “QTL-hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars
Chellapilla Bharadwaj, Shailesh Tripathi, Khela R. Soren, Mahendar Thudi, Rajesh K. Singh, Seema Sheoran, Manish Roorkiwal, Basavanagouda Siddanagouda Patil, Annapurna Chitikineni, Ramesh Palakurthi, Anilkumar Vemula, Abhishek Rathore, Yogesh Kumar, Sushil K. Chaturvedi, Biswajit Mondal, Pichandampalayam Subramaniam Shanmugavadivel, Avinash K. Srivastava, Girish P. Dixit, Narendra P. Singh, Rajeev K. Varshney,
- The Plant Genome
- 22 January 2021
- 78
SPECIAL ISSUE: ADVANCES IN GENOMIC SELECTION AND APPLICATION OF MACHINE LEARNING IN GENOMIC PREDICTION
Open access
Multitrait machine‐ and deep‐learning models for genomic selection using spectral information in a wheat breeding program
- The Plant Genome
- 5 September 2021
- 39
ORIGINAL RESEARCH
Open access
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
Philipp E. Bayer, Babu Valliyodan, Haifei Hu, Jacob I. Marsh, Yuxuan Yuan, Tri D. Vuong, Gunvant Patil, Qijian Song, Jacqueline Batley, Rajeev K. Varshney, Hon-Ming Lam, David Edwards, Henry T. Nguyen,
- The Plant Genome
- 24 June 2021
- 33
ORIGINAL RESEARCH
Open access
Global profiling of N6-methyladenosine methylation in maize callus induction
Xuemei Du, Ting Fang, Yan Liu, Meng Wang, Maosen Zang, Liying Huang, Sihan Zhen, Jie Zhang, Zichen Shi, Guoying Wang, Junjie Fu, Yunjun Liu,
- The Plant Genome
- 17 April 2020
- 21
ORIGINAL RESEARCH
Open access
Genome‐based prediction of multiple wheat quality traits in multiple years
Maria Itria Ibba, Jose Crossa, Osval A. Montesinos-López, Abelardo Montesinos-López, Philomin Juliana, Carlos Guzman, Emily Delorean, Susanne Dreisigacker, Jesse Poland,
- The Plant Genome
- 25 July 2020
- 26
ORIGINAL RESEARCH
Open access
Advancing provitamin A biofortification in sorghum: Genome‐wide association studies of grain carotenoids in global germplasm
Clara Cruet-Burgos, Sarah Cox, Brian P. Ioerger, Ramasamy Perumal, Zhenbin Hu, Thomas J. Herald, Scott R. Bean, Davina H. Rhodes,
- The Plant Genome
- 26 March 2020
- 24
ORIGINAL RESEARCH
Open access
A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome
Lillian K. Padgitt-Cobb, Sarah B. Kingan, Jackson Wells, Justin Elser, Brent Kronmiller, Daniel Moore, Gregory Concepcion, Paul Peluso, David Rank, Pankaj Jaiswal, John Henning, David A. Hendrix,
- The Plant Genome
- 18 February 2021
- 25
SPECIAL ISSUE: ADVANCES IN GENOMIC SELECTION AND APPLICATION OF MACHINE LEARNING IN GENOMIC PREDICTION
Open access
The application of pangenomics and machine learning in genomic selection in plants
Philipp E. Bayer, Jakob Petereit, Monica Furaste Danilevicz, Robyn Anderson, Jacqueline Batley, David Edwards,
- The Plant Genome
- 20 July 2021
- 22
ORIGINAL RESEARCH
Open access
Genome‐based prediction of Bayesian linear and non‐linear regression models for ordinal data
Paulino Pérez-Rodríguez, Samuel Flores-Galarza, Humberto Vaquera-Huerta, David Hebert del Valle-Paniagua, Osval A. Montesinos-López, José Crossa,
- The Plant Genome
- 14 May 2020
- 15
ORIGINAL RESEARCH
Open access
Genome‐wide association study identifies five new cadmium uptake loci in wheat
Luqman Bin Safdar, Fakhrah Almas, Sidra Sarfraz, Muhammad Ejaz, Zeshan Ali, Zahid Mahmood, Li Yang, Muhammad Massub Tehseen, Muhammad Ikram, Shengyi Liu, Umar Masood Quraishi,
- The Plant Genome
- 24 June 2020
- 18
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