Who’s who in the plant gene world?

2025

Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes

MacNish, T. R., Al-Mamun, H. A., Bayer, P. E., McPhan, C., Fernandez, C. G. T., Upadhyaya, S. R., Liu, S., Batley, J., Parkin, I. A. P., Sharpe, A. G. & Edwards, D., Mar 2025, In: Plant Genome. 18, 1, 11 p., e20535.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Citations (Scopus)

Changes of gene content in four crop species during domestication and breeding

Petereit, J., Bayer, P. E., Tay Fernandez, C. G., Batley, J. & Edwards, D., Mar 2025, In: Agriculture Communications. 3, 1, 4 p., 100077.

Research output: Contribution to journal › Article › peer-review

Open Access

Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large-scale soybean dataset

Al-Mamun, H. A., Danilevicz, M. F., Marsh, J. I., Gondro, C. & Edwards, D., Mar 2025, In: Plant Genome. 18, 1, 20 p., e20503.

Research output: Contribution to journal › Article › peer-review

Open Access

2024

Adaptive gene loss in the common bean pan-genome during range expansion and domestication

Cortinovis, G., Vincenzi, L., Anderson, R., Marturano, G., Marsh, J. I., Bayer, P. E., Rocchetti, L., Frascarelli, G., Lanzavecchia, G., Pieri, A., Benazzo, A., Bellucci, E., Di Vittori, V., Nanni, L., Ferreira Fernández, J. J., Rossato, M., Aguilar, O. M., Morrell, P. L., Rodriguez, M. & Gioia, T. & 9 others, Neumann, K., Alvarez Diaz, J. C., Gratias, A., Klopp, C., Bitocchi, E., Geffroy, V., Delledonne, M., Edwards, D. & Papa, R., 7 Aug 2024, In: Nature Communications. 15, 1, 15 p., 6698.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Citations (Web of Science)

Focus on the Crop Not the Weed: Canola Identification for Precision Weed Management Using Deep Learning

Mckay, M., Danilevicz, M. F., Ashworth, M. B., Rocha, R. L., Upadhyaya, S. R., Bennamoun, M. & Edwards, D., 6 Jun 2024, In: Remote Sensing. 16, 11, 19 p., 2041.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Citations (Scopus)

Genome-wide identification and prediction of disease resistance genes in Hirschfeldia incana

Wu, T., Al-Mamun, H. A., Edwards, D., Batley, J. & Dolatabadian, A., Sept 2024, In: Agriculture Communications. 2, 3, 10 p., 100049.

Research output: Contribution to journal › Article › peer-review

Open Access

In silico prediction and analysis of transmembrane-coiled-coil resistance gene analogues in 27 Brassicaceae species

Cantila, A. Y., Thomas, W. J. W., Bayer, P. E., Edwards, D. & Batley, J., Jan 2024, In: Plant Pathology. 73, 1, p. 115-130 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Citation (Web of Science)

Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean

Mohamedikbal, S., Al-Mamun, H. A., Marsh, J. I., Upadhyaya, S., Danilevicz, M. F., Nguyen, H. T., Valliyodan, B., Mahan, A., Batley, J. & Edwards, D., Dec 2024, In: Plant Genome. 17, 4, 17 p., e20528.

Research output: Contribution to journal › Article › peer-review

Open Access

Multimodal Deep Learning Integration of Image, Weather, and Phenotypic Data Under Temporal Effects for Early Prediction of Maize Yield

Shamsuddin, D., Danilevicz, M. F., Al-Mamun, H. A., Bennamoun, M. & Edwards, D., Nov 2024, In: Remote Sensing. 16, 21, 27 p., 4043.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Citation (Scopus)

2023

Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)

Amas, J. C., Bayer, P. E., Hong Tan, W., Tirnaz, S., Thomas, W. J. W., Edwards, D. & Batley, J., Oct 2023, In: Plant Biotechnology Journal. 21, 10, p. 2100-2112 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Citations (Scopus)

Diversity of fatty acid biosynthesis genes across the soybean pangenome

Derbyshire, M. C., Marsh, J., Tirnaz, S., Nguyen, H. T., Batley, J., Bayer, P. E. & Edwards, D., Jun 2023, In: Plant Genome. 16, 2, e20334.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Citations (Web of Science)

Diversity of Phytosterols in Leaves of Wild Brassicaceae Species as Compared to Brassica napus Cultivars: Potential Traits for Insect Resistance and Abiotic Stress Tolerance

Bootter, M. B., Li, J., Zhou, W., Edwards, D. & Batley, J., 1 May 2023, In: Plants. 12, 9, 15 p., 1866.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Citations (Scopus)

Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus

Cantila, A. Y., Thomas, W. J. W., Saad, N. S. M., Severn-Ellis, A. A., Anderson, R., Bayer, P. E., Edwards, D., Van de Wouw, A. P. & Batley, J., 14 Feb 2023, In: Frontiers in Plant Science. 14, 10 p., 1051994.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Citations (Scopus)

Legume-wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression and stress responsive genomic context

Marsh, J. I., Nestor, B. J., Petereit, J., Tay Fernandez, C. G., Bayer, P. E., Batley, J. & Edwards, D., Jul 2023, In: The Plant Journal. 115, 1, p. 68-80 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Citations (Web of Science)

Segmentation of Sandplain Lupin Weeds from Morphologically Similar Narrow-Leafed Lupins in the Field

Danilevicz, M. F., Rocha, R. L., Batley, J., Bayer, P. E., Bennamoun, M., Edwards, D. & Ashworth, M. B., Apr 2023, In: Remote Sensing. 15, 7, 1817.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Citations (Scopus)

The conservation of gene models can support genome annotation

Tay Fernandez, C. G., Bayer, P. E., Petereit, J., Varshney, R., Batley, J. & Edwards, D., Sept 2023, In: Plant Genome. 16, 3, e20377.

Research output: Contribution to journal › Article › peer-review

Open Access

Updated guidelines for gene nomenclature in wheat

the Wheat Initiative, Apr 2023, In: Theoretical and Applied Genetics. 136, 4, 16 p., 72.

Research output: Contribution to journal › Article › peer-review

Open Access

32 Citations (Scopus)

2022

Copy Number Variation among Resistance Genes Analogues in Brassica napus

Dolatabadian, A., Yuan, Y., Bayer, P., Petereit, J., Severn-Ellis, A., Tirnaz, S., Patel, D., Edwards, D. & Batley, J., 4 Nov 2022, In: Genes. 13, 11, p. 1-17 17 p., 2037.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Citations (Scopus)

Evaluating Plant Gene Models Using Machine Learning

Upadhyaya, S. R., Bayer, P. E., Tay Fernandez, C. G., Petereit, J., Batley, J., Bennamoun, M., Boussaid, F. & Edwards, D., 1 Jun 2022, In: Plants. 11, 12, 1619.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Citations (Scopus)

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Marsh, J. I., Hu, H., Petereit, J., Bayer, P. E., Valliyodan, B., Batley, J., Nguyen, H. T. & Edwards, D., Apr 2022, In: Theoretical and Applied Genetics. 135, 4, p. 1443-1455 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Citations (Scopus)

Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale

Petereit, J., Tay Fernandez, C., Marsh, J. I., Bayer, P. E., Thomas, W. J. W., Aliyeva, A. J., Karafiátová, M., Doležel, J., Batley, J. & Edwards, D., Oct 2022, In: International Journal of Molecular Sciences. 23, 19, 8 p., 11106.

Research output: Contribution to journal › Article › peer-review

Open Access

Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction

Gill, M., Anderson, R., Hu, H., Bennamoun, M., Petereit, J., Valliyodan, B., Nguyen, H. T., Batley, J., Bayer, P. E. & Edwards, D., Dec 2022, In: BMC Plant Biology. 22, 1, 180.

Research output: Contribution to journal › Article › peer-review

Open Access

34 Citations (Scopus)

Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana

Cantila, A. Y., Neik, T. X., Tirnaz, S., Thomas, W. J. W., Bayer, P. E., Edwards, D. & Batley, J., Jun 2022, In: Biology. 11, 6, 821.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Citations (Web of Science)

Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species

Cantila, A. Y., Thomas, W. J. W., Bayer, P. E., Edwards, D. & Batley, J., Nov 2022, In: Plants. 11, 22, 3010.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Citations (Scopus)

The pangenome of banana highlights differences between genera and genomes

Rijzaani, H., Bayer, P. E., Rouard, M., Doležel, J., Batley, J. & Edwards, D., Mar 2022, In: The Plant Genome. 15, 1, e20100.

Research output: Contribution to journal › Article › peer-review

Open Access

37 Citations (Scopus)

Wheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes

Bayer, P. E., Petereit, J., Durant, É., Monat, C., Rouard, M., Hu, H., Chapman, B., Li, C., Cheng, S., Batley, J. & Edwards, D., Sept 2022, In: The Plant Genome. 15, 3, p. e20221 e20221.

Research output: Contribution to journal › Article › peer-review

Open Access