The University of Queensland

The use of genome sequencing to improve crops for tropical agriculture

Okemo, Pauline, Wijesundra, Upendra, Nakandala, Upuli, Ananda, Galaihalage K.S., Vanambathina, Prameela, Hasan, Sharmin, Abdulla, Muhammad, Sharma, Priyanka, Manatunga, Sachini, Pazhany, Adhini, Kharabian Masouleh, Ardy, Nath, Onkar, Mitter, Neena, Furtado, Agnelo and Henry, Robert J. (2022). The use of genome sequencing to improve crops for tropical agriculture. Next-generation sequencing and agriculture. (pp. 59-91) edited by Philipp E. Bayer and David Edwards. Wallingford, Oxfordshire, United Kingdom: CAB International. doi: 10.1079/9781789247848.0004

Development of Transcriptome Analysis Methods

Rangan, Parimalan, Furtado, Agnelo, Henry, Robert and Gaikwad, Ambika (2021). Development of Transcriptome Analysis Methods. Comprehensive Foodomics. (pp. 462-471) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22752-2

RNA extraction for transcriptome analysis

Furtado, Agnelo and Henry, Robert J. (2021). RNA extraction for transcriptome analysis. Comprehensive foodomics. (pp. 440-450) edited by Alejandro Cifuentes. Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22727-3

RNA extraction from plant seeds

Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2021). RNA extraction from plant seeds. Comprehensive foodomics. (pp. 451-461) edited by Alejandro Cifuentes. Oxford, United Kingdom: Elsevier. doi: 10.1016/b978-0-08-100596-5.22751-0

RNA-Seq to understand transcriptomes and application in improving crop quality

Kuram Tirumala, Ravikiran, Subbaiyan, Gopala Krishnan, Singh, Ashok Kumar, Furtado, Agnelo and Henry, Robert James (2021). RNA-Seq to understand transcriptomes and application in improving crop quality. Comprehensive foodomics. (pp. 472-485) edited by Alejandro Cifuentes. Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22728-5

Wheat Grain Transcriptome

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert (2021). Wheat Grain Transcriptome. Comprehensive Foodomics. (pp. 501-512) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22730-3

Re-sequencing resources to improve starch and grain quality in rice

Subbaiyan, Gopala Krishnan, Masouleh, Ardashir K., Furtado, Agnelo, Waters, Daniel L. E. and Henry, Robert J. (2019). Re-sequencing resources to improve starch and grain quality in rice. Rice Grain Quality. (pp. 201-240) edited by Nese Sreenivasulu. New York, NY, United States: Humana Press Inc.. doi: 10.1007/978-1-4939-8914-0_12

Cloning of DNA fragments: Ligation reactions in agarose gel

Furtado, Agnelo (2014). Cloning of DNA fragments: Ligation reactions in agarose gel. Cereal genomics: methods and protocols. (pp. 117-121) edited by Robert J. Henry and Agnelo Furtado. New York, United States: Humana Press. doi: 10.1007/978-1-62703-715-0_10

DNA extraction from vegetative tissue for next-generation sequencing

Furtado, Agnelo (2014). DNA extraction from vegetative tissue for next-generation sequencing. Cereal genomics: methods and protocols. (pp. 1-5) edited by Robert J. Henry and Agnelo Furtado. New York, NY United States: Humana Press. doi: 10.1007/978-1-62703-715-0-1

Preface

Henry, Robert J. and Furtado, Agnelo (2014). Preface. Cereal genomics: methods and protocols. (pp. v-v) New York, NY, United States: Humana Press.

RNA extraction from developing or mature wheat seeds

Furtado, Agnelo (2014). RNA extraction from developing or mature wheat seeds. Cereal Genomics: Methods and Protocols. (pp. 23-28) edited by Robert J. Henry and Agnelo Furtado. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-715-0-4

Structural genomics of eucalypts

Healey, Adam, Furtado, Agnelo and Henry, Robert J. (2014). Structural genomics of eucalypts. Genetics, genomics and breeding of eucalypts. (pp. 103-120) edited by Robert Henry and Chittaranjan Kole. Boca Raton, FL, United States: CRC Press. doi: 10.1201/b17154

The genome of Citrus australasica reveals disease resistance and other species specific genes

Nakandala, Upuli, Furtado, Agnelo, Masouleh, Ardashir Kharabian, Smith, Malcolm W., Williams, Darren C. and Henry, Robert J. (2024). The genome of Citrus australasica reveals disease resistance and other species specific genes. BMC Plant Biology, 24 (1) 260. doi: 10.1186/s12870-024-04988-8

A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data

Rangan, Parimalan, Furtado, Agnelo, Chinnusamy, Viswanathan and Henry, Robert (2024). A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data. BioSystems, 238 105195, 105195. doi: 10.1016/j.biosystems.2024.105195

The complex polyploid genome architecture of sugarcane

Healey, A. L., Garsmeur, O., Lovell, J. T., Shengquiang, S., Sreedasyam, A., Jenkins, J., Plott, C. B., Piperidis, N., Pompidor, N., Llaca, V., Metcalfe, C. J., Doležel, J., Cápal, P., Carlson, J. W., Hoarau, J. Y., Hervouet, C., Zini, C., Dievart, A., Lipzen, A., Williams, M., Boston, L. B., Webber, J., Keymanesh, K., Tejomurthula, S., Rajasekar, S., Suchecki, R., Furtado, A., May, G., Parakkal, P. ... D’Hont, A. (2024). The complex polyploid genome architecture of sugarcane. Nature, 1-7. doi: 10.1038/s41586-024-07231-4

A chromosome‐level genome of mango exclusively from long‐read sequence data

Wijesundara, Upendra Kumari, Masouleh, Ardashir Kharabian, Furtado, Agnelo, Dillon, Natalie L. and Henry, Robert J. (2024). A chromosome‐level genome of mango exclusively from long‐read sequence data. The Plant Genome, e20441. doi: 10.1002/tpg2.20441

Differentially expressed genes in Jojoba (Simmondsia chinensis) when subjected to water-stress

Al-Dossary, Othman, Furtado, Agnelo, Kharabian Masouleh, Ardashir, Alsubaie, Bader, Al-Mssallem, Ibrahim and Henry, Robert J. (2024). Differentially expressed genes in Jojoba (Simmondsia chinensis) when subjected to water-stress. Current Plant Biology, 37 100311, 100311. doi: 10.1016/j.cpb.2023.100311

An improved haplotype resolved genome reveals more rice genes

Abdullah, Muhammad, Furtado, Agnelo, Masouleh, Ardashir Kharabian, Okemo, Pauline and Henry, Robert (2024). An improved haplotype resolved genome reveals more rice genes. Tropical Plants, 3 (1). doi: 10.48130/tp-0024-0007

Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows

Al-Dossary, Othman, Furtado, Agnelo, KharabianMasouleh, Ardashir, Alsubaie, Bader, Al-Mssallem, Ibrahim and Henry, Robert J. (2023). Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows. Plant Methods, 19 (1) 112, 112. doi: 10.1186/s13007-023-01091-1

Loss of plastid ndh genes in an autotropic desert plant

Kharabian-Masouleh, Ardashir, Furtado, Agnelo, Alsubaie, Bader, Al-Dossary, Othman, Wu, Alex, Al-Mssalem, Ibrahim and Henry, Robert (2023). Loss of plastid ndh genes in an autotropic desert plant. Computational and Structural Biotechnology Journal, 21, 5016-5027. doi: 10.1016/j.csbj.2023.10.023

Highly sex specific gene expression in Jojoba

Alsubaie, Bader, Kharabian-Masouleh, Ardashir, Furtado, Agnelo, Al-Dossary, Othman, Al-Mssallem, Ibrahim and Henry, Robert J. (2023). Highly sex specific gene expression in Jojoba. BMC Plant Biology, 23 (1) 440, 440. doi: 10.1186/s12870-023-04444-z

Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum

Thirugnanasambandam, Prathima Perumal, Singode, Avinash, Thalambedu, Lakshmi Pathy, Athiappan, Selvi, Krishnasamy, Mohanraj, Purakkal, Sobhakumari Valiya, Govind, Hemaprabha, Furtado, Agnelo and Henry, Robert (2023). Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum. Frontiers in Plant Science, 14 1199748, 1-15. doi: 10.3389/fpls.2023.1199748

Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes

Nakandala, Upuli, Masouleh, Ardashir Kharabian, Smith, Malcolm W., Furtado, Agnelo, Mason, Patrick, Constantin, Lena and Henry, Robert J. (2023). Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes. Horticulture Research, 10 (05) uhad058, 1-14. doi: 10.1093/hr/uhad058

Analysis of domestication loci in wild rice populations

Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2023). Analysis of domestication loci in wild rice populations. Plants, 12 (3) 489, 1-14. doi: 10.3390/plants12030489

Organ-specific expression of genes associated with the UDP-glucose metabolism in sugarcane (Saccharum spp. hybrids)

Mason, Patrick J., Hoang, Nam V., Botha, Frederik C., Furtado, Agnelo, Marquardt, Annelie and Henry, Robert J. (2023). Organ-specific expression of genes associated with the UDP-glucose metabolism in sugarcane (Saccharum spp. hybrids). BMC Genomics, 24 (1) 18, 1-18. doi: 10.1186/s12864-023-09124-8

Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes

Nakandala, Upuli, Furtado, Agnelo, Smith, Malcolm W., Williams, Darren C. and Henry, Robert J. (2023). Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes. Tropical Plants, 1-8. doi: 10.48130/tp-2023-0021

Variant analysis of grain size related genes in the genus Sorghum

Ananda, Galaihalage K. S., Norton, Sally L., Barnes, Eve, Furtado, Agnelo, Møller, Birger Lindberg, Gleadow, Roslyn and Henry, Robert J. (2022). Variant analysis of grain size related genes in the genus Sorghum. Genetic Resources and Crop Evolution, 70 (5), 1377-1394. doi: 10.1007/s10722-022-01508-1

Gene expression in the developing seed of wild and domesticated rice

Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2022). Gene expression in the developing seed of wild and domesticated rice. International Journal of Molecular Sciences, 23 (21) 13351, 1-21. doi: 10.3390/ijms232113351

Transcriptome and metabolome integration in sugarcane through culm development

Perlo, Virginie, Furtado, Agnelo, Botha, Frederik C., Margarido, Gabriel R. A., Hodgson‐Kratky, Katrina, Choudhary, Hemant, Gladden, John, Simmons, Blake and Henry, Robert J. (2022). Transcriptome and metabolome integration in sugarcane through culm development. Food and Energy Security, 11 (4) e421, 1-16. doi: 10.1002/fes3.421

A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

Nath, Onkar, Fletcher, Stephen J., Hayward, Alice, Shaw, Lindsay M., Kharabian Masouleh, Ardashir, Furtado, Agnelo, Henry, Robert J. and Mitter, Neena (2022). A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes. Horticulture Research, 9 uhac157, 1-10. doi: 10.1093/hr/uhac157

The long read transcriptome of rice (oryza sativa ssp. japonica var. Nipponbare) reveals novel transcripts

Hasan, Sharmin, Huang, Lichun, Liu, Qiaoquan, Perlo, Virginie, O'Keeffe, Angela, Margarido, Gabriel Rodrigues Alves, Furtado, Agnelo and Henry, Robert J (2022). The long read transcriptome of rice (oryza sativa ssp. japonica var. Nipponbare) reveals novel transcripts. Rice, 15 (1) 29, 29. doi: 10.1186/s12284-022-00577-1

Allele expression biases in mixed-ploid sugarcane accessions

Correr, Fernando Henrique, Furtado, Agnelo, Franco Garcia, Antonio Augusto, Henry, Robert James and Rodrigues Alves Margarido, Gabriel (2022). Allele expression biases in mixed-ploid sugarcane accessions. Scientific Reports, 12 (1) 8778, 1-10. doi: 10.1038/s41598-022-12725-0

Potential of genome editing to capture diversity from Australian wild rice relatives

Abdullah, Muhammad, Okemo, Pauline, Furtado, Agnelo and Henry, Robert (2022). Potential of genome editing to capture diversity from Australian wild rice relatives. Frontiers in Genome Editing, 4 875243. doi: 10.3389/fgeed.2022.875243

Reticulate evolution in AA-genome wild rice in Australia

Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2022). Reticulate evolution in AA-genome wild rice in Australia. Frontiers in Plant Science, 13 767635, 767635. doi: 10.3389/fpls.2022.767635

Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content

Perlo, Virginie, Margarido, Gabriel R. A., Botha, Frederik C., Furtado, Agnelo, Hodgson-Kratky, Katrina, Correr, Fernando H. and Henry, Robert J. (2022). Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. Theoretical and Applied Genetics, 135 (5), 1619-1636. doi: 10.1007/s00122-022-04058-3

Transcript profiles of wild and domesticated sorghum under water-stressed conditions and the differential impact on dhurrin metabolism

Ananda, Galaihalage K. S., Norton, Sally L., Blomstedt, Cecilia, Furtado, Agnelo, Møller, Birger Lindberg, Gleadow, Roslyn and Henry, Robert J. (2022). Transcript profiles of wild and domesticated sorghum under water-stressed conditions and the differential impact on dhurrin metabolism. Planta, 255 (2) 51, 51. doi: 10.1007/s00425-022-03831-4

A comprehensive high-quality DNA and RNA extraction protocol for a range of cultivars and tissue types of the woody crop avocado

Nath, Onkar, Fletcher, Stephen J., Hayward, Alice, Shaw, Lindsay M., Agarwal, Rimjhim, Furtado, Agnelo, Henry, Robert J. and Mitter, Neena (2022). A comprehensive high-quality DNA and RNA extraction protocol for a range of cultivars and tissue types of the woody crop avocado. Plants, 11 (3) 242. doi: 10.3390/plants11030242

Cyanogenesis in the Sorghum Genus: From Genotype to Phenotype

Cowan, Max, Møller, Birger Lindberg, Norton, Sally, Knudsen, Camilla, Crocoll, Christoph, Furtado, Agnelo, Henry, Robert, Blomstedt, Cecilia and Gleadow, Roslyn M. (2022). Cyanogenesis in the Sorghum Genus: From Genotype to Phenotype. Genes, 13 (1) 140, 1-17. doi: 10.3390/genes13010140

Comparison of the root, leaf and internode transcriptomes in sugarcane (Saccharum spp. hybrids)

Mason, Patrick J., Hoang, Nam V., Botha, Frederik C., Furtado, Agnelo, Marquardt, Annelie and Henry, Robert J. (2022). Comparison of the root, leaf and internode transcriptomes in sugarcane (Saccharum spp. hybrids). Current Research in Biotechnology, 4, 167-178. doi: 10.1016/j.crbiot.2022.02.005

Limited allele-specific gene expression in highly polyploid sugarcane

Rodrigues Alves Margarido, Gabriel, Correr, Fernando Henrique, Furtado, Agnelo, Botha, Frederik C. and Henry, Robert J. (2021). Limited allele-specific gene expression in highly polyploid sugarcane. Genome Research, 32 (2), 297-308. doi: 10.1101/gr.275904.121

The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding

Sharma, Priyanka, Murigneux, Valentine, Haimovitz, Jasmine, Nock, Catherine J., Tian, Wei, Kharabian Masouleh, Ardashir, Topp, Bruce, Alam, Mobashwer, Furtado, Agnelo and Henry, Robert J. (2021). The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding. Plant Direct, 5 (12) e364, e364. doi: 10.1002/pld3.364

Single kernel sorting of high and normal oleic acid peanuts using near infrared spectroscopy

O’Connor, Daniel J., Meder, Roger, Furtado, Angelo, Henry, Robert J., Wright, Graeme C. and Rachaputi, Rao C.N. (2021). Single kernel sorting of high and normal oleic acid peanuts using near infrared spectroscopy. Journal of Near Infrared Spectroscopy, 29 (6), 366-370. doi: 10.1177/09670335211053502

Denovo chromosome level assembly of a plant genome from long read sequence data

Sharma, Priyanka, Kharabian Masouleh, Ardashir, Topp, Bruce, Furtado, Agnelo and Henry, Robert J. (2021). Denovo chromosome level assembly of a plant genome from long read sequence data. The Plant Journal, 109 (3), 727-736. doi: 10.1111/tpj.15583

Secondary genepool of Australian Cajanus species contains sources of resistance to Helicoverpa armigera (Hübner)

Vanambathina, Prameela, Henry, Robert J., Rachaputi, Rao C. N. and Furtado, Agnelo (2021). Secondary genepool of Australian Cajanus species contains sources of resistance to Helicoverpa armigera (Hübner). Annals of Applied Biology, 180 (2), 259-272. doi: 10.1111/aab.12730

The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant

Al‐Dossary, Othman, Alsubaie, Bader, Kharabian‐Masouleh, Ardashir, Al‐Mssallem, Ibrahim, Furtado, Agnelo and Henry, Robert J (2021). The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant. The Plant Journal, 108 (5), 1283-1294. doi: 10.1111/tpj.15509

Identification of genes associated with chapatti quality using transcriptome analysis

Survase, Abhijeet, Furtado, Agnelo, Thengane, Ratnakar and Henry, Robert (2021). Identification of genes associated with chapatti quality using transcriptome analysis. Journal of Cereal Science, 101 103276, 1-11. doi: 10.1016/j.jcs.2021.103276

Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes

Ananda, Galaihalage, Norton, Sally, Blomstedt, Cecilia, Furtado, Agnelo, Møller, Birger, Gleadow, Roslyn and Henry, Robert (2021). Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes. The Plant Genome, 14 (3) e20123, e20123. doi: 10.1002/tpg2.20123

Fragrance in Pandanus amaryllifolius Roxb. Despite the presence of a betaine aldehyde dehydrogenase 2

Bhatt, Vacha, Barvkar, Vitthal T., Furtado, Agnelo, Henry, Robert J. and Nadaf, Altafhusain (2021). Fragrance in Pandanus amaryllifolius Roxb. Despite the presence of a betaine aldehyde dehydrogenase 2. International Journal of Molecular Sciences, 22 (13) 6968, 1-18. doi: 10.3390/ijms22136968

Improvements in the sequencing and assembly of plant genomes

Sharma, Priyanka, Al-Dossary, Othman, Alsubaie, Bader, Al-Mssallem, Ibrahim, Nath, Onkar, Mitter, Neena, Rodrigues Alves Margarido, Gabriel, Topp, Bruce, Murigneux, Valentine, Kharabian Masouleh, Ardashir, Furtado, Agnelo and Henry, Robert J. (2021). Improvements in the sequencing and assembly of plant genomes. Gigabyte, 2021, 1-10. doi: 10.46471/gigabyte.24

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora

Healey, Adam L., Shepherd, Mervyn, King, Graham J., Butler, Jakob B., Freeman, Jules S., Lee, David J., Potts, Brad M., Silva-Junior, Orzenil B., Baten, Abdul, Jenkins, Jerry, Shu, Shengqiang, Lovell, John T., Sreedasyam, Avinash, Grimwood, Jane, Furtado, Agnelo, Grattapaglia, Dario, Barry, Kerrie W., Hundley, Hope, Simmons, Blake A., Schmutz, Jeremy, Vaillancourt, René E. and Henry, Robert J. (2021). Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. Communications Biology, 4 (1) 537, 1-13. doi: 10.1038/s42003-021-02009-0

Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin

Hodgson-Kratky, K., Perlo, V., Furtado, A., Choudhary, H., Gladden, J. M., Simmons, B. A., Botha, F. and Henry, R. J. (2021). Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. Plant Molecular Biology, 106 (1-2), 173-192. doi: 10.1007/s11103-021-01136-w

Comparison of long-read methods for sequencing and assembly of a plant genome

Murigneux, Valentine, Rai, Subash Kumar, Furtado, Agnelo, Bruxner, Timothy J. C., Tian, Wei, Harliwong, Ivon, Wei, Hanmin, Yang, Bicheng, Ye, Qianyu, Anderson, Ellis, Mao, Qing, Drmanac, Radoje, Wang, Ou, Peters, Brock A, Xu, Mengyang, Wu, Pei, Topp, Bruce, Coin, Lachlan J. M. and Henry, Robert J. (2020). Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience, 9 (12) giaa146. doi: 10.1093/gigascience/giaa146

Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots

Mason, Patrick J., Furtado, Agnelo, Marquardt, Annelie, Hodgson-Kratky, Katrina, Hoang, Nam V., Botha, Frederik C., Papa, Gabriella, Mortimer, Jenny C., Simmons, Blake and Henry, Robert J. (2020). Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots. Biotechnology for Biofuels, 13 (1) 201, 1-19. doi: 10.1186/s13068-020-01837-2

Pathways of photosynthesis in non-leaf tissues

Henry, Robert J., Furtado, Agnelo and Rangan, Parimalan (2020). Pathways of photosynthesis in non-leaf tissues. Biology, 9 (12) 438, 1-13. doi: 10.3390/biology9120438

Sequence variants linked to key traits in interspecific crosses between African and Asian rice

Badro, Hayba, Ndjiondjop, Marie-Noelle, Furtado, Agnelo and Henry, Robert (2020). Sequence variants linked to key traits in interspecific crosses between African and Asian rice. Plants, 9 (12) 1653, 1-21. doi: 10.3390/plants9121653

Metabolic changes in the developing sugarcane culm associated with high yield and early high sugar content

Perlo, Virginie, Botha, Frederik C., Furtado, Agnelo, Hodgson‐Kratky, Katrina and Henry, Robert J. (2020). Metabolic changes in the developing sugarcane culm associated with high yield and early high sugar content. Plant Direct, 4 (11) e00276, e00276. doi: 10.1002/pld3.276

Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production

Moner, Ali Mohammad, Furtado, Agnelo and Henry, Robert J. (2020). Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production. BMC Plant Biology, 20 (1) 472, 1-9. doi: 10.1186/s12870-020-02689-6

Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741)

Nock, Catherine J., Baten, Abdul, Mauleon, Ramil, Langdon, Kirsty S., Topp, Bruce, Hardner, Craig, Furtado, Agnelo, Henry, Robert J. and King, Graham J. (2020). Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741). G3: Genes, Genomes, Genetics, 10 (10), 3497-3504. doi: 10.1534/g3.120.401326

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning

Correr, Fernando Henrique, Hosaka, Guilherme Kenichi, Barreto, Fernanda Zatti, Valadão, Isabella Barros, Balsalobre, Thiago Willian Almeida, Furtado, Agnelo, Henry, Robert James, Carneiro, Monalisa Sampaio and Margarido, Gabriel Rodrigues Alves (2020). Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning. BMC Genomics, 21 (1) 673, 673. doi: 10.1186/s12864-020-07091-y

Wild sorghum as a promising resource for crop improvement

Ananda, Galaihalage K. S., Myrans, Harry, Norton, Sally L., Gleadow, Roslyn, Furtado, Agnelo and Henry, Robert J. (2020). Wild sorghum as a promising resource for crop improvement. Frontiers in Plant Science, 11 1108, 1108. doi: 10.3389/fpls.2020.01108

Slower development of lower canopy beans produces better coffee

Cheng, Bing, Smyth, Heather E., Furtado, Agnelo and Henry, Robert J. (2020). Slower development of lower canopy beans produces better coffee. Journal of Experimental Botany, 71 (14), 4201-4214. doi: 10.1093/jxb/eraa151

Structural elements that modulate the substrate specificity of plant purple acid phosphatases: avenues for improved phosphorus acquisition in crops

Feder, Daniel, McGeary, Ross P., Mitić, Natasa, Lonhienne, Thierry, Furtado, Agnelo, Schulz, Benjamin L., Henry, Robert J., Schmidt, Susanne, Guddat, Luke W. and Schenk, Gerhard (2020). Structural elements that modulate the substrate specificity of plant purple acid phosphatases: avenues for improved phosphorus acquisition in crops. Plant Science, 294 110445, 110445. doi: 10.1016/j.plantsci.2020.110445

Transcriptome profiling of wheat genotypes under heat stress during grain-filling

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert (2020). Transcriptome profiling of wheat genotypes under heat stress during grain-filling. Journal of Cereal Science, 91 102895, 102895. doi: 10.1016/j.jcs.2019.102895

Relationships between Iraqi rice varieties at the nuclear and plastid genome levels

Badro, Hayba, Furtado, Agnelo and Henry, Robert (2019). Relationships between Iraqi rice varieties at the nuclear and plastid genome levels. Plants, 8 (11) 481, 481. doi: 10.3390/plants8110481

Relationship between sugarcane culm and leaf biomass composition and saccharification efficiency

Hodgson-Kratky, K., Papa, G., Rodriguez, A., Stavila, V., Simmons, B., Botha, F., Furtado, A. and Henry, R. (2019). Relationship between sugarcane culm and leaf biomass composition and saccharification efficiency. Biotechnology for Biofuels, 12 (1) 247, 247. doi: 10.1186/s13068-019-1588-3

Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species

Guyeux, Christophe, Charr, Jean-Claude, Tran, Hue T. M., Furtado, Agnelo, Henry, Robert J., Crouzillat, Dominique, Guyot, Romain and Hamon, Perla (2019). Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. PLoS One, 14 (6) e0216347, e0216347. doi: 10.1371/journal.pone.0216347

Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane

Thirugnanasambandam, Prathima P., Mason, Patrick J., Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C. and Henry, Robert J. (2019). Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane. BMC Plant Biology, 19 (1) 160, 160. doi: 10.1186/s12870-019-1733-y

Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm

Nirmal, Ravi C., Singh, Amit Kumar, Furtado, Agnelo and Henry, Robert J. (2019). Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm. Journal of Cereal Science, 85, 62-69. doi: 10.1016/j.jcs.2018.11.010

The impact of cDNA normalization on long-read sequencing of a complex transcriptome

Hoang, Nam V., Furtado, Agnelo, Perlo, Virginie, Botha, Frederik C. and Henry, Robert (2019). The impact of cDNA normalization on long-read sequencing of a complex transcriptome. Frontiers in Genetics, 10 (JUN) 654, 654. doi: 10.3389/fgene.2019.00654

Differential response of wheat genotypes to heat stress during grain filling

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert (2018). Differential response of wheat genotypes to heat stress during grain filling. Experimental Agriculture, 55 (5), 818-827. doi: 10.1017/s0014479718000406

Breeding for improved blanchability in peanut: phenotyping, genotype × environment interaction and selection

Wright, G. C., Borgognone, M. G., Connor, D. J.O., Rachaputi, R. C.N., Henry, R. J., Furtado, A., Anglin, N. L. and Freischfresser, D. B. (2018). Breeding for improved blanchability in peanut: phenotyping, genotype × environment interaction and selection. Crop & Pasture Science, 69 (12), 1237-1250. doi: 10.1071/CP18156

SNP in the Coffea arabica genome associated with coffee quality

Tran, Hue T. M., Furtado, Agnelo, Vargas, Carlos Alberto Cordero, Smyth, Heather, Lee, L. Slade and Henry, Robert (2018). SNP in the Coffea arabica genome associated with coffee quality. Tree Genetics & Genomes, 14 (5) 72. doi: 10.1007/s11295-018-1282-9

Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content

Kasirajan, Lakshmi, Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C. and Henry, Robert J. (2018). Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content. Scientific Reports, 8 (1) 11612, 11612. doi: 10.1038/s41598-018-30033-4

The coffee bean transcriptome explains the accumulation of the major bean components through ripening

Cheng, Bing, Furtado, Agnelo and Henry, Robert J. (2018). The coffee bean transcriptome explains the accumulation of the major bean components through ripening. Scientific Reports, 8 (1) 11414, 11414. doi: 10.1038/s41598-018-29842-4

Wheat seed transcriptome reveals genes controlling key traits for human preference and crop adaptation

Henry, Robert J., Furtado, Agnelo and Rangan, Parimalan (2018). Wheat seed transcriptome reveals genes controlling key traits for human preference and crop adaptation. Current Opinion in Plant Biology, 45 (Pt B), 231-236. doi: 10.1016/j.pbi.2018.05.002

Chloroplast phylogeny of AA genome rice species

Mohammad Moner, Ali, Furtado, Agnelo and Henry, Robert J (2018). Chloroplast phylogeny of AA genome rice species. Molecular Phylogenetics and Evolution, 127, 475-487. doi: 10.1016/j.ympev.2018.05.002

Diversity and evolution of rice progenitors in Australia

Moner, Ali M., Furtado, Agnelo, Chivers, Ian, Fox, Glen, Crayn, Darren and Henry, Robert J. (2018). Diversity and evolution of rice progenitors in Australia. Ecology and Evolution, 8 (8), 4360-4366. doi: 10.1002/ece3.3989

De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts

Hoang, Nam V., Furtado, Agnelo, Thirugnanasambandam, Prathima P., Botha, Frederik C. and Henry, Robert J. (2018). De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts. Heliyon, 4 (3) e00583, e00583. doi: 10.1016/j.heliyon.2018.e00583

Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content

Tran, Hue T. M., Ramaraj, Thiruvarangan, Furtado, Agnelo, Lee, L. Slade and Henry, Robert J. (2018). Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant Biotechnology Journal, 16 (10), 1756-1766. doi: 10.1111/pbi.12912

Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae

Healey, Adam, Lee, David J., Furtado, Agnelo and Henry, Robert J. (2018). Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae. Australian Journal of Botany, 66 (5), 369-378. doi: 10.1071/BT18028

Phylogeny and Molecular Evolution of miR820 and miR396 microRNA Families in Oryza AA Genomes

Singh, Amit Kumar, Furtado, Agnelo, Brozynska, Marta, Mishra, Neeti Sanan and Henry, Robert J (2017). Phylogeny and Molecular Evolution of miR820 and miR396 microRNA Families in Oryza AA Genomes. Tropical Plant Biology, 11 (1-2), 1-16. doi: 10.1007/s12042-017-9197-4

Association of variation in the sugarcane transcriptome with sugar content

Thirugnanasambandam, Prathima P, Hoang, Nam V, Furtado, Agnelo, Botha, Frederick C and Henry, Robert J (2017). Association of variation in the sugarcane transcriptome with sugar content. BMC genomics, 18 (909) 909, 1-22. doi: 10.1186/s12864-017-4302-5

The transcriptome of the developing grain: A resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert J. (2017). The transcriptome of the developing grain: A resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. BMC Genomics, 18 (1) 766, 766-776. doi: 10.1186/s12864-017-4154-z

Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat

Nirmal, Ravi C., Furtado, Agnelo, Rangan, Parimalan and Henry, Robert J. (2017). Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat. Scientific Reports, 7 (1) 12539, 12539. doi: 10.1038/s41598-017-12845-y

Molecular structures and properties of starches of Australian wild rice

Tikapunya, Tiparat, Zou, Wei, Yu, Wenwen, Powell, Prudence O., Fox, Glen P., Furtado, Agnelo, Henry, Robert J. and Gilbert, Robert G. (2017). Molecular structures and properties of starches of Australian wild rice. Carbohydrate Polymers, 172, 213-222. doi: 10.1016/j.carbpol.2017.05.046

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

Cheng, Bing, Furtado, Agnelo and Henry, Robert J (2017). Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. GigaScience, 6 (11) gix086, 1-13. doi: 10.1093/gigascience/gix086

Effects of genotype and temperature on accumulation of plant secondary metabolites in Canadian and Australian wheat grown under controlled environments

Shamloo, Maryam, Babawale, Elizabeth A., Furtado, Agnelo, Henry, Robert J., Eck, Peter K. and Jones, Peter J. H. (2017). Effects of genotype and temperature on accumulation of plant secondary metabolites in Canadian and Australian wheat grown under controlled environments. Scientific Reports, 7 (1) 9133, 9133. doi: 10.1038/s41598-017-09681-5

Association of gene expression with biomass content and composition in sugarcane

Hoang, Nam V., Furtado, Agnelo, O'Keeffe, Angela J., Botha, Frederik C. and Henry, Robert J. (2017). Association of gene expression with biomass content and composition in sugarcane. PLoS One, 12 (8) e0183417, e0183417. doi: 10.1371/journal.pone.0183417

Does C-4 Photosynthesis Occur in Wheat Seeds?

Henry, Robert J., Rangan, Parimalan and Furtado, Agnelo (2017). Does C-4 Photosynthesis Occur in Wheat Seeds?. Plant Physiology, 174 (4), 1992-1993. doi: 10.1104/pp.17.00837

Does C-4 Photosynthesis Occur in Wheat Seeds?

Henry, Robert J., Rangan, Parimalan, Furtado, Agnelo, Busch, Florian A. and Farquhar, Graham D. (2017). Does C-4 Photosynthesis Occur in Wheat Seeds?. Plant Physiology, 174 (4), 1994-1995.

Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice

Wambugu, Peterson, Ndjiondjop, Marie-Noelle, Furtado, Agnelo and Henry, Robert (2017). Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice. Plant Biotechnology Journal, 16 (1), 100-110. doi: 10.1111/pbi.12752

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brozynska, Marta, Copetti, Dario, Furtado, Agnelo, Wing, Rod A., Crayn, Darren, Fox, Glen, Ishikawa, Ryuji and Henry, Robert J. (2017). Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnology Journal, 15 (6), 765-774. doi: 10.1111/pbi.12674

Variation in bean morphology and biochemical composition measured in different genetic groups of arabica coffee (Coffea arabica L.)

Tran, Hue T. M., Vargas, Carlos Alberto Cordero, Lee, L. Slade, Furtado, Agnelo, Smyth, Heather and Henry, Robert (2017). Variation in bean morphology and biochemical composition measured in different genetic groups of arabica coffee (Coffea arabica L.). Tree Genetics and Genomes, 13 (3) 54. doi: 10.1007/s11295-017-1138-8

A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

Hoang, Nam V., Furtado, Agnelo, Mason, Patrick J., Marquardt, Annelie, Kasirajan, Lakshmi, Thirugnanasambandam, Prathima P., Botha, Frederik C. and Henry, Robert J. (2017). A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics, 18 (1) 395, 395. doi: 10.1186/s12864-017-3757-8

Comparison of chapatti and breadmaking quality of wheat genotypes

Survase, Abhijeet, Furtado, Agnelo, Thengane, Ratnakar, Fox, Glen, Taylor, Terence and Henry, Robert (2017). Comparison of chapatti and breadmaking quality of wheat genotypes. Cereal Chemistry, 94 (3), 409-416. doi: 10.1094/CCEM-04-16-0090-R

High-throughput profiling of the fiber and sugar composition of sugarcane biomass

Hoang, Nam V., Furtado, Agnelo, Donnan, Laura, Keeffe, Eloise C., Botha, Frederik C. and Henry, Robert J. (2016). High-throughput profiling of the fiber and sugar composition of sugarcane biomass. Bioenergy Research, 10 (2), 1-17. doi: 10.1007/s12155-016-9801-8

Influence of genotype and environment on coffee quality

Cheng, Bing, Furtado, Agnelo, Smyth, Heather E. and Henry, Robert J. (2016). Influence of genotype and environment on coffee quality. Trends in Food Science and Technology, 57 (A), 20-30. doi: 10.1016/j.tifs.2016.09.003

Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae)

Nock, Catherine J., Baten, Abdul, Barkla, Bronwyn J., Furtado, Agnelo, Henry, Robert J. and King, Graham J. (2016). Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae). BMC Genomics, 17 (1) 937, 937. doi: 10.1186/s12864-016-3272-3

Commentary: new evidence for grain specific C4 photosynthesis in wheat

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert J. (2016). Commentary: new evidence for grain specific C4 photosynthesis in wheat. Frontiers in Plant Science, 7 (OCTOBER2016) 1537. doi: 10.3389/fpls.2016.01537

Influence of gene expression on hardness in wheat

Nirmal, Ravi C., Furtado, Agnelo, Wrigley, Colin and Henry, Robert J. (2016). Influence of gene expression on hardness in wheat. PLoS ONE, 11 (10) 164746, e0164746. doi: 10.1371/journal.pone.0164746

New evidence for grain specific C4 photosynthesis in wheat

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert J. (2016). New evidence for grain specific C4 photosynthesis in wheat. Scientific Reports, 6 (1) 31721, 31721. doi: 10.1038/srep31721

Advances in genomics for the improvement of quality in coffee

Tran, Hue T. M., Lee, L. Slade, Furtado, Agnelo, Smyth, Heather and Henry, Robert J. (2016). Advances in genomics for the improvement of quality in coffee. Journal of the Science of Food and Agriculture, 96 (10), 3300-3312. doi: 10.1002/jsfa.7692

Functional cereals for production in new and variable climates

Henry, Robert J., Rangan, Parimalan and Furtado, Agnelo (2016). Functional cereals for production in new and variable climates. Current Opinion in Plant Biology, 30, 11-18. doi: 10.1016/j.pbi.2015.12.008

Grain physical characteristics of the Australian wild rices

Tikapunya, Tiparat, Fox, Glen, Furtado, Agnelo and Henry, Robert (2016). Grain physical characteristics of the Australian wild rices. Plant Genetic Resources, 15 (5), 1-12. doi: 10.1017/S1479262116000083

Efficient eucalypt cell wall deconstruction and conversion for sustainable lignocellulosic biofuels

Healey, Adam L., Lee, David J., Furtado, Agnelo, Simmons, Blake A. and Henry, Robert J. (2015). Efficient eucalypt cell wall deconstruction and conversion for sustainable lignocellulosic biofuels. Frontiers in Bioengineering and Biotechnology, 3 (NOV) 190, 190.1-190.14. doi: 10.3389/fbioe.2015.00190

Potential for genetic improvement of sugarcane as a source of biomass for biofuels

Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C., Simmons, Blake A. and Henry, Robert J. (2015). Potential for genetic improvement of sugarcane as a source of biomass for biofuels. Frontiers in Bioengineering and Biotechnology, 3 (NOV) 182, 1-15. doi: 10.3389/fbioe.2015.00182

Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

Wambugu, Peterson W., Brozynska, Marta, Furtado, Agnelo, Waters, Daniel L. and Henry, Robert J. (2015). Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Scientific Reports, 5 (Art No.: 13957) 13957, 13957. doi: 10.1038/srep13957

Genomics of crop wild relatives: Expanding the gene pool for crop improvement

Brozynska, Marta., Furtado, Agnelo. and Henry, Robert J. (2015). Genomics of crop wild relatives: Expanding the gene pool for crop improvement. Plant Biotechnology Journal, 14 (4), 1070-1085. doi: 10.1111/pbi.12454

Next Generation Sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy

Hoang, Nam V., Furtado, Agnelo, McQualter, Richard B. and Henry, Robert J. (2015). Next Generation Sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy. New Negatives in Plant Science, 1-2, 33-45. doi: 10.1016/j.neps.2015.10.001

A novel highly differentially expressed gene in wheat endosperm associated with bread quality

Furtado, A., Bundock, P. C., Banks, P. M., Fox, G., Yin, X. and Henry, R. J. (2015). A novel highly differentially expressed gene in wheat endosperm associated with bread quality. Scientific Reports, 5 (10446) 10446, 1-14. doi: 10.1038/srep10446

Modifying plants for biofuel and biomaterial production

Furtado, Agnelo, Lupoi, Jason S., Hoang, Nam V., Healey, Adam, Singh, Seema, Simmons, Blake A. and Henry, Robert J. (2014). Modifying plants for biofuel and biomaterial production. Plant Biotechnology Journal, 12 (9), 1246-1258. doi: 10.1111/pbi.12300

Chloroplast genome of novel rice germplasm identified in Northern Australia

Brozynska, Marta, Omar, Ernnie Syafika, Furtado, Agnelo, Crayn, Darren, Simon, Bryan, Ishikawa, Ryuji and Henry, Robert James (2014). Chloroplast genome of novel rice germplasm identified in Northern Australia. Tropical Plant Biology, 7 (3-4), 111-120. doi: 10.1007/s12042-014-9142-8

Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding

Brozynska, Marta, Furtado, Agnelo and Henry, Robert James (2014). Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One, 9 (10) e110387, e110387.1-e110387.10. doi: 10.1371/journal.pone.0110387

Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species

Healey, Adam, Furtado, Agnelo, Cooper, Tal and Henry, Robert J. (2014). Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods, 10 (1) 21, 1-8. doi: 10.1186/1746-4811-10-21

Conservation and utilization of African Oryza genetic resources

Wambugu, Peterson W., Furtado, Agnelo, Le Waters, Daniel, Nyamongo, Desterio O. and Henry, Robert J. (2013). Conservation and utilization of African Oryza genetic resources. Rice, 6 (1) 29, 29.1-29.13. doi: 10.1186/1939-8433-6-29

Gene expression in the developing aleurone and starchy endosperm of wheat

Gillies, Susan A., Futardo, Agnelo and Henry, Robert J. (2012). Gene expression in the developing aleurone and starchy endosperm of wheat. Plant Biotechnology Journal, 10 (6), 668-679. doi: 10.1111/j.1467-7652.2012.00705.x

Analysis of promoters in transgenic barley and wheat

Furtado, Agnelo, Henry, Robert J. and Pellegrineschi, Alessandro (2009). Analysis of promoters in transgenic barley and wheat. Plant Biotechnology Journal, 7 (3), 240-253. doi: 10.1111/j.1467-7652.2008.00394.x

Comparison of promoters in transgenic rice

Furtado, Agnelo, Henry, Robert J. and Takaiwa, Fumio (2008). Comparison of promoters in transgenic rice. Plant Biotechnology Journal, 6 (7), 679-693. doi: 10.1111/j.1467-7652.2008.00352.x

DNA banks and their role in facilitating the application of genomics to plant germplasm

Rice, Nicole, Cordeiro, Giovanni, Shepherd, Mervyn, Bundock, Peter, Bradbury, Louis, Pacey-Miller, Toni, Furtado, Agnelo and Henry, Robert (2006). DNA banks and their role in facilitating the application of genomics to plant germplasm. Plant Genetic Resources: Characterization and Utilization, 4 (01), 64-70. doi: 10.1079/pgr2006113

The wheat Em promoter drives reporter gene expression in embryo and aleurone tissue of transgenic barley and rice

Furtado, Agnelo and Henry, Robert James (2005). The wheat Em promoter drives reporter gene expression in embryo and aleurone tissue of transgenic barley and rice. Plant Biotechnology Journal, 3 (4), 421-434. doi: 10.1111/j.1467-7652.2005.00135.x

Randomly Amplified DNA Fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification

Waldron, Julie, Peace, Cameron P., Searle, Iain R., Furtado, Agnelo, Wade, Nick, Findlay, Ian, Graham, Michael W. and Carroll, Bernard J. (2003). Randomly Amplified DNA Fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification. Journal of Biomedicine and Biotechnology, 2 (3), 141-150. doi: 10.1155/S1110724302206026

The promoter of the asi gene directs expression in the maternal tissues of the seed in transgenic barley

Furtado, A, Henry, R, Scott, K and Meech, S (2003). The promoter of the asi gene directs expression in the maternal tissues of the seed in transgenic barley. PLANT MOLECULAR BIOLOGY, 52 (4), 787-799. doi: 10.1023/A:1025097218768

Measurement of green fluorescent protein concentration in single cells by image analysis

Furtado, A and Henry, R (2002). Measurement of green fluorescent protein concentration in single cells by image analysis. ANALYTICAL BIOCHEMISTRY, 310 (1), 84-92. doi: 10.1016/S0003-2697(02)00281-6

Control of sugar and fibre: insights from sugarcane transcriptome analyses

Thirugnanasambandam, Prathima Perumal, Kasirajan, Lakshmi, Furtado, Agnelo, Botha, Frikkie C. and Henry, Robert J. (2020). Control of sugar and fibre: insights from sugarcane transcriptome analyses. The Third International Tropical Agriculture Conference, Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036204

Analysis of differences in gene expression associated with variation in biomass composition in sugarcane

Perlo, Virginie, Furtado, Agnelo, Botha, Frikkie and Henry, Robert (2020). Analysis of differences in gene expression associated with variation in biomass composition in sugarcane. The Third International Tropical Agriculture Conference, Brisbane, QLD Australia, 13-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036164

Isolation and characterization of full-length phenylalanine ammonium lyase and cinnamyl alcohol dehydrogenase genes involved in lignin biosynthesis of Erianthus arundinaceus

Kasirajan, Lakshmi, Thirugnanasambandam, Prathima Perumal, Furtado, Agnelo, Botha, Frikkie C. and Henry, Robert J. (2020). Isolation and characterization of full-length phenylalanine ammonium lyase and cinnamyl alcohol dehydrogenase genes involved in lignin biosynthesis of Erianthus arundinaceus. The Third International Tropical Agriculture Conference (TROPAG 2019), Brisbane, QLD, Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036174

Transcriptomics analysis for the detection of novel drought tolerance genes in Jojoba (Simmondsia Chinensis)

Al-Dossary, Othman, Kharabian, Ardashir, Al-Mssallem, Ibrahim, Furtado, Agnelo and Henry, Robert (2020). Transcriptomics analysis for the detection of novel drought tolerance genes in Jojoba (Simmondsia Chinensis). The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036135

Relationships between Iraqi rice varieties at the nuclear and plastid genome levels

Badro, Hayba, Furtado, Agnelo and Henry, Robert (2019). Relationships between Iraqi rice varieties at the nuclear and plastid genome levels. The Third International Tropical Agriculture Conference, Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI AG. doi: 10.3390/proceedings2019036024

SNPs Linked to Key Traits in Hybrids between African and Asian Rice

Badro, Hayba, Ndjiondjop, Marie-Noelle, Furtado, Agnelo and Henry, Robert (2019). SNPs Linked to Key Traits in Hybrids between African and Asian Rice. The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036025

Determination of Phylogenetic Relationships of the Genus Sorghum Using Nuclear and Chloroplast Genome Assembly

Ananda, Galaihalage, Gleadow, Roslyn, Norton, Sally, Furtado, Agnelo and Henry, Robert (2019). Determination of Phylogenetic Relationships of the Genus Sorghum Using Nuclear and Chloroplast Genome Assembly. The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036017

Diversity of domestication loci in wild rice populations

Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2019). Diversity of domestication loci in wild rice populations. The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036014

Analysis of the chloroplast genome of a coffee relative from northern Australia

Cooper, T., Furtado, A., Henry, R. J. and Crayn, D. (2015). Analysis of the chloroplast genome of a coffee relative from northern Australia. International Horticultural Congress, Brisbane, QLD, Australia, 17-22 August 2014. Leuven, Belgium: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2015.1101.27

Developing cereals acceptable to consumers for production in new and variable climates

Henry, Robert J., Rangan, Parimalan and Furtado, Agnelo (2015). Developing cereals acceptable to consumers for production in new and variable climates. Agriculture and Climate Change - Adapting Crops to Increased Uncertainty (AGRI 2015), Amsterdam, Netherlands, 15-17 February 2015. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.proenv.2015.07.128

Identification of molecular markers to smut resistance in sugarcane

Furtado, A., Piperidus, G., Croft, B. J., Cox, M., Mcintyre, C. L., Smith, G. R. and Brumbley, S. M. (2003). Identification of molecular markers to smut resistance in sugarcane. IVth International Workshop on Plant Biotechnology and Sustainable Development (BioVeg) 2003, Ciego de Avila, Cuba, 14-19 April 2003.

Identification of molecular markers to smut resistance in sugarcane

Furtado, A., Piperidus, G., Croft, B. J., Cox, M., Mcintyre, C. L., Smith, G. R. and Brumbley, S. M. (2003). Identification of molecular markers to smut resistance in sugarcane. ISSCT Molecular Biology - Genome Analysis and Molecular Physiology, Montpellier, France, 7-11 April 2003.

Transposon tagging of DNA sequences for alleviating transgene silencing

Reyes, M., Waldron, J., Furtado, A., Klimyuk, V., Jones, J. D., Wang, J. S., Scott, K. J. and Carroll, B. J. (2000). Transposon tagging of DNA sequences for alleviating transgene silencing. The Genome Conference 2000, Lorne, Victoria, Australia, 13 - 17 February 2000. Australia: Lorne Genome Conference.

Transposon tagging of chromosomal regions responsible for alleviating transgene silencing

Waldron, J., Reyes, M., Furtado, A., Klimyuk, V., Wang, J. S., Godwin, I. D., Scott, K. J., Jones, J. D. and Carroll, B. J. (1999). Transposon tagging of chromosomal regions responsible for alleviating transgene silencing. Human Genome Meeting, Brisbane Convention Cen., Brisbane, 27th -30th March, 1999. Nature Publishing Co.: Nature Genetics.

Transposon tagging or DNA sequences for alleviating transgene silencing

Carroll, B. J., Reyes, M., Waldron, J., Furtado, A., Klimyuk, V., Wang, J. S., Scott, K. J. and Jones, J. D. (1999). Transposon tagging or DNA sequences for alleviating transgene silencing. ComBio 99, Conrad Jupiters Casino, Gold Coast, 27-30 September, 1999. Kent Town, SA: Aust. Society for Biochemistry & Molecular Biology ..

Plant Genomics Sequence Data archive.

Furtado Agnelo (2016). Plant Genomics Sequence Data archive.. The University of Queensland. (Dataset) doi: 10.48610/a97b567