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2. Crop Lodging Prediction from UAV-Acquired Images of Wheat and Canola using a DCNN Augmented with Handcrafted Texture Features

Author

Mardanisamani, Sara, Maleki, Farhad, Kassani, Sara Hosseinzadeh, Rajapaksa, Sajith, Duddu, Hema, Wang, Menglu, Shirtliffe, Steve, Ryu, Seungbum, Josuttes, Anique, Zhang, Ti, Vail, Sally, Pozniak, Curtis, Parkin, Isobel, Stavness, Ian, and Eramian, Mark

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Lodging, the permanent bending over of food crops, leads to poor plant growth and development. Consequently, lodging results in reduced crop quality, lowers crop yield, and makes harvesting difficult. Plant breeders routinely evaluate several thousand breeding lines, and therefore, automatic lodging detection and prediction is of great value aid in selection. In this paper, we propose a deep convolutional neural network (DCNN) architecture for lodging classification using five spectral channel orthomosaic images from canola and wheat breeding trials. Also, using transfer learning, we trained 10 lodging detection models using well-established deep convolutional neural network architectures. Our proposed model outperforms the state-of-the-art lodging detection methods in the literature that use only handcrafted features. In comparison to 10 DCNN lodging detection models, our proposed model achieves comparable results while having a substantially lower number of parameters. This makes the proposed model suitable for applications such as real-time classification using inexpensive hardware for high-throughput phenotyping pipelines. The GitHub repository at https://github.com/FarhadMaleki/LodgedNet contains code and models.

Published
2019

7. Genome structural evolution in Brassica crops

Author

He, Zhesi, Ji, Ruiqin, Havlickova, Lenka, Wang, Lihong, Li, Yi, Lee, Huey Tyng, Song, Jiaming, Koh, Chushin, Yang, Jinghua, Zhang, Mingfang, Parkin, Isobel A. P., Wang, Xiaowu, Edwards, David, King, Graham J., Zou, Jun, Liu, Kede, Snowdon, Rod J., Banga, Surinder S., Machackova, Ivana, and Bancroft, Ian

Published
2021
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8. A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds.

Author

Wentao Zhang, Higgins, Erin E., Robinson, Stephen J., Clarke, Wayne E., Boyle, Kerry, Sharpe, Andrew G., Fobert, Pierre R., and Parkin, Isobel A. P.

Subjects
RAPESEED, GENE regulatory networks, QUANTITATIVE genetics, LOCUS (Genetics), GENOMICS, OILSEEDS
Abstract

Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eightythree subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality. [ABSTRACT FROM AUTHOR]

Published
2024
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25. A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

Author

Clarke, Wayne E., Higgins, Erin E., Plieske, Joerg, Wieseke, Ralf, Sidebottom, Christine, Khedikar, Yogendra, Batley, Jacqueline, Edwards, Dave, Meng, Jinling, Li, Ruiyuan, Lawley, Cynthia Taylor, Pauquet, Jérôme, Laga, Benjamin, Cheung, Wing, Iniguez-Luy, Federico, Dyrszka, Emmanuelle, Rae, Stephen, Stich, Benjamin, Snowdon, Rod J., Sharpe, Andrew G., Ganal, Martin W., and Parkin, Isobel A. P.

Published
2016
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28. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Author

Chalhoub, Boulos, Denoeud, France, Liu, Shengyi, Parkin, Isobel A. P., Tang, Haibao, Wang, Xiyin, Chiquet, Julien, Belcram, Harry, Tong, Chaobo, Samans, Birgit, Corréa, Margot, Da Silva, Corinne, Just, Jérémy, Falentin, Cyril, Koh, Chu Shin, Le Clainche, Isabelle, Bernard, Maria, Bento, Pascal, Noel, Benjamin, Labadie, Karine, Alberti, Adriana, Charles, Mathieu, Arnaud, Dominique, Guo, Hui, Daviaud, Christian, Alamery, Salman, Jabbari, Kamel, Zhao, Meixia, Edger, Patrick P., Chelaifa, Houda, Tack, David, Lassalle, Gilles, Mestiri, Imen, Schnel, Nicolas, Le Paslier, Marie-Christine, Fan, Guangyi, Renault, Victor, Bayer, Philippe E., Golicz, Agnieszka A., Manoli, Sahana, Lee, Tae-Ho, Thi, Vinh Ha Dinh, Chalabi, Smahane, Hu, Qiong, Fan, Chuchuan, Tollenaere, Reece, Lu, Yunhai, Battail, Christophe, Shen, Jinxiong, Sidebottom, Christine H. D., Wang, Xinfa, Canaguier, Aurélie, Chauveau, Aurélie, Bérard, Aurélie, Deniot, Gwenaëlle, Guan, Mei, Liu, Zhongsong, Sun, Fengming, Lim, Yong Pyo, Lyons, Eric, Town, Christopher D., Bancroft, Ian, Wang, Xiaowu, Meng, Jinling, Ma, Jianxin, Pires, J. Chris, King, Graham J., Brunel, Dominique, Delourme, Régine, Renard, Michel, Aury, Jean-Marc, Adams, Keith L., Batley, Jacqueline, Snowdon, Rod J., Tost, Jorg, Edwards, David, Zhou, Yongming, Hua, Wei, Sharpe, Andrew G., Paterson, Andrew H., Guan, Chunyun, and Wincker, Patrick

Published
2014

32. Sequencing of Camelina neglecta, a diploid progenitor of the hexaploid oilseed Camelina sativa.

Author

Chaudhary, Raju, Koh, Chu Shin, Perumal, Sampath, Jin, Lingling, Higgins, Erin E., Kagale, Sateesh, Smith, Mark A., Sharpe, Andrew G., and Parkin, Isobel A. P.

Subjects
CAMELINA, BRASSICA, CHROMOSOMAL rearrangement, CROP improvement, ARABIDOPSIS thaliana, WHOLE genome sequencing
Abstract

Summary: Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance while providing a tool to study the evolution of polyploids. A highly contiguous chromosome‐level genome sequence of C. neglecta with an N50 size of 29.1 Mb was generated utilizing Pacific Biosciences (PacBio, Menlo Park, CA) long‐read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C. sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34 061 genes suggested subgenome 1 of C. sativa directly descended from C. neglecta around 1.2 mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C. sativa in comparison with C. neglecta, and the complete lack of fractionation of meiosis‐specific genes attests to the neopolyploid status of C. sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow for the identification and exploitation of novel variation for Camelina crop improvement. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Identification of QTL and alleles for agronomic and seed quality traits in C genome using a Brassica napus population diversified with B. oleracea.

Author

Nikzad, Azam, Kebede, Berisso, Megha, Swati, Buchwaldt, Miles, Parkin, Isobel, and Rahman, Habibur

Subjects
COLE crops, LOCUS (Genetics), RAPESEED, ALLELES in plants, SEED quality, ALLELES, GENOMES
Abstract

A genome‐wide association study (GWAS) was carried out by using a Brassica napus population of 175 lines, developed from six B. napus × B. oleracea interspecific crosses, and 5,743 single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) for agronomic and seed quality traits and to understand the effect of B. oleracea alleles on these traits. Heritability of these traits varied from 52.9 to 84.1%. About 79% of the SNPs were positioned to the nine C genome chromosomes, while only 21% to the 10 A genome chromosomes; this was largely due to little genetic variation in the A genome of this population, as expected. However, the SNPs were distributed throughout the entire length of the chromosomes suggesting their usefulness in GWAS. The C genome SNPs detected nine genomic regions affecting these traits. This included the genomic regions of C2 and C5 affecting days to flowering, C1 affecting the duration of grain‐filling period, C1, C5, and C8 affecting oil content, and C1, C2, and C6 affecting glucosinolate content; among these, some of the loci has not been reported previously. The QTL alleles of B. oleracea which can be beneficial in oilseed B. napus, such as the C5 QTL allele for the earliness of flowering, were also identified. Several putative candidate genes were identified in the QTL regions. Thus, the results provided evidence of the utility of the B. oleracea gene pool for use in unveiling the unidentified QTL in B. napus as well as its use in breeding. Core Ideas: C genome alleles from six vegetable Brassica oleracea accessions were introgressed into oilseed B. napus.Quantitative trait loci for agronomic and seed quality traits were mapped and the effect of Brassica oleracea alleles in B. napus were detected.Beneficial quantitative trait loci allele of Brassica oleracea were identified for use in B. napus breeding.C genome quantitative trait loci that has not been reported previously were disclosed. [ABSTRACT FROM AUTHOR]

Published
2023
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38. Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Author

Chawla, Harmeet Singh, Lee, HueyTyng, Gabur, Iulian, Vollrath, Paul, Tamilselvan‐Nattar‐Amutha, Suriya, Obermeier, Christian, Schiessl, Sarah V., Song, Jia‐Ming, Liu, Kede, Guo, Liang, Parkin, Isobel A. P., and Snowdon, Rod J.

Subjects
genome rearrangement, Polyploidy, presence–absence variants, Brassica napus, food and beverages, PAV, Humans, Polymorphism, Single Nucleotide, Research Articles, Genome, Plant, Research Article, Disease Resistance
Abstract

Summary Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single‐nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small‐ (30–10 000 bp) to mid‐scale (10 000–30 000 bp) SV and their impact on evolution and adaptation‐related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high‐throughput genome screening methods. Here, we describe how long‐read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small‐ to mid‐scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small‐ to mid‐scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short‐read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco‐geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium‐coverage long‐read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

Published
2020

46. Identification of QTL and alleles for agronomic and seed quality traits in C genome using a Brassica napuspopulation diversified with B. oleracea

Author

Nikzad, Azam, Kebede, Berisso, Megha, Swati, Buchwaldt, Miles, Parkin, Isobel, and Rahman, Habibur

Abstract

A genome‐wide association study (GWAS) was carried out by using a Brassica napuspopulation of 175 lines, developed from six B. napus × B. oleraceainterspecific crosses, and 5,743 single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) for agronomic and seed quality traits and to understand the effect of B. oleraceaalleles on these traits. Heritability of these traits varied from 52.9 to 84.1%. About 79% of the SNPs were positioned to the nine C genome chromosomes, while only 21% to the 10 A genome chromosomes; this was largely due to little genetic variation in the A genome of this population, as expected. However, the SNPs were distributed throughout the entire length of the chromosomes suggesting their usefulness in GWAS. The C genome SNPs detected nine genomic regions affecting these traits. This included the genomic regions of C2 and C5 affecting days to flowering, C1 affecting the duration of grain‐filling period, C1, C5, and C8 affecting oil content, and C1, C2, and C6 affecting glucosinolate content; among these, some of the loci has not been reported previously. The QTL alleles of B. oleraceawhich can be beneficial in oilseed B. napus, such as the C5 QTL allele for the earliness of flowering, were also identified. Several putative candidate genes were identified in the QTL regions. Thus, the results provided evidence of the utility of the B. oleraceagene pool for use in unveiling the unidentified QTL in B. napusas well as its use in breeding. C genome alleles from six vegetable Brassica oleraceaaccessions were introgressed into oilseed B. napus.Quantitative trait loci for agronomic and seed quality traits were mapped and the effect of Brassica oleraceaalleles in B. napuswere detected.Beneficial quantitative trait loci allele of Brassica oleraceawere identified for use in B. napusbreeding.C genome quantitative trait loci that has not been reported previously were disclosed.

Published
2023
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50. ePlant in 2021: New Species, Viewers, Data Sets, and Widgets

Author

Waese-Perlman, Ben, primary, Pasha, Asher, additional, Ho, Chantal, additional, Azhieh, Amirahmad, additional, Liu, Yushan, additional, Sullivan, Alexander, additional, Lau, Vincent, additional, Esteban, Eddi, additional, Waese, Jamie, additional, Ly, George, additional, Hooper, Cornelia, additional, Staton, S. Evan, additional, Brereton, Nicholas, additional, Le, Cuong, additional, Nelson, Rex, additional, Lumba, Shelley, additional, Goodstein, David, additional, Millar, A. Harvey, additional, Parkin, Isobel, additional, Lukens, Lewis, additional, Ehlting, Juergen, additional, Rieseberg, Loren, additional, Pitre, Frédéric, additional, Brown, Anne, additional, and Provart, Nicholas J., additional

Published
2021
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