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Book ; Online ; E-Book: The flax genome

You, Frank M. / Fofana, Bourlaye

(Compendium of Plant Genomes Series)

2023

Abstract: The Flax Genome is a comprehensive compilation of most recent studies focused on reference genome, genetic resources and molecular diversity, breeding, QTL mapping, gene editing tools, functional genomics and metabolomics, molecular breeding via genomic ... ...

Author's details	Frank M. You and Bourlaye Fofana, editors
Series title	Compendium of Plant Genomes Series
Abstract	The Flax Genome is a comprehensive compilation of most recent studies focused on reference genome, genetic resources and molecular diversity, breeding, QTL mapping, gene editing tools, functional genomics and metabolomics, molecular breeding via genomic selection, and genomic resources. The flax genome reference sequences and the new genome assemblies are presented. A list of flax QTL and candidate genes associated with more than 35 traits, including yield and agronomic, seed quality and fatty acid composition, fibre quality and yield, abiotic stress, and disease resistance traits, are summarized. A QTL- based genomic selection strategy and genome–editing tools are systematically introduced. In addition, huge amounts of flax genomic resources generated in the last decade are summarized. The book contains 13 chapters with about 390 pages authored by globally reputed researchers in the relevant fields to this crop The book is intended to be useful to students, teachers, and researchers interested in traditional and molecular breeding, pathology, molecular genetics and breeding, bioinformatics and computational biology, and functional genomics.
Keywords	Flax ; Flax industry
Subject code	633.85
Language	English
Size	1 online resource (301 pages)
Edition	1st ed. 2023.
Publisher	Springer Nature Switzerland AG
Publishing place	Cham, Switzerland
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
ISBN	3-031-16061-4 ; 9783031160608 ; 978-3-031-16061-5 ; 3031160606
DOI	10.1007/978-3-031-16061-5
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article: Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes.

Fofana, Bourlaye / Soto-Cerda, Braulio / Zaidi, Moshin / Main, David / Fillmore, Sherry

Frontiers in genetics

2024 Volume 14, Page(s) 1306519

Abstract: Cultivated potato ( ...

Abstract	Cultivated potato (
Language	English
Publishing date	2024-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1306519
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Article: Aluminum in plant: Benefits, toxicity and tolerance mechanisms.

Ofoe, Raphael / Thomas, Raymond H / Asiedu, Samuel K / Wang-Pruski, Gefu / Fofana, Bourlaye / Abbey, Lord

Frontiers in plant science

2023 Volume 13, Page(s) 1085998

Abstract: Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental ... ...

Abstract	Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental age, and growing conditions. Although Al can be beneficial to plants by stimulating growth and mitigating biotic and abiotic stresses, it remains unknown how Al mediates these effects since its biological significance in cellular systems is still unidentified. Al is considered a major limiting factor restricting plant growth and productivity in acidic soils. It instigates a series of phytotoxic symptoms in several Al-sensitive crops with inhibition of root growth and restriction of water and nutrient uptake as the obvious symptoms. This review explores advances in Al benefits, toxicity and tolerance mechanisms employed by plants on acidic soils. These insights will provide directions and future prospects for potential crop improvement.
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2022.1085998
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Article ; Online: Structure and genetic diversity of Canadian Maritimes wild hops.

Somalraju, Ashok / Soto-Cerda, Braulio / Ghose, Kaushik / McCallum, Jason / Knox, Ron / Fofana, Bourlaye

Genome

2023 Volume 67, Issue 1, Page(s) 24–30

Abstract: Studies on the northeastern American native hops ( ...

Abstract	Studies on the northeastern American native hops (
MeSH term(s)	Canada ; Humulus/genetics ; Humulus/chemistry ; Haplotypes ; Microsatellite Repeats ; Genetic Variation
Language	English
Publishing date	2023-09-22
Publishing country	Canada
Document type	Journal Article
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/gen-2023-0045
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Article: Foliar selenium application reduces late blight severity and incidence in potato and acts as a pathogen growth inhibitor and elicitor of induced plant defence

Somalraju, Ashok / Mccallum, Jason L. / Main, David / Peters, Rick D. / Fofana, Bourlaye

Canadian journal of plant pathology. 2022 Jan. 02, v. 44, no. 1

2022

Abstract: Late blight caused by Phytophthora infestans is a serious threat to potato production. Currently, solutions to manage late blight in organic systems are scarce. This study was undertaken to evaluate the effect of selenium (Se) on plant emergence from ... ...

Abstract	Late blight caused by Phytophthora infestans is a serious threat to potato production. Currently, solutions to manage late blight in organic systems are scarce. This study was undertaken to evaluate the effect of selenium (Se) on plant emergence from seed pre-treated with Se and the seed decay pathogens Pectobacterium carotovorum ssp. carotovorum and Fusarium sambucinum, and on foliar potato late blight following inoculation with P. infestans and foliar treatment with Se. The potential modes of action of Se were also evaluated. Following inoculation of the seed decay pathogens on potato seed pre-treated with different rates of Se, plant emergence was not affected by Se treatment. By pre-treating potato seed with different Se rates, and applying different foliar Se rates on potato plants subsequently inoculated with the late blight pathogen in a greenhouse setting, we showed that foliar Se application alone or combined with Se seed treatment reduced the severity and incidence of late blight, and activated the production of secondary metabolites in potato leaves and tubers. Further, in vitro studies showed that Se directly inhibited the mycelial growth of P. infestans and other important plant pathogens, including Fusarium graminearum and Sclerotinia sclerotiorum. The data suggest that Se acts as an inducer of plant defences, while also inhibiting fungal growth. The study highlights the potential of Se for managing late blight, and suggests that its application could contribute to improving plant health in greenhouse production systems by helping to control diseases caused by P. infestans, F. graminearum and S. sclerotiorum.
Keywords	Fusarium graminearum ; Fusarium sambucinum ; Phytophthora infestans ; Sclerotinia sclerotiorum ; elicitors ; fungal growth ; greenhouse production ; greenhouses ; growth inhibitors ; mycelium ; plant pathology ; potatoes ; pretreatment ; secondary metabolites ; seed treatment ; selenium
Language	English
Dates of publication	2022-0102
Size	p. 39-55.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	763044-x
ISSN	0706-0661 ; 1715-2992
ISSN	0706-0661 ; 1715-2992
DOI	10.1080/07060661.2021.1954093
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Genetic Dissection of Nitrogen Use-Related Traits in Flax (

Soto-Cerda, Braulio J / Larama, Giovanni / Cloutier, Sylvie / Fofana, Bourlaye / Inostroza-Blancheteau, Claudio / Aravena, Gabriela

International journal of molecular sciences

2023 Volume 24, Issue 24

Abstract: Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops ...

Abstract	Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43,
MeSH term(s)	Flax/genetics ; Flax/metabolism ; Genome-Wide Association Study ; Genomics ; Nitrogen/metabolism ; Plant Breeding ; RNA-Seq ; Seedlings/metabolism
Chemical Substances	Nitrogen (N762921K75)
Language	English
Publishing date	2023-12-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms242417624
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Article: Seed priming with pyroligneous acid mitigates aluminum stress, and promotes tomato seed germination and seedling growth

Ofoe, Raphael / Gunupuru, Lokanadha R. / Wang-Pruski, Gefu / Fofana, Bourlaye / Thomas, Raymond H. / Abbey, Lord

Plant Stress. 2022 Apr., v. 4

2022

Abstract: Aluminum (Al) toxicity in acidic soils is a major constraint for seed germination and crop growth. Pyroligneous acid (PA) is rich in bioactive compounds that can enhance crop growth and tolerance to environmental stresses including toxic trace elements, ... ...

Abstract	Aluminum (Al) toxicity in acidic soils is a major constraint for seed germination and crop growth. Pyroligneous acid (PA) is rich in bioactive compounds that can enhance crop growth and tolerance to environmental stresses including toxic trace elements, but under studied. In this study, we investigated the effect of tomato (Solanum lycopersicum L. ‘Scotia’) seed priming with different rates of PA (i.e., 0, 0.5:100, 1:100, 1:300, 1:600, 1:900, 1:1200, and 2:100 PA/ddH₂O (v/v)) on germination and seedling growth under different growing medium Al concentrations (i.e., 0, 0.5, and 1.25 mM aluminum chloride termed Al). The results showed that priming tomato seed with 2:100 PA for 24 hr significantly (p < 0.01) enhanced seed germination indices and seedling growth. PA significantly (p < 0.05) improved seed germination index and seedling vigor irrespective of the imposed Al stress compared to the control, but not seed germination percentage. Priming with PA also increased the total lengths and surface areas of seedling hypocotyls and roots, root volume, and seedling fresh weight. In most cases, seedling growth of both the control and the PA primed groups were not affected by the 0.5 mM Al. Additionally, hydrogen peroxide and malonaldehyde contents of seedlings were reduced while proline and soluble protein contents were significantly (p < 0.001) increased in PA primed seedlings compared to the control. Furthermore, PA-primed seedlings exhibited enhanced peroxidase (POD) activities, and relatively high expression of auxin response factor and antioxidant genes (i.e., glutathione reductase, POD, superoxide dismutase, catalase, and ascorbate peroxidase 1). These findings suggest that seed priming with PA can mitigates Al stress, and improve tomato seed germination and seedling growth via improving antioxidant defense system against Al-induced oxidative stress. Future studies will be required to investigate molecular mechanisms.
Keywords	Solanum lycopersicum ; aluminum ; aluminum chloride ; antioxidant activity ; ascorbate peroxidase ; auxins ; catalase ; glutathione-disulfide reductase ; hydrogen peroxide ; hypocotyls ; malondialdehyde ; oxidative stress ; peroxidase ; plant stress ; proline ; seed germination ; seedling growth ; seedlings ; superoxide dismutase ; tomatoes ; toxicity ; vigor
Language	English
Dates of publication	2022-04
Publishing place	Elsevier B.V.
Document type	Article
ISSN	2667-064X
DOI	10.1016/j.stress.2022.100083
Database	NAL-Catalogue (AGRICOLA)

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Article: Choice of cover crop influences soil fungal and bacterial communities in Prince Edward Island, Canada

Aiyer, Harini / Fofana, Bourlaye / Fraser, Tandra / Caldwell, Claude / McKenzie-Gopsill, Andrew / Mills, Aaron / Foster, Adam

Canadian journal of microbiology. 2022 Mar. 28, v. 68, no. 7

2022

Abstract: Soil fungal and bacterial communities play various roles in agroecosystems and are significantly influenced by agricultural management practices. Currently, little is known about the effects of selected cover crops on soil fungal and bacterial ... ...

Abstract	Soil fungal and bacterial communities play various roles in agroecosystems and are significantly influenced by agricultural management practices. Currently, little is known about the effects of selected cover crops on soil fungal and bacterial communities in no-till systems. In this study, eight cover crops, three mixed crops, and an unmanaged fallow control were evaluated over 2 years for their effects on the soil microbiome. Internal transcribed spacer (ITS) and 16S rRNA amplicon sequencing was performed to characterize fungal and bacterial communities in the soil during the cover crop growing season, and in the subsequent year. Fungal and bacterial alpha diversity significantly increased over time and were influenced in the subsequent growing season by choice of cover crops. Some fungal and bacterial trophic and functional groups were also affected by crop choice. Fungal pathotroph abundance was positively associated with oilseed radish, alfalfa, and phacelia, but negatively associated with sorghum–sudangrass. Beneficial symbiotrophic fungi and functional nitrification-related bacterial groups were also associated with sorghum–sudangrass and buckwheat. These findings suggest that choice of cover crops influences the soil microbial community composition and may impact plant health in the subsequent crops.
Keywords	Sorghum bicolor subsp. drummondii ; agroecosystems ; alfalfa ; buckwheat ; community structure ; cover crops ; internal transcribed spacers ; no-tillage ; oilseeds ; plant health ; radishes ; soil ; soil fungi ; species diversity ; Prince Edward Island
Language	English
Dates of publication	2022-0328
Size	p. 465-482.
Publishing place	Canadian Science Publishing
Document type	Article
ZDB-ID	280534-0
ISSN	1480-3275 ; 0008-4166
ISSN (online)	1480-3275
ISSN	0008-4166
DOI	10.1139/cjm-2021-0360
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Choice of cover crop influences soil fungal and bacterial communities in Prince Edward Island, Canada.

Aiyer, Harini / Fofana, Bourlaye / Fraser, Tandra / Caldwell, Claude / McKenzie-Gopsill, Andrew / Mills, Aaron / Foster, Adam

Canadian journal of microbiology

2022 Volume 68, Issue 7, Page(s) 465–482

Abstract	Soil fungal and bacterial communities play various roles in agroecosystems and are significantly influenced by agricultural management practices. Currently, little is known about the effects of selected cover crops on soil fungal and bacterial communities in no-till systems. In this study, eight cover crops, three mixed crops, and an unmanaged fallow control were evaluated over 2 years for their effects on the soil microbiome. Internal transcribed spacer (ITS) and 16S rRNA amplicon sequencing was performed to characterize fungal and bacterial communities in the soil during the cover crop growing season, and in the subsequent year. Fungal and bacterial alpha diversity significantly increased over time and were influenced in the subsequent growing season by choice of cover crops. Some fungal and bacterial trophic and functional groups were also affected by crop choice. Fungal pathotroph abundance was positively associated with oilseed radish, alfalfa, and phacelia, but negatively associated with sorghum-sudangrass. Beneficial symbiotrophic fungi and functional nitrification-related bacterial groups were also associated with sorghum-sudangrass and buckwheat. These findings suggest that choice of cover crops influences the soil microbial community composition and may impact plant health in the subsequent crops.
MeSH term(s)	Bacteria/genetics ; Crops, Agricultural/microbiology ; Prince Edward Island ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology
Chemical Substances	RNA, Ribosomal, 16S ; Soil
Language	English
Publishing date	2022-03-28
Publishing country	Canada
Document type	Journal Article
ZDB-ID	280534-0
ISSN	1480-3275 ; 0008-4166
ISSN (online)	1480-3275
ISSN	0008-4166
DOI	10.1139/cjm-2021-0360
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Article: Integrating multi-locus genome-wide association studies with transcriptomic data to identify genetic loci underlying adult root trait responses to drought stress in flax (Linum usitatissimum L.)

Soto-Cerda, Braulio J. / Larama, Giovanni / Gajardo, Humberto / Inostroza-Blancheteau, Claudio / Cloutier, Sylvie / Fofana, Bourlaye / Abanto, Michel / Aravena, Gabriela

Environmental and experimental botany. 2022 Oct., v. 202

2022

Abstract: Water stress is a major constraint on crop production and, root systems are one of the key features of plants determining drought tolerance and yield. In this study, five root morphological traits and their stability indices were evaluated at the ... ...

Abstract	Water stress is a major constraint on crop production and, root systems are one of the key features of plants determining drought tolerance and yield. In this study, five root morphological traits and their stability indices were evaluated at the reproductive stage on an association panel consisting of 120 diverse Linum usitatissimum accessions grown under well-watered and water-limiting conditions. To identify quantitative trait loci (QTL) and candidate genes positively influencing root traits under drought, combined multi-locus genome-wide association studies (ML-GWAS) and transcriptomic data analysis were carried out. A total of 112 QTL were identified accounting for 0.45–24.28 % of the phenotypic variation for root-related traits. Fifty QTL were detected by at least two ML-GWAS models, and 26 were co-located with previously reported QTL associated with yield-related traits under drought and early root and shoot development. Phenotypic differences between two contrasting subsets of accessions for the traits assessed were attributable to the accumulation of positive QTL alleles (PQTL), where the subset with the largest number of PQTL registered 154 % and 69 % greater total root length and yield under drought stress, respectively, than the subset with the fewest PQTL. Transcriptomic data analysis identified 766 differentially expressed genes (DEGs) responsive to drought stress in 108 QTL. Annotation of the 766 DEGs yielded functional genes involved in root development, stomatal closure, ROS (reactive oxygen species) scavenging, and hormone responses, among others. Taken together, the combined use of GWAS and transcriptomic data analyses provide the foundation for our enhanced understanding of root trait morphological changes in response to drought stress, and to achieve superior yield resilience/stability under water shortages in flax through enhanced molecular breeding. All data supporting the findings of this study are available within the paper and within its Supplementary data
Keywords	Linum usitatissimum ; adults ; crop production ; drought ; drought tolerance ; flax ; gene expression regulation ; phenotype ; phenotypic variation ; quantitative traits ; stomatal movement ; transcriptomics ; water shortages ; water stress
Language	English
Dates of publication	2022-10
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	195968-2
ISSN	0098-8472
ISSN	0098-8472
DOI	10.1016/j.envexpbot.2022.105019
Database	NAL-Catalogue (AGRICOLA)

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