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  1. AU="Odeny, D A"
  2. AU="Naserghandi, Alvand"
  3. AU="Nelson, Eric Andrew"
  4. AU=Verkman Alan S.
  5. AU=Garg Parvesh M
  6. AU="Luigi Aprea"
  7. AU="Cortes, Jorge Alberto"
  8. AU="Malehi, Amal Saki"
  9. AU=Rieber Nikolaus
  10. AU="Jennifer R Habel"
  11. AU="Sun, Yan Ni"
  12. AU="Nath, Sujith S"
  13. AU=Gao Xuesong
  14. AU="Tankelevich, Michael"
  15. AU=Jean Guillaume
  16. AU=Xiong J
  17. AU="Rollins, Alicia"
  18. AU="Shufang Sun"
  19. AU="Daisuke Kasai"
  20. AU="Bernadette L. Jenner"
  21. AU=Zhang Jing
  22. AU="Stoica, Maria"
  23. AU="Romina Valentini"
  24. AU="Bagó, György Attila"
  25. AU="Bahrar, Harsh"
  26. AU="Judd, Dallin"

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  1. Artikel ; Online: The African Eggplant

    Moenga, S M / Odeny, D A

    2022  

    Abstract: The African eggplant (Solanum aethiopicum L.) is a promising nutritious African vegetable that is also grown in South and Central America and certain parts of Italy and France. There are four known cultivar groups of the African eggplant, which together ... ...

    Abstract The African eggplant (Solanum aethiopicum L.) is a promising nutritious African vegetable that is also grown in South and Central America and certain parts of Italy and France. There are four known cultivar groups of the African eggplant, which together with its progenitor, Solanum anguivi, form the hypervariable scarlet eggplant complex. Despite its importance as food, medicine, and source of disease resistance genes, there has been limited research investment in the improvement of the African eggplant and it remains an orphan crop. We review the botanical description of the cultivar groups, the available genetic and genomic resources, and the germplasm conservation efforts within the primary and secondary genepools. We present the recently published draft genome sequence and make detailed comparisons of the genome with other genomes within the Solanaceae family. We further demonstrate the immediate utilization of the draft genome for gene discovery by retrieving orthologous seed dormancy candidate genes that can be characterized to improve this trait in the African eggplant. We finally provide evidence of why the African eggplant is underutilized and make some recommendations for future breeding, research investment, and marketing efforts that promise to enhance its utilization.
    Schlagwörter Genetics and Genomics
    Thema/Rubrik (Code) 940
    Erscheinungsdatum 2022-11-04
    Verlag Springer Nature
    Erscheinungsland in
    Dokumenttyp Artikel ; Online
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  2. Artikel ; Online: Physicochemical and sensory attributes of gluten-free sourdough breads produced from underutilised African cereal flours and flour blends

    Adepehin, J O / Enujiugha, V N / Badejo, A A / Young, G M / Odeny, D A

    2022  

    Abstract: To seek potential alternative(s) for imported wheat in the African baking industry, the physicochemical parameters and sensory attributes of sourdough breads developed from locally sourced underutilised cereals and their blends were assessed. Processed ... ...

    Abstract To seek potential alternative(s) for imported wheat in the African baking industry, the physicochemical parameters and sensory attributes of sourdough breads developed from locally sourced underutilised cereals and their blends were assessed. Processed sorghum (Sorghum bicolour), finger millet (Eleusine coracana) and pearl millet (Pennisetum glaucum) and their composites (50:50) were used to produce sourdough. Sourdough and flour-sourdough blends (30% sourdough) were used in making gluten-free breads. The protein content of the breads ranged from 16.29% to 39.26%, whereas the fat, crude fibre, ash and carbohydrate contents fell between 14.02–18.80%, 0.55–1.22%, 1.90–3.32% and 42.16–65.61%, respectively. The calculated energy value of the gluten-free breads (405.99–446.39 Kcal per 100 g) exceeded that of wheat bread (396.43 Kcal per 100 g), while the specific loaf volume varied from 1.46 to 1.80 cm3 g-1. Although the produced gluten-free breads have improved nutritional content compared to conventional wheat bread, they were at best moderately liked. This is perhaps due to the non-cohesive nature of the crumbs and psychological preference for known products. Further research targeted at improving the organoleptic properties of these sourdough breads is recommended.
    Schlagwörter Pearl Millet ; Finger Millet ; Sorghum
    Sprache Englisch
    Erscheinungsdatum 2022-09-17
    Verlag Wiley
    Erscheinungsland in
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    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Plant genome resequencing and population genomics

    Song, B / Ning, W / Wei, D / Jiang, M / Zhu, K / Wang, X / Edwards, D / Odeny, D A / Cheng, S

    Current status and future prospects

    2023  

    Abstract: Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance ... ...

    Abstract Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
    Schlagwörter Genetic Engineering ; Genetics and Genomics
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2023-08-31
    Verlag Cell Press
    Erscheinungsland in
    Dokumenttyp Artikel ; Online
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  4. Artikel ; Online: Genomic and phenotypic characterization of finger millet indicates a complex diversification history

    Bančič, J / Odeny, D A / Ojulong, H F / Josiah, S M / Buntjer, J / Gaynor, R C / Hoad, S P / Gorjanc, G

    2023  

    Abstract: Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide ... ...

    Abstract Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.
    Schlagwörter Finger Millet ; Genetics and Genomics
    Thema/Rubrik (Code) 571
    Sprache Englisch
    Erscheinungsdatum 2023-11-20
    Verlag Crop Science Society of America
    Erscheinungsland in
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  5. Artikel ; Online: Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources

    Ruperao, P / Gandham, P / Odeny, D A / Mayes, S / Selvanayagam, S / Thirunavukkarasu, N / Das, R R / Srikanda, M / Gandhi, H / Habyarimana, E / Manyasa, E / Nebie, B / Deshpande, S P / Rathore, A

    2023  

    Abstract: Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific ... ...

    Abstract Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.
    Schlagwörter Sorghum
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2023-03-23
    Verlag Frontiers
    Erscheinungsland in
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  6. Artikel ; Online: Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources

    Ruperao, P / Gandham, P / Odeny, D A / Mayes, S / Selvanayagam, S / Thirunavukkarasu, N / Das, R R / Srikanda, M / Gandhi, H / Habyarimana, E / Manyasa, E / Nebie, B / Deshpande, S P / Rathore, A

    2023  

    Abstract: Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific ... ...

    Abstract Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.
    Schlagwörter Sorghum ; Genetics and Genomics
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2023-03-17
    Verlag Frontiers Media
    Erscheinungsland in
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Genome‑wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection

    Achola, E / Wasswa, P / Fonceka, D / Clevenger, J P / Bajaj, P / Ozias‑Akins, P / Rami, J / Deom, C M / Hoisington, D A / Edema, R / Odeny, D A / Okello, D K

    2023  

    Abstract: Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: ... ...

    Abstract Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523 high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1 on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.
    Schlagwörter Groundnut ; Plant Pathology ; Africa
    Thema/Rubrik (Code) 630
    Sprache Englisch
    Erscheinungsdatum 2023-03-10
    Verlag Springer
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    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: First Report of Sweet potato badnavirus A and Sweet potato badnavirus B in South Africa.

    Nhlapo, T F / Mulabisana, J M / Odeny, D A / Rey, M E C / Rees, D J G

    Plant disease

    2018  Band 102, Heft 9, Seite(n) 1865

    Mesh-Begriff(e) Badnavirus/classification ; Badnavirus/genetics ; Badnavirus/physiology ; DNA, Viral/genetics ; Ipomoea batatas/virology ; Plant Diseases/virology ; South Africa
    Chemische Substanzen DNA, Viral
    Sprache Englisch
    Erscheinungsdatum 2018-07-23
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 754182-x
    ISSN 1943-7692 ; 0191-2917
    ISSN (online) 1943-7692
    ISSN 0191-2917
    DOI 10.1094/PDIS-08-17-1235-PDN
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Heritability Analysis and Phenotypic Characterization of Spider Plant (Cleome gynandra L.) for Yield

    Kangai Munene, A / Nzuve, F / Ambuko, J / Odeny, D A

    2018  

    Abstract: Knowledge on phenotypic diversity among existing spider plant accessions is a milestone in the improvement of spider plant, which is a highly nutritious indigenous vegetable in Kenya. A study involving agronomic and morphological characterization of 49 ... ...

    Abstract Knowledge on phenotypic diversity among existing spider plant accessions is a milestone in the improvement of spider plant, which is a highly nutritious indigenous vegetable in Kenya. A study involving agronomic and morphological characterization of 49 spider plant accessions assembled from East and South Africa was carried out at the University of Nairobi Field Station for two seasons in a randomized complete block design with three replications. Phenotypic data was collected on growth habit, flower, petiole, leaf and stem colour, petiole, leaf and stem hairiness, number of leaves per plant, plant height, number of primary branches, leaf length and width, single leaf area, and chlorophyll content according to FAO descriptors with modifications. Data was analyzed using both DARwin software V6 and Genstat Version 14. We observed significant differences among the traits implying great genetic variability among the evaluated spider plant accessions. The high genetic variation was further validated using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) clustering method with stem and flower colour as key traits. The 49-spider plant accessions were clustered into 2 major groups, each consisting of Kenyan and South African accessions. Stepwise regression revealed that plant height had the most influence on yield in terms of number of leaves per plant. We also observed high heritability for several traits including days to flowering (91%), number of leaves per plant (99%), plant height (99%), number of primary branches (94%), chlorophyll content (94%), and single leaf area (87%). Our results reveal the high genetic variation between different spider plant accessions, especially from different regions of Africa that could be further exploited to improve productivity in the plant. The high heritability of most of the yield related traits is promising for improving yield in the crop through direct selection.
    Schlagwörter Biotechnology ; Molecular Biology ; Plant Breeding ; Genetics and Genomics ; African Agriculture ; Kenya
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Verlag Hindawi Publishing Corporation
    Erscheinungsland in
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Heritability Analysis and Phenotypic Characterization of Spider Plant (Cleome gynandra L.) for Yield

    Kangai Munene, A / Nzuve, F / Ambuko, J / Odeny, D A

    2018  

    Abstract: Knowledge on phenotypic diversity among existing spider plant accessions is a milestone in the improvement of spider plant, which is a highly nutritious indigenous vegetable in Kenya. A study involving agronomic and morphological characterization of 49 ... ...

    Abstract Knowledge on phenotypic diversity among existing spider plant accessions is a milestone in the improvement of spider plant, which is a highly nutritious indigenous vegetable in Kenya. A study involving agronomic and morphological characterization of 49 spider plant accessions assembled from East and South Africa was carried out at the University of Nairobi Field Station for two seasons in a randomized complete block design with three replications. Phenotypic data was collected on growth habit, flower, petiole, leaf and stem colour, petiole, leaf and stem hairiness, number of leaves per plant, plant height, number of primary branches, leaf length and width, single leaf area, and chlorophyll content according to FAO descriptors with modifications. Data was analyzed using both DARwin software V6 and Genstat Version 14. We observed significant differences among the traits implying great genetic variability among the evaluated spider plant accessions. The high genetic variation was further validated using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) clustering method with stem and flower colour as key traits. The 49-spider plant accessions were clustered into 2 major groups, each consisting of Kenyan and South African accessions. Stepwise regression revealed that plant height had the most influence on yield in terms of number of leaves per plant. We also observed high heritability for several traits including days to flowering (91%), number of leaves per plant (99%), plant height (99%), number of primary branches (94%), chlorophyll content (94%), and single leaf area (87%). Our results reveal the high genetic variation between different spider plant accessions, especially from different regions of Africa that could be further exploited to improve productivity in the plant. The high heritability of most of the yield related traits is promising for improving yield in the crop through direct selection.
    Schlagwörter Biotechnology ; Molecular Biology ; Plant Breeding ; Genetics and Genomics ; African Agriculture ; Kenya
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Verlag Hindawi Publishing Corporation
    Erscheinungsland in
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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