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Obonyo D, Ouma G, Ikawa R, Odeny DA. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology 2024; 593:110011. [PMID: 38367474 DOI: 10.1016/j.virol.2024.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. METHODS We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. RESULTS Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. CONCLUSION Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
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Affiliation(s)
- Dennis Obonyo
- Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - George Ouma
- Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Rachel Ikawa
- Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Eastern and Southern Africa, P.O Box 39063-00623, Nairobi, Kenya.
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2
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Bančič J, Odeny DA, Ojulong HF, Josiah SM, Buntjer J, Gaynor RC, Hoad SP, Gorjanc G, Dawson IK. Genomic and phenotypic characterization of finger millet indicates a complex diversification history. Plant Genome 2024; 17:e20392. [PMID: 37986545 DOI: 10.1002/tpg2.20392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 11/22/2023]
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 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.
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Affiliation(s)
- Jon Bančič
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
- Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, UK
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, ICRAF House, Gigiri Nairobi, Kenya
| | - Henry F Ojulong
- International Crops Research Institute for the Semi-Arid Tropics, ICRAF House, Gigiri Nairobi, Kenya
| | - Samuel M Josiah
- Department of Horticulture, University of Georgia, Athens, Georgia, USA
| | - Jaap Buntjer
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
| | - R Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
| | - Stephen P Hoad
- Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
| | - Ian K Dawson
- Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, UK
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3
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Gimode DM, Ochieng G, Deshpande S, Manyasa EO, Kondombo CP, Mikwa EO, Avosa MO, Kunguni JS, Ngugi K, Sheunda P, Jumbo MB, Odeny DA. Validation of sorghum quality control (QC) markers across African breeding lines. Plant Genome 2024:e20438. [PMID: 38409578 DOI: 10.1002/tpg2.20438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho ) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.
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Affiliation(s)
- Davis M Gimode
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Grace Ochieng
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-arid Tropics-Patancheru, Patancheru, Telangana, India
| | - Eric O Manyasa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Clarisse P Kondombo
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Erick O Mikwa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Millicent O Avosa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | | | - Kahiu Ngugi
- Department of Plant Science & Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Patrick Sheunda
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
- The Kenya Seed Company Limited, Kitale Branch, Kitale, Kenya
| | - McDonald Bright Jumbo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
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4
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. Mol Plant 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
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 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.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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5
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Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 2023; 14:3694. [PMID: 37344528 DOI: 10.1038/s41467-023-38915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 06/23/2023] Open
Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
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Affiliation(s)
- Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Davis M Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| | - Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
- Ethiopian Agricultural Transformation Agency, Addis Ababa, Bole, Ethiopia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- UR Ventures, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas H Pendergast
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- ICAR-Central Research Institute for Jute and Allied Fibers, Kolkata, West Bengal, 700120, India
| | - Gurjot S Sidhu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Santosh Deshpande
- ICRISAT, Patancheru, 502 324, T.S., India
- Hytech Seed India Pvt. Ltd., Ravalkol Village, Medcahl-Malkajgiri Dist-, 501 401, Hubballi, T.S, India
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, 80108, Kenya
- Pwani University Biosciences Research Center (PUBReC), Kilifi, 80108, Kenya
| | - Mathews M Dida
- Department of Crop and Soil Science, Maseno University, P.O. 333, Maseno, Kenya
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Emmarold E Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar Es Salaam, Tanzania
- Biotechnology Society of Tanzania, P.O. Box 10257, Dar es Salaam, Tanzania
| | - Henry F Ojulong
- ICRISAT, Matopos Research Station, P.O. Box 776, Bulawayo, Zimbabwe
| | - Michael C Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
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Odeny DA, Okoth MA. Africa-led group generates lablab crop genome. Nature 2023; 617:37-38. [PMID: 37069304 DOI: 10.1038/d41586-023-01022-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
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7
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Ruperao P, Gandham P, Odeny DA, Mayes S, Selvanayagam S, Thirunavukkarasu N, Das RR, Srikanda M, Gandhi H, Habyarimana E, Manyasa E, Nebie B, Deshpande SP, Rathore A. Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources. Front Plant Sci 2023; 14:1143512. [PMID: 37008459 PMCID: PMC10063887 DOI: 10.3389/fpls.2023.1143512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
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 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.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, LA, United States
| | - Damaris A. Odeny
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research (ICAR) - Indian Institute of Millets Research, Hyderabad, India
| | - Roma R. Das
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manasa Srikanda
- Department of Statistics, Osmania University, Hyderabad, India
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | | | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India
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8
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. Plant Cell 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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9
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Mallu TS, Irafasha G, Mutinda S, Owuor E, Githiri SM, Odeny DA, Runo S. Mechanisms of pre-attachment Striga resistance in sorghum through genome-wide association studies. Mol Genet Genomics 2022; 297:751-762. [PMID: 35305146 DOI: 10.1007/s00438-022-01882-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/26/2022] [Indexed: 11/30/2022]
Abstract
Witchweeds (Striga spp.) greatly limit production of Africa's most staple crops. These parasitic plants use strigolactones (SLs)-chemical germination stimulants, emitted from host's roots to germinate, and locate their hosts for invasion. This information exchange provides opportunities for controlling the parasite by either stimulating parasite seed germination without a host (suicidal germination) or by inhibiting parasite seed germination (pre-attachment resistance). We sought to determine genetic factors that underpin Striga pre-attachment resistance in sorghum using the genome wide association study (GWAS) approach. Results revealed that Striga germination was associated with genes encoding hormone signaling functions, e.g., the Novel interactor of jaz (NINJA) and, Abscisic acid-insensitive 5 (ABI5). This pointed toward abscisic acid (ABA) and gibberellic acid (GA) as probable determinants of Striga germination. To test this hypothesis, we conditioned Striga using: ABA, ABA + its inhibitor fluridone (FLU), GA or water. Unexpectedly, Striga conditioned with FLU germinated after 4 days without SL. Upon germination stimulation using sorghum root exudate or the synthetic SL GR24, we found that ABA conditioned seeds had above 20-fold reduction in germination. Conversely, FLU conditioned seeds recorded above 20-fold increase in germination. Conditioning with GA reduced Striga seed germination 1.5-fold only in the GR24 treatment. Germination assays using seeds of a related parasitic plant (Alectra vogelii) showed similar degrees of stimulation and reduction of germination by the hormones further affirming the hormonal crosstalk. Our findings have far-reaching implications in the control of some of the most noxious pathogens of crops in Africa.
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Affiliation(s)
- Tesfamichael S Mallu
- Pan African University Institute for Basic Sciences, Technology and Innovation, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya.,Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Gilles Irafasha
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Sylvia Mutinda
- Pan African University Institute for Basic Sciences, Technology and Innovation, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya.,Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Erick Owuor
- International Crops Research Institute for the Semi-Arid Tropics, P. O. Box 39063-00623, Nairobi, Kenya
| | - Stephen M Githiri
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, P. O. Box 39063-00623, Nairobi, Kenya.
| | - Steven Runo
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya.
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10
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Muchira N, Ngugi K, Wamalwa LN, Avosa M, Chepkorir W, Manyasa E, Nyamongo D, Odeny DA. Genotypic Variation in Cultivated and Wild Sorghum Genotypes in Response to Striga hermonthica Infestation. Front Plant Sci 2021; 12:671984. [PMID: 34305972 PMCID: PMC8296141 DOI: 10.3389/fpls.2021.671984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/03/2021] [Indexed: 05/23/2023]
Abstract
Striga hermonthica is the most important parasitic weed in sub-Saharan Africa and remains one of the most devastating biotic factors affecting sorghum production in the western regions of Kenya. Farmers have traditionally managed Striga using cultural methods, but the most effective and practical solution to poor smallholder farmers is to develop Striga-resistant varieties. This study was undertaken with the aim of identifying new sources of resistance to Striga in comparison with the conventional sources as standard checks. We evaluated 64 sorghum genotypes consisting of wild relatives, landraces, improved varieties, and fourth filial generation (F4) progenies in both a field trial and a pot trial. Data were collected for days to 50% flowering (DTF), dry panicle weight (DPW, g), plant height (PH, cm), yield (YLD, t ha-1), 100-grain weight (HGW, g), overall disease score (ODS), overall pest score (OPS), area under Striga number progress curve (ASNPC), maximum above-ground Striga (NSmax), and number of Striga-forming capsules (NSFC) at relevant stages. Genetic diversity and hybridity confirmation was determined using Diversity Arrays Technology sequencing (DArT-seq). Residual heterosis for HGW and NSmax was calculated as the percent increase or decrease in performance of F4 crossover midparent (MP). The top 10 best yielding genotypes were predominantly F4 crosses in both experiments, all of which yielded better than resistant checks, except FRAMIDA in the field trial and HAKIKA in the pot trial. Five F4 progenies (ICSVIII IN × E36-1, LANDIWHITE × B35, B35 × E36-1, F6YQ212 × B35, and ICSVIII IN × LODOKA) recorded some of the highest HGW in both trials revealing their stability in good performance. Three genotypes (F6YQ212, GBK045827, and F6YQ212xB35) and one check (SRN39) were among the most resistant to Striga in both trials. SNPs generated from DArT-seq grouped the genotypes into three major clusters, with all resistant checks grouping in the same cluster except N13. We identified more resistant and high-yielding genotypes than the conventional checks, especially among the F4 crosses, which should be promoted for adoption by farmers. Future studies will need to look for more diverse sources of Striga resistance and pyramid different mechanisms of resistance into farmer-preferred varieties to enhance the durability of Striga resistance in the fields of farmers.
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Affiliation(s)
- Nicoleta Muchira
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
- International Crops Research Institute for the Semi-Arid Tropics-Kenya, Nairobi, Kenya
| | - Kahiu Ngugi
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Lydia N. Wamalwa
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Millicent Avosa
- International Crops Research Institute for the Semi-Arid Tropics-Kenya, Nairobi, Kenya
| | - Wiliter Chepkorir
- International Crops Research Institute for the Semi-Arid Tropics-Kenya, Nairobi, Kenya
| | - Eric Manyasa
- International Crops Research Institute for the Semi-Arid Tropics-Kenya, Nairobi, Kenya
| | - Desterio Nyamongo
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, Kikuyu, Kenya
| | - Damaris A. Odeny
- International Crops Research Institute for the Semi-Arid Tropics-Kenya, Nairobi, Kenya
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11
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Bančič J, Werner CR, Gaynor RC, Gorjanc G, Odeny DA, Ojulong HF, Dawson IK, Hoad SP, Hickey JM. Modeling Illustrates That Genomic Selection Provides New Opportunities for Intercrop Breeding. Front Plant Sci 2021; 12:605172. [PMID: 33633761 PMCID: PMC7902002 DOI: 10.3389/fpls.2021.605172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/05/2021] [Indexed: 05/14/2023]
Abstract
Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pests and diseases. Especially in subsistence agriculture, intercropping has great potential to optimize farming and increase profitability. However, breeding for intercrop varieties is complex as it requires simultaneous improvement of two or more component crops that combine well in the field. We hypothesize that genomic selection can significantly simplify and accelerate the process of breeding crops for intercropping. Therefore, we used stochastic simulation to compare four different intercrop breeding programs implementing genomic selection and an intercrop breeding program entirely based on phenotypic selection. We assumed three different levels of genetic correlation between monocrop grain yield and intercrop grain yield to investigate how the different breeding strategies are impacted by this factor. We found that all four simulated breeding programs using genomic selection produced significantly more intercrop genetic gain than the phenotypic selection program regardless of the genetic correlation with monocrop yield. We suggest a genomic selection strategy which combines monocrop and intercrop trait information to predict general intercropping ability to increase selection accuracy in the early stages of a breeding program and to minimize the generation interval.
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Affiliation(s)
- Jon Bančič
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter Bush Research Centre, Midlothian, United Kingdom
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
| | - Christian R. Werner
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter Bush Research Centre, Midlothian, United Kingdom
| | - R. Chris Gaynor
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter Bush Research Centre, Midlothian, United Kingdom
| | - Gregor Gorjanc
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter Bush Research Centre, Midlothian, United Kingdom
| | - Damaris A. Odeny
- International Crops Research Institute for the Semi-Arid Tropics, ICRAF House, Nairobi, Kenya
| | - Henry F. Ojulong
- International Crops Research Institute for the Semi-Arid Tropics, ICRAF House, Nairobi, Kenya
| | - Ian K. Dawson
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
| | | | - John M. Hickey
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter Bush Research Centre, Midlothian, United Kingdom
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12
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Ruperao P, Thirunavukkarasu N, Gandham P, Selvanayagam S, Govindaraj M, Nebie B, Manyasa E, Gupta R, Das RR, Odeny DA, Gandhi H, Edwards D, Deshpande SP, Rathore A. Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. Front Plant Sci 2021; 12:666342. [PMID: 34140962 PMCID: PMC8204017 DOI: 10.3389/fpls.2021.666342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/28/2021] [Indexed: 05/05/2023]
Abstract
Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
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Affiliation(s)
- Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | - Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | | | - Baloua Nebie
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, Mali
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Damaris A. Odeny
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Harish Gandhi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- Santosh P. Deshpande
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- *Correspondence: Abhishek Rathore
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13
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Tamiru A, Paliwal R, Manthi SJ, Odeny DA, Midega CAO, Khan ZR, Pickett JA, Bruce TJA. Genome wide association analysis of a stemborer egg induced "call-for-help" defence trait in maize. Sci Rep 2020; 10:11205. [PMID: 32641801 PMCID: PMC7343780 DOI: 10.1038/s41598-020-68075-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 06/15/2020] [Indexed: 11/30/2022] Open
Abstract
Tritrophic interactions allow plants to recruit natural enemies for protection against herbivory. Here we investigated genetic variability in induced responses to stemborer egg-laying in maize Zea mays (L.) (Poaceae). We conducted a genome wide association study (GWAS) of 146 maize genotypes comprising of landraces, inbred lines and commercial hybrids. Plants were phenotyped in bioassays measuring parasitic wasp Cotesia sesamiae (Cameron) (Hymenoptera: Braconidae) attraction to volatiles collected from plants exposed to stemborer Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) eggs. Genotyping-by-sequencing was used to generate maize germplasm SNP data for GWAS. The egg-induced parasitoid attraction trait was more common in landraces than in improved inbred lines and hybrids. GWAS identified 101 marker-trait associations (MTAs), some of which were adjacent to genes involved in the JA-defence pathway (opr7, aos1, 2, 3), terpene biosynthesis (fps3, tps2, 3, 4, 5, 7, 9, 10), benzoxazinone synthesis (bx7, 9) and known resistance genes (e.g. maize insect resistance 1, mir1). Intriguingly, there was also association with a transmembrane protein kinase that may function as a receptor for the egg elicitor and other genes implicated in early plant defence signalling. We report maize genomic regions associated with indirect defence and provide a valuable resource for future studies of tritrophic interactions in maize. The markers identified may facilitate selection of indirect defence by maize breeders.
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Affiliation(s)
- Amanuel Tamiru
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100, Nairobi, Kenya
| | - Rajneesh Paliwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), P.O. Box 39063-00623, Nairobi, Kenya.,International Institute of Tropical Agriculture (IITA), 5320, Ibadan, Nigeria
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), P.O. Box 39063-00623, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), P.O. Box 39063-00623, Nairobi, Kenya
| | - Charles A O Midega
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100, Nairobi, Kenya
| | - Zeyaur R Khan
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100, Nairobi, Kenya
| | - John A Pickett
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Toby J A Bruce
- School of Life Sciences, Keele University, Staffordshire, ST5 5BG, UK.
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14
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Nhlapo TF, Mulabisana JM, Odeny DA, Rey MEC, Rees DJG. First Report of Sweet potato badnavirus A and Sweet potato badnavirus B in South Africa. Plant Dis 2018; 102:1865. [PMID: 30125171 DOI: 10.1094/pdis-08-17-1235-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- T F Nhlapo
- Biotechnology Platform, Agricultural Research Council, Onderstepoort 0110, South Africa
| | - J M Mulabisana
- Vegetable and Ornamental Plant Institute, Agricultural Research Council, Pretoria 0001, South Africa
| | - D A Odeny
- ICRISAT (ICRAF Campus), Nairobi, Kenya
| | - M E C Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - D J G Rees
- Department of Life and Consumer Sciences, University of South Africa, Florida 1710, South Africa
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15
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Rauwane ME, Odeny DA, Millar I, Rey C, Rees J. The early transcriptome response of cassava (Manihot esculenta Crantz) to mealybug (Phenacoccus manihoti) feeding. PLoS One 2018; 13:e0202541. [PMID: 30133510 PMCID: PMC6105004 DOI: 10.1371/journal.pone.0202541] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/06/2018] [Indexed: 11/18/2022] Open
Abstract
The mealybug, Phenacoccus manihoti, is a leading pest of cassava (Manihot esculenta Crantz), damaging this crop globally. Although the biological control of this mealybug using natural predators has been established, resistance breeding remains an important means of control. Understanding plant responses to insect herbivory, by determining and identifying differentially expressed genes (DEGs), is a vital step towards the understanding of molecular mechanisms of defence responses in plants and the development of resistant cultivars by gene editing. Morphological and molecular analysis confirmed the mealybug identity as Phenacoccus manihoti (Matile-Ferrero). The transcriptome response of the green mite resistant cassava genotype AR23.1 was compared to P40/1 with no known resistance at 24 and 72 hours of mealybug infestation compared to non-infested mock. A total of 301 and 206 genes were differentially expressed at 24 and 72 of mealybug infestation for AR23.1 and P40/1 genotypes respectively, using a log2 fold change and P-value ≤ 0.05. Gene ontology functional classification revealed an enrichment of genes in the secondary metabolic process category in AR23.1 in comparison with P40/1, while genes in the regulation of molecular function, cellular component biogenesis and electron carrier categories were more significantly enriched in P40/1 than in AR23.1. Biological pathway analysis, based on KEGG, revealed a significant enrichment of plant-pathogen interaction and plant hormonal signal transduction pathways for a cohort of up-regulated and down-regulated DEGs in both genotypes. Defence-related genes such as 2-oxogluterate, gibberellin oxidase and terpene synthase proteins were only induced in genotype AR23.1 and not in P40/1, and subsequently validated by RT-qPCR. The study revealed a difference in response to mealybug infestation in the two genotypes studied, with AR23.1 showing a higher number of differentially expressed transcripts post mealybug infestation at 24 and 72 hours. Candidate defence-related genes that were overexpressed in the AR23.1 genotype post mealybug infestation will be useful in future functional studies towards the control of mealybugs.
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Affiliation(s)
- Molemi E. Rauwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
| | | | - Ian Millar
- Biosystematics Division, Plant Protection Research Institute, Agricultural Research Council, Queenswood, Pretoria, South Africa
| | - Chrissie Rey
- University of the Witwatersrand, Johannesburg, South Africa
| | - Jasper Rees
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
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16
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Viljoen E, Odeny DA, Coetzee MPA, Berger DK, Rees DJG. Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. J Mol Evol 2018; 86:216-239. [PMID: 29556741 DOI: 10.1007/s00239-018-9837-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023]
Abstract
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.
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Affiliation(s)
- Erika Viljoen
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa.,Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Martin P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa.
| | - David J G Rees
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa.,Department of Life and Consumer Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida, 1710, South Africa
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17
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Mbuvi DA, Masiga CW, Kuria E, Masanga J, Wamalwa M, Mohamed A, Odeny DA, Hamza N, Timko MP, Runo S. Novel Sources of Witchweed ( Striga) Resistance from Wild Sorghum Accessions. Front Plant Sci 2017; 8:116. [PMID: 28220136 PMCID: PMC5292437 DOI: 10.3389/fpls.2017.00116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/19/2017] [Indexed: 05/04/2023]
Abstract
Sorghum is a major food staple in sub-Saharan Africa (SSA), but its production is constrained by the parasitic plant Striga that attaches to the roots of many cereals crops and causes severe stunting and loss of yield. Away from cultivated farmland, wild sorghum accessions grow as weedy plants and have shown remarkable immunity to Striga. We sought to determine the extent of the resistance to Striga in wild sorghum plants. Our screening strategy involved controlled laboratory assays of rhizotrons, where we artificially infected sorghum with Striga, as well as field experiments at three sites, where we grew sorghum with a natural Striga infestation. We tested the resistance response of seven accessions of wild sorghum of the aethiopicum, drummondii, and arundinaceum races against N13, which is a cultivated Striga resistant landrace. The susceptible control was farmer-preferred variety, Ochuti. From the laboratory experiments, we found three wild sorghum accessions (WSA-1, WSE-1, and WSA-2) that had significantly higher resistance than N13. These accessions had the lowest Striga biomass and the fewest and smallest Striga attached to them. Further microscopic and histological analysis of attached Striga haustorium showed that wild sorghum accessions hindered the ingression of Striga haustorium into the host endodermis. In one of the resistant accessions (WSE-1), host and parasite interaction led to the accumulation of large amounts of secondary metabolites that formed a dark coloration at the interphase. Field experiments confirmed the laboratory screening experiments in that these same accessions were found to have resistance against Striga. In the field, wild sorghum had low Area under the Striga Number Progressive curve (AUSNPC), which measures emergence of Striga from a host over time. We concluded that wild sorghum accessions are an important reservoir for Striga resistance that could be used to expand the genetic basis of cultivated sorghum for resistance to the parasite.
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Affiliation(s)
- Dorothy A. Mbuvi
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | - Clet W. Masiga
- Tropical Institute of Development InnovationsKampala, Uganda
- Sudan Academy of SciencesKhartoum, Sudan
| | - Eric Kuria
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | - Joel Masanga
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | - Mark Wamalwa
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | | | - Damaris A. Odeny
- International Crops Research Institute for the Semi-Arid TropicsNairobi, Kenya
| | - Nada Hamza
- Sudan Academy of SciencesKhartoum, Sudan
- Commission for Biotechnology and Genetic Engineering, National Centre for ResearchKhartoum, Sudan
| | - Michael P. Timko
- Department of Biology, University of VirginiaCharlottesville, VA, USA
| | - Steven Runo
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
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Gimode D, Odeny DA, de Villiers EP, Wanyonyi S, Dida MM, Mneney EE, Muchugi A, Machuka J, de Villiers SM. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies. PLoS One 2016; 11:e0159437. [PMID: 27454301 PMCID: PMC4959724 DOI: 10.1371/journal.pone.0159437] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/01/2016] [Indexed: 01/18/2023] Open
Abstract
Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity.
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Affiliation(s)
- Davis Gimode
- Kenyatta University, P.O. Box 43844–00100, Nairobi, Kenya
| | | | | | | | | | - Emmarold E. Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar-Es-Salaam, Tanzania
| | - Alice Muchugi
- Kenyatta University, P.O. Box 43844–00100, Nairobi, Kenya
- ICRAF-Nairobi, P.O Box 30677, Nairobi, Kenya
| | - Jesse Machuka
- Kenyatta University, P.O. Box 43844–00100, Nairobi, Kenya
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Kunguni JS, Odeny DA, Dangasuk OG, Matasyoh LG, Oduori CO. Response of Elite Kenyan Finger Millet (<i>Eleusine coracana, </i>L. Gaertn) Genotypes to Ethrel Application. ILNS 2015. [DOI: 10.56431/p-hy36u6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Finger millet is a staple food crop of many communities in Africa. The crop is highly nutritious and has incredible grain storage quality. Limited research investment in finger millet in the past has resulted in poor yields and there are currently no commercial hybrids. We investigated the response of different finger millet genotypes (Okhale-1, Gulu-E, KACCIMMI-72, IE 2872, IE 4115 and U-15) to the application of a plant growth regulator hormone (Ethrel). Six elite Kenyan finger millet varieties with contrasting agronomic traits were crossed in a 6 x 6 diallel pattern. To enhance male sterility across female parents, we subjected the plants to Ethrel at concentrations of 1,500ppm, 1,750ppm and 2,000ppm against a 0ppm check. Dwarfing of sprayed plants that resulted in less lodging and ultimately higher yields were observed among plants sprayed with Ethrel at different concentrations. Ethrel application at 2,000ppm had the most dwarfing effect on plants while spraying plants with 1,500ppm of Ethrel resulted in increased grain weight. Although our results demonstrate overall positive effect of Ethrel on finger millet production, the optimum concentrations for more efficient hybridization will still need to be determined.
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Affiliation(s)
| | - Damaris A. Odeny
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT)
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Kunguni JS, Odeny DA, Dangasuk OG, Matasyoh LG, Oduori CO. Response of Elite Kenyan Finger Millet (<i>Eleusine coracana, </i>L. Gaertn) Genotypes to Ethrel Application. ILNS 2015. [DOI: 10.18052/www.scipress.com/ilns.48.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Finger millet is a staple food crop of many communities in Africa. The crop is highly nutritious and has incredible grain storage quality. Limited research investment in finger millet in the past has resulted in poor yields and there are currently no commercial hybrids. We investigated the response of different finger millet genotypes (Okhale-1, Gulu-E, KACCIMMI-72, IE 2872, IE 4115 and U-15) to the application of a plant growth regulator hormone (Ethrel). Six elite Kenyan finger millet varieties with contrasting agronomic traits were crossed in a 6 x 6 diallel pattern. To enhance male sterility across female parents, we subjected the plants to Ethrel at concentrations of 1,500ppm, 1,750ppm and 2,000ppm against a 0ppm check. Dwarfing of sprayed plants that resulted in less lodging and ultimately higher yields were observed among plants sprayed with Ethrel at different concentrations. Ethrel application at 2,000ppm had the most dwarfing effect on plants while spraying plants with 1,500ppm of Ethrel resulted in increased grain weight. Although our results demonstrate overall positive effect of Ethrel on finger millet production, the optimum concentrations for more efficient hybridization will still need to be determined.
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Affiliation(s)
| | - Damaris A. Odeny
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT)
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Odeny DA, Jayashree B, Gebhardt C, Crouch J. New microsatellite markers for pigeonpea (cajanus cajan (L.) millsp.). BMC Res Notes 2009; 2:35. [PMID: 19284532 PMCID: PMC2660351 DOI: 10.1186/1756-0500-2-35] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/06/2009] [Indexed: 12/01/2022] Open
Abstract
Background Pigeonpea is a nutritious tropical legume with several desirable characteristics but has been relatively neglected in terms of research. More efficient improvement can be achieved in this crop through molecular breeding but adequate molecular markers are lacking and no linkage map has been developed so far. Microsatellites remain the markers of choice due to their high polymorphism and their transferability from closely related genera. The overall objective of this study was to develop microsatellite markers from an enriched library of pigeonpea as well as testing the transferability of soybean microsatellites in pigeonpea. Results Primers were designed for 113 pigeonpea genomic SSRs, 73 of which amplified interpretable bands. Thirty-five of the primers revealed polymorphism among 24 pigeonpea breeding lines. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. GT/CA and GAA class of repeats were the most abundant di-nucleotide and tri-nucleotide repeats respectively. Additionally, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands. Conclusion Despite the observed morphological diversity, there is little genetic diversity within cultivated pigeonpea as revealed by the developed microsatellites. Although some of the tested soybean microsatellites may be transferable to pigeonpea, lack of useful polymorphism may hinder their full use. A robust set of markers will still have to be developed for pigeonpea genome if molecular breeding is to be achieved.
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Affiliation(s)
- D A Odeny
- University of Bonn, Centre for Development Research (ZEFc), Walter-Flex Str,3 53113 Bonn, Germany.
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