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Cycle 8 (2019 Deadline)
Deploying Striga Smart Sorghum: the last mile
PI: Steven Runo (smruno@gmail.com), Kenyatta University
U.S. Partner: Emily Bellis, Arkansas State University
Project dates: January 2020 - March 2022
Project Overview
 | | Dr. Runo conducts field work with students (photo courtesy of Dr. Runo). |
Crop losses caused by parasitic plants of the genus Striga pose a great danger to the livelihoods of millions of smallholder farmers in Africa. The parasite attaches to host crops and siphons nutrients, leading to severe growth retardation and death of infected plants. One efficient and cost-effective way to control infestations would be to develop crops that are resistant to Striga. Extensive searches have led to the identification of cultivars and wild relatives of crops that are resistant to Striga parasitism, and subsequently resistant varieties have been introduced in some breeding programs in sub-Saharan Africa. However, the resistance often is weak and tends to break down.
This PEER project sought to develop a platform to deploy sorghum varieties with durable resistance to Striga. Dr. Steven Runo and his team aimed to improve the sustainability of food crop production systems and contribute to the alleviation of hunger and poverty of smallholder farmers by reducing the risk of crop failure, increasing profit margins, protecting yield, and extending the life of varieties that farmers have adopted. The PEER team also linked farmers to the extended sorghum value chain. Because sorghum is considered a “women’s” crop in most Kenyan communities, this economic advancement will directly impact women.
The PI and his team worked with local farmers and extension officers to select, from a set of Striga resistant varieties already tested under laboratory and field conditions, sorghum varieties with preferable traits. The researchers also leveraged Striga genetic diversity data generated by U.S. partner Dr. Emily Bellis to determine how Striga adapts to various environments and determines host compatibility, including seeking eco-geographic regions with the most aggressive Striga and compatibility or incompatibility between Striga ecotypes and selected sorghum varieties.
Final Summary of Project Activities
The PEER team worked with farmers to grow sorghum varieties in their farms before making their preferred selection. The researchers carried out field evaluations of Striga-resistant sorghum in four field sites for one season (April–August 2021) and two sites for two seasons (September–December 2021), collecting data on farmer selection and Striga resistance. The farmers preferred grains that are bird resistant (high in tannin), Striga resistant, early maturing, and that have large heads, a dual purpose for feed. Some Striga-resistant sorghum identified in the team’s study had traits desirable to farmers. Other sorghum varieties were more desirable for industrial uses, including one for brewing.
To develop varieties of sorghum that have more desirable traits in addition to Striga resistance, the PEER team developed a breeding platform for sorghum to introgress more traits into Striga resistance. Research assistant Cecilia Shinda made several crosses, including Striga-resistant sorghum with brewing quality, Striga-resistant and bird resistant, and crosses of sorghum with more than one mechanism of resistance. To identify early maturing sorghum with Striga resistance, PhD student Sylvia Mutinda screened the sorghum accession panel (SAP) and identified 12 new Striga-resistant early maturity sorghum varieties. The PEER team therefore created a solid foundation for carrying out the screening of these varieties under field conditions.
The researchers used genomic sequence data from the U.S. partner Dr. Bellis to determine the distribution of Striga pathotypes (variants) in various regions in western Kenya. They identified genetic variants of Striga that may cause differences in virulence (aggressiveness of infection). The data have been used to develop virulence maps. The team also analyzed samples from Striga growing on various Striga-resistant sorghum lines in different locations and carried out a transcriptome analysis of sorghum varieties having distinct mechanisms of Striga resistance.
Genomic analysis of Striga and sorghum data showed specific adaptation of the parasite to some hosts. Further work revealed the evolution of the parasite to overcome host resistance. This will inform specific guidelines for the deployment of the resistant varieties. Genomic data and transcriptome analysis revealed distinct mechanisms of resistance in sorghum. This work led to the identification of more Striga-resistant sorghum varieties and inspired further work to impart Striga resistance in sorghum using genome editing. In the short term, varieties will be registered and deployed to improve livelihoods in Kenya.
The PEER team received three additional grants to continue this work, including from the King Abdullah University of Science and Technology and the Mawazo Foundation. The team and U.S. partner also delivered a virtual workshop on genomics and R tools in spatial data analysis. More than 100 people from Africa, Asia, the United States, and Europe participated.
Publications
Gilles Irafasha, Sylvia Mutinda, Fredrick Mobegi, Brett Hale, George Omwenga, Asela J. Wijeratne, Susann Wicke, Emily S. Bellis, and Steven Runo. 2023. Transcriptome atlas of Striga germination: Implications for managing an intractable parasitic plant. Plants People Planet 2023;1–15. https://doi.org/10.1002/ppp3.10395
Sylvia Mutinda, Fredrick M. Mobegi, Brett Hale, Olivier Dayou, Elijah Ateka, Asela Wijeratne, Susann Wicke, Emily S. Bellis, and Steven Runo. 2023. Resolving intergenotypic Striga resistance in sorghum. Journal of Experimental Botany 74(17): 5294–5306. https://doi.org/10.1093/jxb/erad210
Gilles Irafasha, Sylvia Mutinda, Fredrick Mobegi, Brett Hale, George Omwenga, Asela J. Wijeratne, Susann Wicke, Emily S. Bellis, and Steven Runo. 2022. A transcriptome atlas of Striga hermonthica germination. BioRxiv preprint. https://doi.org/10.1101/2022.12.14.520245
Joel Masanga, Richard Oduor, Amos Alakonya, Mathew Ngugi, Patroba Ojola, Emily S. Bellis, and Steven Runo. 2022. Comparative phylogeographic analysis of Cuscuta campestris and Cuscuta reflexa in Kenya: Implications for management of highly invasive vines. Plants People Planet 4(2): 182–193. https://doi.org/10.1002/ppp3.10236
Emily S. Bellis, Clara S. von Münchow, Alan Kronberger, Calvins O. Odero, Elizabeth A. Kelly, Tian Xia, Xiuzhen Huang, Susann Wicke, Steven M. Runo, Claude W. dePamphilis, and Jesse R. Lasky. 2022. Genomic signatures of host-specific selection in a parasitic plant. BioRxiv preprint. https://doi.org/10.1101/2022.02.01.478712
Tesfamichael S. Mallu, Gilles Irafasha, Sylvia Mutinda, Erick Owuor, Stephen M. Githiri, Damaris A. Odeny, and Steven Runo. 2022. Mechanisms of pre- attachment Striga resistance in sorghum through genome-wide association studies. Molecular Genetics and Genomics 297: 751–762. https://doi.org/10.1007/s00438-022-01882-6
Leena Tripathi, Kanwarpal S. Dhugga, Valentine O. Ntui, Steven Runo, Easter D. Syombua, Samwel Muiruri, Zhengyu Wen, and Jaindra N. Tripathi. 2022. Genome editing for sustainable agriculture in Africa. Frontiers in Genome Editing 4: 876697. https://doi.org/10.3389/fgeed.2022.876697
Joel Masanga, Beatrice Njoki Mwangi, Willy Kibet, Philip Sagero, Mark Wamalwa, Richard Oduor, Mathew Ngugi, Amos Alakonya, Patroba Ojola, Emily S. Bellis, and Steven Runo. 2021. Physiological and ecological warnings that dodders pose an exigent threat to farmlands in Eastern Africa. Plant Physiology 185: 1457-1467. https://doi.org/10.1093/plphys/kiab034
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