Genome Wide Association Studies Of Striga Hermonthica (Del.) Benth. Resistance in the Sorghum Diversity Panel
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Date
2023
Authors
Kavuluko, Jacinta Muthini
Journal Title
Journal ISSN
Volume Title
Publisher
kenyatta university
Abstract
Enhancing parasite resistance in sorghum (Sorghum bicolor (L.) Moench.), a crucial cereal for the vast majority of inhabitants of sub-Saharan Africa (SSA), is vital to safeguarding food security. Striga hermonthica (Delile) Benth. being the most widespread and destructive hemiparasitic root weed of the family Orobanchaceae, is of economic concern. Developing crops that are resistant to Striga is one of the most efficient and economical methods to manage this parasite. Many researchers in the past have identified Striga resistant sorghum which have through the years been incorporated into existing breeding programs in SSA. However, the resistance has not been durable and disintegrates when new Striga ecotypes emerge. The current study sought to screen a diverse collection from the sorghum diversity panel to identify various sources of post- attachment resistance against S. hermonthica (Kibos ecotype). Subsequently, the laboratory resistance of twenty-one accessions was validated in Kibos (Western Kenya) for two rainy seasons in 2018-2019. The study further elucidated the associated genomic regions using Genome Wide Association Studies. To determine the resistance response of 151 sorghum accessions against S. hermonthica, root observation chambers (rhizotrons) were used. Further, the extent of parasitism was studied by dissecting small sections of parasite-host root attachments from sorghum roots nine days after infection. To determine the field response of 21 sorghum accessions with varying post-attachment resistance to S. hermonthica, the average maximum number of emerged Striga plants and the Area Under Striga Number Progress Curve were used as measures to indicate the level of Striga resistance. Relative grain yield loss due to Striga infestation was used as a measure of tolerance. Population stratification of the sorghum diversity panel was evaluated using the ADMIXTURE software, principal component analysis (PCA), and neighbour joining (NJ) phylogeny. Association scans were performed using Fixed and random model Circulating Probability Unification algorithm implemented in the Genomic Association and Prediction Integrated Tool. There were significant differences in resistance responses of sorghum accessions to Striga infection with regard to numbers, size and biomass of attached Striga. A total of ten accessions were resistant or highly resistant by the three metrics. Three diverse resistant mechanisms were observed ranging from hypersensitive reaction, resistance due to mechanical barriers and resistance attributed to the parasites inability to differentiate. The sorghum accessions displayed varied levels of Striga resistance in the field. The yields of the accessions differed significantly between the Striga-infested and non-Striga fields in both seasons. The varied Striga resistance responses exhibited in the laboratory was validated in the natural Striga environments in Kibos for most sorghum accessions. The NJ tree showed that the population structure of most accessions followed the pattern of morphological type within geographic origin. This was further supported by ADMIXTURE and PCA biplot analyses. Association Mapping identified several single nucleotide polymorphism (SNP) markers significantly associated with genes involved in cell wall modifications, innate immunity, systemic acquired immunity, and pathogenesis-related proteins. The newly identified high-yielding Striga-resistant sorghum landraces have great potential for immediate integration into breeding programs. Furthermore, in future breeding programs, the identified multiple genes can be combined in a single farmer-preferred sorghum cultivar to establish a more durable and broad-spectrum Striga resistance.
Description
A Thesis Submitted in Fulfilment of the Requirements for the Award of the Degree of Doctor of Philosophy (Biotechnology) in the School of Pure and Applied Sciences of Kenyatta University
Keywords
Genome, Striga Hermonthica (Del.), Sorghum Diversity Panel