Genetic analysis of resistance to Fusarium stalk rot (Fusarium thapsinum) in sorghum (Sorghum bicolor (L) Moench)

Abstract

Sorghum is a climate-resilient C4 plant best suited for the drier areas of the world. It is the fifth most widely cultivated cereal for food, feed, and biofuel production. Fusarium stalk rot, caused by Fusarium thapsinum, is among the predominant sorghum diseases in Kansas, affecting economic traits including grain yield, sugar yield, quality, and biomass. Resistant variety is the most viable way to manage the disease and minimize the associated losses. Adequate knowledge of genetic mechanisms associated with the development of the disease is a prerequisite for progress toward developing resistant hybrids. This dissertation comprises three separate experiments aimed at understanding the genetics of stalk rot resistance in sorghum, identifying genes and/or genomic regions associated with the disease, understanding molecular pathways responsible for resistance, and assessing the potential of selected resistant lines as parents for resistance breeding. The first experiment focuses on mapping QTLs associated with disease resistance and dissecting the QTL by environment interactions. Two hundred and thirty-three recombinant inbred lines (RILs) developed from crosses of BTx3042 (susceptible) ⨯ SC599 (resistant) were evaluated for reaction to infection by F. thapsinum in the 2018, 2019, and 2020 field seasons. The genotypes were artificially inoculated by F. thapsinum, and disease development was rated as lesion length and the number of diseased nodes. Flowering time, plant height, and lodging data were recorded. The RILs were genotyped using genotyping-by-sequencing, and 3297 polymorphic SNP markers were used for linkage mapping and QTL analysis. The analysis of phenotypic data showed significant differences and transgressive segregation for disease parameters. Heritability was 66% for major lesion length and 92% for plant height. The SNPs covered 3070.8 cM with an average distance of 1.8 cM between markers. Inclusive composite interval mapping detected four stable additive QTLs across environments on chromosomes 1, 3, 5, and 9 for major lesion length. The results from this study may serve as a basis for future mapping studies on Fusarium stalk rot to aid resistant germplasm development through breeding. In the second experiment, the RIL founder parents, SC599 (resistant) and BTx3042 (susceptible), were used for the transcriptome analysis to investigate genes regulating disease resistance and identify the molecular basis of host plant resistance. Early activation of the defense response was observed in the resistant line at 24 hours post-infection (hpi). Differentially expressed genes (DEGs) such as nucleotide-binding site leucine-rich repeat (SbRWRKY1, SbLRx4, and Sobic.005G226400), pathogenesis-related (PR10 Sobic.001G401200), disease resistance-response (Sobic.009G021300), wall-associated kinase (Sobic.008G170800 and Sobic.002G249600), peroxidase (SbPrx34 and SbPrx30), chalcone synthase (SbCHS1 and SbCHS5), and flavonoid synthase genes (SbDFR3) were upregulated in the resistant and downregulated in the susceptible genotypes at 24 hpi. The resistant genotype displayed a time-regulated transcriptome response showing that defense regulation might be related to the pathogen's hemi-biotrophic nature. This result provides a foundation for future studies to understand genes and pathways involved in the molecular mechanisms of Fusarium stalk rot resistance in sorghum. The third experiment aimed to identify the genetic mechanisms associated with stalk rot resistance, lodging, and agronomic traits and pinpoint key traits related to stalk rot resistance. Sixty-one lines from the BTx3042 (susceptible) ⨯ SC599 (resistant) RIL population representing the susceptible, intermediate, and resistant categories were crossed with three standard seed parents in a factorial mating design to generate 183 F1 hybrids. The hybrids and 64 inbred parents were grown in an alpha lattice incomplete block design in three replications at four environments in Kansas. Data were collected on days to flowering, plant height, major lesion length, total lesion length, number of diseased nodes, grain yield, and stalk lodging. Significant differences were observed between entries for all traits. Likewise, the male and female effects and their interaction with the environment were significant for most traits, indicating that the general combining ability (GCA) effect had a large role in regulating plant response to F. thapsinum infection. The male-by-female interaction effect also known as the specific combining ability (SCA) was also significant. Grain yield had a negative genotypic correlation with all disease traits and lodging, indicating that stalk rot infection does affect yield performance.