Genetic and Genomic Studies on Diseases of Watermelon and Onion in Texas

Abstract

Fungi and bacteria cause economically important diseases of watermelon and onions in Texas, one of the leading states producing both crops. Anthracnose is a major fungal disease in watermelon and is the only disease listed in the grading standards of the United States Department of Agriculture and is critical to the quality and marketability of the produce in watermelon growing regions, including Texas. Bacterial diseases cause a significant loss in onion production and productivity, but there is very limited research on bacterial diseases of onions in Texas. The objectives of this dissertation are: i) to identify QTL associated with race 1 anthracnose resistance and develop markers for use in marker-assisted breeding for watermelon, ii) to understand the mode of inheritance, identify the QTL, and develop markers associated with race 2 anthracnose resistance in watermelon, iii) to isolate and identify bacteria from onion bulb and leaf samples, and test for pathogenicity, and iv) to further understand the pathogenic bacterial isolates using molecular techniques. The first study in this dissertation (Chapter 2) is aimed at determining quantitative trait loci (QTL) associated with anthracnose race 1 resistance in watermelon. The mapping population for race 1 anthracnose (F2 individuals) was derived from cross: ‘Charleston Gray’ x ‘New Hampshire Midget’. The second study in this dissertation (Chapter 3) is aimed at understanding the mode of inheritance of race 2 anthracnose resistance in watermelon. The third study in this dissertation (Chapter 4) is aimed at determining quantitative trait loci (QTL) associated with race 2 anthracnose resistance in watermelon. For Chapters 3 and 4, mapping populations (F2 individuals) were derived from crosses of Population 1 (PI 189225 x ‘New Hampshire Midget’), Population 2 (‘Perola’ x PI 189225), and Population 3 (‘Verona’ x PI 189225). The phenotypic (disease rating) and genotypic data were combined to delineate QTL associated with anthracnose resistance in watermelon. Results showed that a region in Chromosome 8 (Qar1-8) in watermelon harbors race 1 anthracnose resistance, whereas a region in Chromosome 3 (Qar2-3) governs race 2 anthracnose resistance in watermelon. The studies also designed and validated diagnostic PCR allelic competitive extension markers in the QTL region for race 1 (marker S8_5149002) and race 2 (markers S3_7469753, S3_8226811, and S3_11094483) anthracnose resistance. As part of the fourth study (Chapter 5) in the dissertation, major onion growing regions in Texas (the Rio Grande Valley and Winter Garden) were surveyed and symptomatic onion foliage and bulbs were collected. Further, bacteria were isolated from collected onion samples, identified (total 208 strains), characterized, pathogenicity tested, whole genome sequenced, and annotated. The top five genera identified were Pantoea, Pseudomonas, Enterobacter, Bacillus, and Erwinia. Only 2% of the total bacteria were found to be pathogenic in the red scale necrosis assay. The annotation of the whole genome of pathogenic strains, 21TX0081 and 21TX0197, indicated that they possess several sulfur and copper-tolerance related genes, which might help bacteria withstand antimicrobial compounds of onion and tolerate copper-based bactericides. Overall, these studies deployed genetic and genomic tools to expand the current understanding of important diseases in watermelons and onions. The diagnostic markers identified from the study would help breeders conduct marker-assisted selection for anthracnose resistance in watermelon. Also, findings on the prevalence and occurrence of onion bacteria would help breeders, plant pathologists, and others to develop cultivars for disease resistance, create diagnostic assays for pathogenic bacteria, and initiate disease best management practices.