BACKGROUND: Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. RESULTS: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F₂:₃ progenies and identified one major QTL and three minor QTLs. CONCLUSION: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

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Rice is one of the most important cereal crops for the world population. Flowering time and seed development of rice are directly related to plant regional and ecological adaptions, and productive yield. In this dissertation, to gain knowledge of seed development in rice, the status of post-translational modifications (PTMs) in developing rice seeds was investigated. Numerous modified lysine sites in developing rice seeds were identified utilizing antibody-based affinity enrichment approaches and nano-HPLC/MS/MS analyses of acetylated, succinylated, crotonylated and 2-hydroxyisobutyrylated peptides. Functional annotation analyses indicated that a wide variety of vital biological processes were targeted by lysine PTMs. A number of modified histone and non-histone proteins were found to harbor multiple PTMs, and our findings showed that many modified histone sites were conserved across plant, human, and animal systems. Comprehensive analyses of lysine modification sites illustrated that the sites were highly sequence-specific for distinct motifs. Overall, this study provides a systematic analysis of lysine PTM proteome in plants, which will serve as the basis for future investigations of the regulatory mechanisms and functions of lysine PTMs. The mechanisms of flowering time variances in response to different photoperiods were further studied in the rice mutant, HSS. QTL-seq analysis identified a major effect on chromosome 6 responsible for the phenotypic divergence between Nipponbare (wild-type) and HSS rice. Sequence and mRNA expression analyses confirmed that allelic variants of Hd1 make HSS plants less sensitive to photoperiod by altering expression level of Hd3a. Diurnal expression pattern analyses revealed that DTH8 transcripts were largely affected by Hd1 expression level in both LD and SD. This result suggested that Hd1 may able to regulate DTH8 and DTH8-Hd1 complex abundance in response to day length in rice flowering time regulation. In addition, we discussed the functions of PTMs in flowering time regulation in rice.

Migratory insects are vital components of global ecosystems and provide important ecosystem services, yet the migration phenomenon is understudied in insects compared to vertebrates. In this thesis, I aim to deepen our understanding of insect migration, using the monarch butterfly Danaus plexippus (L.) and the painted lady butterfly Vanessa cardui (L.) as model systems. Studying insect migration is notoriously difficult given the small size, high abundance, and short lifespans of insects. Isotope geolocation has shown promise for overcoming these obstacles. Here, I develop and apply metals and metal isotopes, specifically strontium isotope ratios (⁸⁷Sr/⁸⁶Sr), to increase the spatial precision of isotope geolocation and demonstrate how isotopic geolocation tools can advance our understanding of insect migration at the population level. In the first chapter, I test the validity of using ⁸⁷Sr/⁸⁶Sr, lead isotopes, and a suite of 23 metals and metalloids to estimate the natal origins of migratory insects, by investigating the pathways of metal incorporation into butterfly wing tissues. Using an 8-week diet-switching experiment, I show that the concentrations of many metals in insect wings can be altered through the adult diet or dust deposition, making them poor candidates for geolocation but potentially interesting tools to study insect physiology, diet, or toxicology. For example, lead was found to accumulate on butterfly wings from external sources, and lead isotopes could potentially be used to quantify the exposure of migratory insects to metal pollution. Some metals, including Ba, Cs, Mg, Na, Rb, Sr, Ti, Tl, and U, are good candidates for developing geolocation tools. I focused on ⁸⁷Sr/⁸⁶Sr and demonstrated that, despite some caveats, this tool is valid for isotope geolocation. In the second chapter, I outline the steps required to use ⁸⁷Sr/⁸⁶Sr for the geolocation of insects, including the calibration of a spatial model of isotopic variation (i.e., an isoscape) using random forest regression. I then combine hydrogen isotope values (δ²H) and ⁸⁷Sr/⁸⁶Sr into a dual assignment framework to estimate the natal origins of a single generation of monarch butterflies in eastern North America. I demonstrate that combining these two isotopes provides a more spatially constrained estimate of natal origin than using either isotope alone. In the third chapter, I apply this framework to characterize the migratory patterns and migratory connectivity of an insect species across a geographical barrier, the Sahara. Painted ladies journeying northwards across the Sahara appear to do so in a gradual progression, although spatiotemporal sampling limitations prevented a complete characterization of this movement. In contrast, painted ladies migrating southwards appear to journey in a broad front, parallel migration pattern with little longitudinal movement. Evidence for a leapfrog migration pattern was found in the western region, wherein butterflies of northernmost origin journey farther south than butterflies bred in more southerly regions. This leapfrog migration pattern suggests distinct migratory behaviours within painted lady butterflies wherein some individuals migrate longer distances than others. In the fourth chapter, I apply isotope geolocation to characterize the migration distances of multiple individuals and assess the potential genetic differentiation of butterflies migrating distinct distances. I use δ²H and ⁸⁷Sr/⁸⁶Sr-based geographic assignment to confirm that some painted ladies migrate up to 4,000 km from Europe to sub-Saharan Africa, while others migrate shorter distances from Europe to the circum-Mediterranean region. Despite these differences in migration distance, genome-wide analysis revealed a lack of adaptive variation between short- and long-distance migrants. Instead, variation in migration distance in painted lady butterflies is likely the result of a plastic response to environmental conditions. Overall, the methodological developments presented in this thesis are a step forward in studying insect migration. The development and application of metals and metal isotopes for insect geolocation opens new avenues to study the migration phenomenon at different scales with widespread relevance for conservation and pest management.