Soybean Seed Quality and Vigor: Influencing Factors, Measurement, and Pathogen Characterization

High seed vigor (SV), or the ability of seed to germinate and grow in a stressful environment is important, as many field emergence conditions are stressful for germination. Soybean SV can be affected by cultivar, seed storage environment conditions, the growing environment during seed development, crop management practices such as foliar fungicide applications, pathogens, and other factors. To assess the effects of some of these factors on soybean, the objectives of this work were to determine 1. the effect of cultivar and foliar azoxystrobin application on soybean yield, germination, vigor, microflora, and their relationships under harvest delay conditions; 2. if amplicon sequence community analysis using next generation sequencing characterized more fungi and bacteria than culture dependent methods; and 3. changes in seed quality and performance of high and low quality soybean seed stored in a commercial warehouse and under controlled conditions during the summer season as measured by SG, vigor, and field emergence. Cultivar had a significant impact on yield and soybean SV, which were at least partly due to differences in seedborne pathogen infection. Differences in pathogen incidence among cultivars appeared to be influenced by genes for disease resistance. Foliar azoxystrobin application affected SV and seedborne pathogen incidence inconsistently, particularly Phomopsis longicolla. Seed infection by fungi and bacteria significantly reduced SV. Seedborne pathogens are problematic in all soybean growing areas. Culture dependent methods, the current standard, may only detect a small portion of the microorganisms in a seed lot. Next generation amplicon sequencing of fungal and bacterial DNA revealed over two dozen seedborne microorganisms. Five fungi and bacteria were found using culture methods from the same seed lot. During storage seed are best maintained by cool and low humidity conditions, which are not always available in seed warehouses. In this study, seed stored in high temperatures and relative humidity had greater reductions of field emergence and SV to a lesser degree than controls. Overall, soybean SV was affected by cultivar, environmental conditions at harvest, and appeared to be affected by conditions of storage, which affected SV through changes in seed physiology and infection by fungal and bacterial pathogens

Gut Microorganisms of Aquatic Animals 2.0

This is a collection of scientific research articles focusing on the associations and/or interactions of various aquatic animals with their microorganisms, focusing mostly on fish and, in particular, gut bacterial communities

Unravelling the complex reproductive tactics of male humpback whales : an integrative analysis of paternity, age, testosterone, and genetic diversity

How the underlying forces of sexual selection impact reproductive tactics including elaborate acoustic displays in cetaceans remains poorly understood. Here, I combined 26 years (1995-2020) of photo-identification, behavioural, (epi)genetic, and endocrine data from an endangered population of humpback whales (New Caledonia), to explore male reproductive success, age, physiology, and population dynamics over almost a third of the lifespan of a humpback whale. First, I conducted a paternity analysis on 177 known mother-offspring pairs and confirmed previous findings of low variation in reproductive success in male humpback whales. Second, epigenetic age estimates of 485 males revealed a left-skewed population age structure in the first half of the study period that became more balanced in the second half. Further, older males (> 23 years) more often engaged in certain reproductive tactics (singing and escorting) and were more successful in siring offspring once the population age structure stabilised, suggesting reproductive tactics and reproductive success in male humpback whales may be age-dependent. Third, using enzyme immunoassays on 457 blubber samples, I observed a seasonal decline in male testosterone in the population over the breeding season. Testosterone levels appeared highest during puberty, then decreased and levelled off at the onset of maturity, yet were highly variable at any point during the breeding season and across males of all ages. Lastly, I investigated the influence of genetic diversity at the major histocompatibility complex (MHC) class I and class IIa (DQB and DRB-a) on patterns of male reproductive success in humpback whales. Mating pairs shared fewer alleles than expected under random mating at MHC class I and IIa, thus, providing evidence of an MHC-mediated female mate choice in humpback whales. This thesis provides novel, critical insights into the evolutionary consequences of commercial whaling on the demography, patterns of reproduction and sexual selection of exploited populations of baleen whales."This work was supported by a University of St Andrews School of Biology Ph.D. Scholarship and the Louis M. Herman Research Scholarship 2022 to Franca Eichenberger. Sample collection and analyses from 2018-2020 were supported by grants to Ellen C. Garland (Royal Society University Research Fellowship (UF160081 & URF\R\221020), Royal Society Research Fellows Enhancement Award (RGF\EA\180213), Royal Society Research Grants for Research Fellows 2018 (RGF\R1\181014), National Geographic Grant (#NGS-50654R-18), Carnegie Trust Research Incentive Grant (RIG007772), British Ecological Society Small Research Grant (SR18/1288) and School of Biology Research Committee funding)."--Fundin

A study of the green leaf volatile biochemical pathway as a source of important flavour and aroma precursors in Sauvignon blanc grape berries

Green leaf volatiles (GLVs) are short-chain acylic aldehydes, alcohols and esters produced by plants via enzymatic metabolism of polyunsaturated fatty acids (PUFAs). GLVs are known to affect flavour and aroma of fruits and vegetables, including grapes. It has also been suggested that C6 and C5 GLVs are the precursors of volatile thiols, the aroma compounds that are important in Sauvignon blanc wine. GLVs are produced during grape berry development and released in high quantities upon berry crush. GLV aldehydes are formed from PUFAs by the action of two enzymes, lipoxygenase (LOX) and hydroperoxide lyase (HPL). This biochemical pathway is well characterised in other plant species and is known as the GLV pathway. To date, the GLV pathway has not been characterised in grapes. This thesis focuses on identification and initial characterisation of LOX and HPL genes and enzymes involved in the GLV-pathway. LOXs are a group of non-haem iron-containing dioxygenases that catalyse oxygenation of PUFAs producing PUFA-hydroperoxides. The most common PUFA substrates in plants are linoleic acid (LA, 18:2) and α-linolenic acid (LnA, 18:3). Depending on the position of oxygenation of the 18-carbon chain PUFAs, all plant LOXs are classified as 13(S) - and 9(S)-LOXs. 13(S)-LOXs are further regarded as type II and type I enzymes, depending on the presence or absence of transit peptides in the amino acid sequences of these enzymes respectively. HPLs belong to the CYP74 enzyme family, which is represented by atypical members of cytochrome P450 oxidases superfamily. HPLs cleave PUFA-hydroperoxides, producing aldehydes and oxoacids. Depending on the substrate specificity, HPLs are classified as 13-HPLs, 9/13-HPLs or 9-HPLs. The research reveals the complexity of the genetic makeup of the GLV metabolic pathway in grapes. Eighteen putative LOX genes and six putative HPL genes were identified in the Pinot noir grape genome. Phylogenetic analysis of the identified grape LOXs classified them as members of two groups, type II 13-LOXs and 9-LOXs, whereas all identified grape HPLs were classified as 13-HPLs (CYP-74B) and 9/13-HPLs (CYP-74C). Several LOX and HPL genes were expressed at different levels in Sauvignon blanc berry. Study of selected LOX and HPL gene expression revealed different levels of expression and differential tissue distribution of individual LOX and HPL genes within the berry. The studied genes also displayed different patterns of expression across different stages of berry development, upon wounding and in berries infected with Botrytis cinerea. Amongst the four LOX gene studied, transcripts of VvLOXA were the most abundant at all stages during berry development. VvLOXO was induced transiently upon berry damage and was a clear candidate involved in berry response to wounding. Expression levels of VvLOXC and VvLOXO were significantly increased in berries infected with Botrytis cinerea compared to the uninfected berries. In vitro biochemical analysis of the reaction products of recombinant VvLOXA (LOXA-TP) and VvLOXO (LOXO-TP) confirmed that these two enzymes are 13-LOXs. Both enzymes preferred LnA as a substrate. Both enzymes had the same temperature optima of 25°C, but preferred different pH conditions. Recombinant LOXA-TP preferred acidic environment and had pH optimum of pH 5.5, while LOXO-TP preferred neutral-to-basic conditions and had pH optimum of pH 7.5. Preliminary experiments with recombinant VvHPLA showed its ability to metabolise 13(S)-hydroperoxides, releasing C6 volatile aldehydes. Recombinant VvHPLA exhibited maximum activity with 13(S)-hydroperoxides of LnA as substrate at pH 5.0