Genetic Variation for Weed Competition and Allelopathy in Rapeseed (Brassica napus L.)

Rapeseed (canola, Brassica napus L.) is the second major oilseed crop of the world and provides a source of healthy oil for human consumption, meal for stock markets and several other by-products. Several weed species afflict the sustainable production and quality of canola. Various agronomic practices such as crop rotation, stubble management (e.g. burning), minimum tillage, application of herbicides and cultivation of herbicide resistant varieties have been deployed to minimise yield losses. There is no doubt that herbicide-tolerant cultivars enable management of weeds which are difficult to control otherwise. However, widespread usage increases the risk of herbicide resistance. This is becoming a major impediment in sustaining high crop productivity. Allelopathic and weed competitive varieties are potential tools to reduce the dependence on herbicides and could be grown to suppress weed growth in commercial canola. Genetic variation and ‘proxy’ traits involved in both crop competition as well as allelopathy have been reported. Further research is required to link genetic variation in weed competition and allelopathy, and genetic/genomic marker technologies to unravel effective alleles to expand breeding activity for weed interference in canola

Genetic studies of salinity tolerance in wheat.

Salinity is an important issue in arid and semi-arid regions of the world, both in irrigated and dryland agriculture. Increasing salinity tolerance of crops is a feasible approach to tackling salinity. Focusing on the physiological traits associated with salinity tolerance such as Na⁺ exclusion and osmotic stress tolerance simplifies the strategies for improving tolerance. The first aim of the study described in this thesis was the development of a high throughput technique for the measurement of osmotic stress tolerance in bread wheat. This technique was then applied to 162 recombinant inbred lines derived from crossing two Australian bread wheat cultivars (Gladius and Drysdale), to identify the loci associated with osmotic stress tolerance and 4th leaf Na⁺ accumulation. This population was grown under two growth conditions – a pot-soil set-up with non-destructive imaging system (LemnaTec Scanalyzer 3D technology) for the estimation of osmotic stress tolerance using high through-put system (conveyor belt system) and a supported hydroponics set-up for 4th leaf Na⁺ and 4th leaf K⁺ accumulation measurements. In the soil based study, QTL analyses revealed two major QTL on the distal regions of the short arms of chromosomes 2B and 1B, where the salinity tolerance index (shoot biomass in saline conditions relative to shoot biomass in control conditions) and osmotic stress tolerance overlapped. Another significant QTL for osmotic stress tolerance was mapped onto the distal region of the long arm of chromosome 5D. In the hydroponics study, two QTL associated with 4th leaf Na⁺ accumulation were mapped to the distal regions of the long arms of chromosomes 1D and 3B. Loci containing a vernalisation gene (VRN-A1), on the long arm of chromosome 5A, and a photoperiod gene (Ppd-D1), on the short arm of chromosome 2D, had an impact on tiller number, shoot biomass and shoot water content in salt and control conditions. The second aim of the research program was to study the genetics of Na⁺ exclusion in two Afghani durum wheat landraces, which accumulated half the amount of 3rd leaf Na⁺ compared to Australian commercial durum wheat cultivars. These landraces were crossed with an Australian durum wheat (cv Jandaroi) and F₂ populations were developed. The parents and F₂ population were grown in a supported hydroponics system at 100 mM NaCl, and the Na⁺+ and K⁺ concentrations in the third leaf was measured after ten days growth in salt. Selective genotyping analysis using DArT markers and bulked segregant analysis (BSA) using SNP markers were carried out to detect the putative genomic regions responsible for salinity tolerance. Both analyses revealed a locus on the distal region of the long arm of chromosome 4B associated with Na⁺ and K⁺ accumulation and the ratio of K⁺/Na⁺ in the third leaf; the favourable allele derived from the Afghani landraces. BSA identified another locus on the distal region of the long arm of chromosome 3B, associated only with 3rd leaf Na⁺ accumulation and the favourable allele was inherited from Jandaroi. These loci on chromosomes 3B and 4B were validated in the entire F₂ population and marker regression analysis showed that both have a significant association with 3rd leaf Na+ accumulation. The putative genomic loci identified in this thesis can be validated further and these would lead to the identification of genes and the development of markers to facilitate the breeding of salt tolerant wheat cultivars.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 201

Quantitative Trait Loci for Genotype and Genotype by Environment Interaction Effects for Seed Yield Plasticity to Terminal Water-Deficit Conditions in Canola (<i>Brassica napus</i> L.)

Canola plants suffer severe crop yield and oil content reductions when exposed to water-deficit conditions, especially during the reproductive stages of plant development. There is a pressing need to develop canola cultivars that can perform better under increased water-deficit conditions with changing weather patterns. In this study, we analysed genetic determinants for the main effects of quantitative trait loci (QTL), (Q), and the interaction effects of QTL and Environment (QE) underlying seed yield and related traits utilising 223 doubled haploid (DH) lines of canola in well-watered and water-deficit conditions under a rainout shelter. Moderate water-deficit at the pre-flowering stage reduced the seed yield to 40.8%. Multi-environmental QTL analysis revealed 23 genomic regions associated with days to flower (DTF), plant height (PH) and seed yield (SY) under well-watered and water-deficit conditions. Three seed yield QTL for main effects were identified on chromosomes A09, C03, and C09, while two were related to QE interactions on A02 and C09. Two QTL regions were co-localised to similar genomic regions for flowering time and seed yield (A09) and the second for plant height and chlorophyll content. The A09 QTL was co-located with a previously mapped QTL for carbon isotope discrimination (Δ13C) that showed a positive relationship with seed yield in the same population. Opposite allelic effects for plasticity in seed yield were identified due to QE interactions in response to water stress on chromosomes A02 and C09. Our results showed that QTL’s allelic effects for DTF, PH, and SY and their correlation with Δ13C are stable across environments (field conditions, previous study) and contrasting water regimes (this study). The QTL and DH lines that showed high yield under well-watered and water-deficit conditions could be used to manipulate water-use efficiency for breeding improved canola cultivars

Additional file 1: of Genetics of Na+ exclusion and salinity tolerance in Afghani durum wheat landraces

Data for seven SNP markers used in this research. Details regarding the markers used in this study, which contains their sequence information and the locus ID of the gene the marker is within. (DOCX 14 kb

SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana.

Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me . Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing. [Abstract copyright: © 2024. The Author(s), under exclusive licence to Springer Nature Limited.