Genomic selection for target traits in the Australian lentil breeding program

Genomic selection (GS) uses associations between markers and phenotypes to predict the breeding values of individuals. It can be applied early in the breeding cycle to reduce the cross-to-cross generation interval and thereby increase genetic gain per unit of time. The development of cost-effective, high-throughput genotyping platforms has revolutionized plant breeding programs by enabling the implementation of GS at the scale required to achieve impact. As a result, GS is becoming routine in plant breeding, even in minor crops such as pulses. Here we examined 2,081 breeding lines from Agriculture Victoria’s national lentil breeding program for a range of target traits including grain yield, ascochyta blight resistance, botrytis grey mould resistance, salinity and boron stress tolerance, 100-grain weight, seed size index and protein content. A broad range of narrow-sense heritabilities was observed across these traits (0.24-0.66). Genomic prediction models were developed based on 64,781 genome-wide SNPs using Bayesian methodology and genomic estimated breeding values (GEBVs) were calculated. Forward cross-validation was applied to examine the prediction accuracy of GS for these targeted traits. The accuracy of GEBVs was consistently higher (0.34-0.83) than BLUP estimated breeding values (EBVs) (0.22-0.54), indicating a higher expected rate of genetic gain with GS. GS-led parental selection using early generation breeding materials also resulted in higher genetic gain compared to BLUP-based selection performed using later generation breeding lines. Our results show that implementing GS in lentil breeding will fast track the development of high-yielding cultivars with increased resistance to biotic and abiotic stresses, as well as improved seed quality traits

Evolutionary genetics of adaptation in Tasmanian blue gum

© 2016 Dr. Hossein Valipour KahroodObjectives The main aim of this thesis was to understand the role of Darwinian positive selection in Eucalyptus evolution and provide persuasive indications of adaptive evolution for forest trees. Background The species-rich genus Eucalyptus L’Héritier De Brutelle (Eucalyptus) forms the dominant canopy species of the Australian landscape and plays an essential role in diverse ecological aspects of its ecosystems including micro and macroclimates, biodiversity, fire spread, and water resources. Species of this genus for their outstanding growth and wood quality constitute the majority of Australian hardwood plantations and are among the major commercial plantation hardwoods in tropical and temperate regions of the world. Understanding evolutionary processes contributing genetic variation of Eucalyptus would aid in deriving more sustainable management strategies of conservation biology and forest tree breeding in Australia and worldwide. In conservation genetics it can help inform public policy directed at the conservation and the short- and long-term adaptability of the species. In breeding programs using association or genomic selection methods, identification of elite trees is influenced by demographic and selective histories of the species. Approach and results The wealth of nucleotide diversity in Eucalyptus, existence of numerous repetitive features of its DNA sequences coupled with the lack of a sophisticated NGS data pipeline at the time hindered obtaining good-quality, long stretch nuclear DNA. This thesis used a significant number of entire chloroplast genomes carrying both divergence and diversity information. In the first study, a phylogeny-based analysis was applied to measure rates of evolution and detect molecular signatures of positive selection of 85 plastid-encoded orthologous genes from 39 Myrtaceae species (interspecific set). Amino acid residues of several genes showed rate acceleration consistent with strong directional selection. The Eucalyptus clade showed elevated substitution rates when compared to its sister Corymbia+Angophora clade, indicating the role of natural selection in adaptation, radiation and/or speciation of the Eucalyptus species when inhabiting new environments. In the second study, a similar analysis was carried out on the same set of genes in 136 individuals from seven populations of Eucalyptus globulus Labill. ssp globulus (E. globulus) to pinpoint its genetic variation in an intraspecific approach. Tasmanian blue gum was used since the species is widely distributed across elevation and annual rainfall classes between southern Victoria and south of Tasmania, encouraging speculation about potential variation. In this study, a smaller number of genes (intraspecific set) were identified as showing similar signature consistent with those identified in the previous study. These included accD, ccsA, matK, ndhD, ndhF, ndhH, rbcL and ycf1, and within those five sites including ndhD-454, ndhF-230, matK-252, rbcL-142 and rbcL-251 were shared between the two datasets. The dataset in this study also enabled for the first time analysis of the phylogeography of E. globulus ssp. globulus as well as studying demographic history of the species using the whole cp genomes. Two distinct origins of E. globulus were confirmed with one lineage being differentiated in mainland Australia and the other one in Tasmania. These two major lineages diverged approximately 5 7 Ma with the second split between the western and eastern mainland sub-lineages taking place around 2 2.5 Ma. The split times of these lineages and sub-lineages coincided with major cooling and/or drying periods in the distant past. It was also shown that the above lineages had expanded their territory from the Mid-Pleistocene onwards, and thus genetic drift has principally affected Eucalyptus genetic variation, in comparison to which natural selection appears to have had local influence. In the last section of this thesis, it is hypothesised that sites with similar signatures between the two datasets are of functional importance. Among those, rbcL, the large subunit of RuBisCo - the most abundant enzyme on Earth and the most critical enzyme in the process of carbon fixation - appeared most amenable for physiological experiments in order to phenotypically validate its putative signatures of selection. A functional link was found between the rbcL haplotypes (PI, PM, TM) and net assimilation rate of CO2, providing an insight into the process of natural selection in deriving adaptive evolution of the species. The glasshouse experiment was followed by protein modelling and the higher photosynthetic rates of the PM and PI haplotypes over TM haplotype was explained. Conclusions The readily hybridising closely-related species of Eucalyptus occur across a large range of contrasting climates, making them an excellent model to explore naturally-occurring genetic variation that is under selection. This thesis reports how genetic variation of a key enzyme in photosynthesis with signatures consistent with having been subject to positive selection can be advantageous under future climate change where higher temperatures and/or prolonged drought are predicted. Apart from the availability of naturally-occurring genetic variations in chloroplast genomes for tree adaption, breeding programs and forest health monitoring, this research also proves that the haploid nature of the chloroplast genome is appropriate for studying phylogeography and evolutionary history of the species. Using the entire chloroplast genome for both interspecific and intraspecific data, a comprehensive demographic history of Tasmanian blue gum, a worldwide commercially important forest tree species, is illustrated. This thesis therefore provides a unique perspective in studying evolutionary genetics of a plant species

Genetic variation of mangrove species Avicennia marina in Iran revealed by microsatellite markers

Mangroves play an essential role in ecosystem dynamics but are reported to be regressing as human pressure increases on coastal zones. In order to ensure conservation of mangroves, genetic diversity in remaining population must be explored. Since Avicennia marina is an environmentally susceptible species, such studies including examination of its genetic variation is done in a worldwide range.During the present study the level of genetic variation of mangrove trees (A. marina) in three coastlines of Bushehr province (Southwest regions of Iran) was examined using microsatellite markers. Threemicrosatellite loci which were applied in the last large-scale study, detected high levels of allelic diversity here (14 alleles in total), essential for an accurate estimation of population genetic parameters.The levels of heterozygosity detected for each population, over all loci, ranged from 0.451 to 0.667 with an average of 0.589, indicating relatively appropriate level of genetic variation. The expectedheterozygosity was larger than the observed heterozygosity leading to positive inbreeding coefficients in all three populations. Highly significant departures from Hardy-Weinberg Equilibrium were detectedin populations. Reduced level of genetic variation was found in the central population indicating strong genetic structure among the other populations with larger area and less exploitation

Development and Application of Image-Based High-Throughput Phenotyping Methodology for Salt Tolerance in Lentils

Soil salinity is a major abiotic stress in Australian lentil-producing areas. It is therefore imperative to identify genetic variation for salt tolerance in order to develop lentil varieties suitable for saline soils. Conventional screening methods include the manual assessment of stress symptoms, which can be very laborious, time-consuming, and error-prone. Recent advances in image-based high-throughput phenotyping (HTP) technologies have provided unparalleled opportunities to screen plants for a range of stresses, such as salt toxicity. The current study describes the development and application of an HTP method for salt toxicity screening in lentils. In a pilot study, six lentil genotypes were evaluated to determine the optimal salt level and the growth stage for distinguishing lentil genotypes using red–green–blue (RGB) images on a LemnaTec Scanalyzer 3D phenomics platform. The optimized protocol was then applied to screen 276 accessions that were also assessed earlier in a conventional phenotypic screen. Detailed phenotypic trait assessments, including plant growth and green/non-green color pixels, were made and correlated to the conventional screen (r = 0.55; p < 0.0001). These findings demonstrated the improved efficacy of an image-based phenotyping approach that is high-throughput, efficient, and better suited to modern breeding programs

Application of Genomics Approaches for the Improvement in Ascochyta Blight Resistance in Chickpea

Advancements in high-throughput genotyping and sequencing technologies are enabling the development of a vast range of genomic tools and resources for a new revolution in plant breeding. Several genotyping-by-sequencing (GBS) methods including capture-based, genome complexity reduction and sequencing of cDNA (GBS-t) are available for application in trait dissection, association mapping, and genomic selection (GS) in crop plants. The aims of this study were to identify genomic regions conferring resistance to Ascochyta blight (AB) introgressed from the wild Cicer echinospernum into the domesticated C. arietinum, through a conventional recombinant inbred population genotyped using a variety of GBS methods. Evaluation of GBS methods revealed that capture-based approaches are robust and reproducible while GBS-t is rapid and flexible. A genetic linkage map consisting of 5886 polymorphic loci spanning 717.26 cM was generated. Using field phenotyping data from two years, a single genomic region on LG4 was identified with quantitative trait loci (QTL) mapping. Both GBS methods reported in this study are well suited for applications in genomics assisted plant breeding. Linked markers for AB resistance, identified in the current study, provide an important resource for the deployment into chickpea breeding programs for marker-assisted selection (MAS)

Small urban stands of the mangrove Avicennia marina are genetically diverse but experience elevated inbreeding

Anthropogenic impacts contribute to the fragmentation of urban mangrove forests, and in the Sydney region of Australia, Avicennia marina is commonly found in small stands of However, genetic diversity may not vary with stand size because insufficient time has passed since stands were established or pollen and propagule dispersal are sufficient to overwhelm the effects of genetic drift and founder events. We tested the predictions that, despite the potential of mangroves for dispersal of propagules by water and long distance dispersal of pollen by honeybees, fragmentation and localized foraging by honeybees causes small stands of A. marina to display reduced genetic diversity and elevated inbreeding. Using four microsatellite markers, we quantified the genetic and genotypic diversity present within samples of 20 adults taken from three large (\u3e1500 trees), intermediate (300-500 trees) and small (\u3c50 \u3etrees) stands within each of two urbanized estuaries and estimated mating system parameters using progeny arrays for sets of five adults within the large and small stands. We detected no significant effect of stand size on levels of single-locus genetic diversity. There were low, although significant, levels of allelic differentiation within (F SE = 0.021, P = 0.003) and among (F ET = 0.055, P = 0.005) estuaries but no evidence of isolation by distance. In contrast, our analysis of progeny arrays revealed that, while all stands displayed high levels of biparental inbreeding, an expected consequence of pollination by honeybees, current outcrossing rates (t m ) were significantly lower in small (0.55) as compared to large (0.75) stands. The genetic makeup of the adult populations imply that stands are interconnected and suggest little impact of habitat fragmentation, while the progeny arrays suggest that plants within small stands may display reduced fitness

Cosmic kidney disease:an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction

Missions into Deep Space are planned this decade. Yet the health consequences of exposure to microgravity and galactic cosmic radiation (GCR) over years-long missions on indispensable visceral organs such as the kidney are largely unexplored. We performed biomolecular (epigenomic, transcriptomic, proteomic, epiproteomic, metabolomic, metagenomic), clinical chemistry (electrolytes, endocrinology, biochemistry) and morphometry (histology, 3D imaging, miRNA-ISH, tissue weights) analyses using samples and datasets available from 11 spaceflight-exposed mouse and 5 human, 1 simulated microgravity rat and 4 simulated GCR-exposed mouse missions. We found that spaceflight induces: 1) renal transporter dephosphorylation which may indicate astronauts' increased risk of nephrolithiasis is in part a primary renal phenomenon rather than solely a secondary consequence of bone loss; 2) remodelling of the nephron that results in expansion of distal convoluted tubule size but loss of overall tubule density; 3) renal damage and dysfunction when exposed to a Mars roundtrip dose-equivalent of simulated GCR.</p