Conservation Genetics for Management of Threatened Plant and Animal Species

This book focuses on conservation genetic (and genomic) papers that demonstrate applied outcomes that inform practical threatened species management. We cover a broad range of species and genetic approaches, but focus on how conservation genetic information is used to underpin management actions for species recovery. Through the exposition of a diversity of approaches, we aim to demonstrate to conservation managers and researchers how conservation genetics can inform on-ground species management

Plant Biodiversity and Genetic Resources

The papers included in this Special Issue address a variety of important aspects of plant biodiversity and genetic resources, including definitions, descriptions, and illustrations of different components and their value for food and nutrition security, breeding, and environmental services. Furthermore, comprehensive information is provided regarding conservation approaches and techniques for plant genetic resources, policy aspects, and results of biological, genetic, morphological, economic, social, and breeding-related research activities. The complexity and vulnerability of (plant) biodiversity and its inherent genetic resources, as an integral part of the contextual ecosystem and the human web of life, are clearly demonstrated in this Special Issue, and for several encountered problems and constraints, possible approaches or solutions are presented to overcome these

Using genomic information to conserve genetic diversity in livestock

Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity. </p

Conserving Australia's iconic marsupials; one genome at a time

In the midst of a global sixth mass extinction event, conservation initiatives are now more crucial than ever. Australia houses the most diverse range of marsupial species in the world; however, the number that are threatened is growing every year. Genetic management of threatened populations is vital in species recovery, yet incorporation of genetic data in conservation management is currently limited. International and national genome sequencing consortia are currently producing reference genomes for a large variety of species, though there is currently a gap between the creation of these genomic resources and their downstream applications, particularly in conservation contexts. One of the major drivers of this gap is due to the bioinformatic expertise and resources that are required to analyse genomic datasets and to translate the findings into conservation management. This PhD employs a variety of bioinformatic and sequencing approaches to develop genomic resources for threatened Australian Marsupials and demonstrates how these resources can be used as a tool to assist species conservation. The value of genomic data for conservation is demonstrated for a range of species under varying scenarios including: i) using existing genomic datasets for the endangered Tasmanian devil to answer new conservation questions relating to reproduction, ii) creating a reference genome for the common brown antechinus, to act as a model species for its threatened congeneric counterparts and iii) generating and uniting a suite of genomic resources to assist in the management of the vulnerable greater bilby. In addition, ten simple rules for getting started with command-line bioinformatics are presented to facilitate the use of genomic data in wildlife conservation. Bridging the research-implementation gap is essential for harnessing the power of genomic resources for the conservation of threatened species. The findings from this PhD provide crucial steps into bridging this gap

Better tools, better resources, better conservation: integrating genome data into the conservation of the pink pigeon Nesoenas mayeri

Humans are driving the sixth mass extinction causing biodiversity to decline at an unprecedented rate. To halt these declines effective conservation strategies are vital, if possible, these should include genetic data to ensure that the extinction risk of a population is not being underestimated. This thesis presents resources and tools that have been used to integrate genetic data into the management of the endangered pink pigeon (Nesoenas mayeri). A pseudo-chromosome assembly enabled the first whole genome analyses of the pink pigeon (Chapter 2), these analyses provided insight into their past demography and revealed a surprisingly large amount of variation within its genome. This challenges previous results obtained using restriction site associated DNA sequencing (RAD-Seq) data from wild pink pigeons but current methods for processing RAD data produce biased data sets that under-estimate diversity. A novel tool, RADiKal is presented (Chapter 3), which extracts information directly from raw RAD reads and avoids biasing data sets with complex parameterisation. The painted chromosomes produced by RADiKal provide an overview about the levels of variation present in the wild population which are comparable to those observed from whole genome analyses. Despite increasing access to genetic data one of the greatest challenges is its integration into management, one solution is the use of population viability analysis (PVA). An updated PVA was produced for pink pigeons showing that without genetic rescue they could face extinction within 100 years (Chapter 4). Selecting which individuals are most valuable for a genetic rescue is not trivial, especially in the absence of empirical data. I Choose You (I.C.Y) is an easy-to-use tool that allows practitioners to select individuals for genetic rescue based on their genetic diversity measured using founder equivalents calculated from studbook data (Chapter 5). Overall this thesis aims to demonstrate how better tools can lead to better resources and better conservation

Abstracts from the 50th European Society of Human Genetics Conference: Posters

International audienc

Physiological and genetic dissection of rice tolerance to water-deficit stress

Rice (Oryza sativa L.) is the world's most important staple food crop, especially in Asia. As a semi-aquatic crop species, water-scarcity and increasing severity of water-deficit stress owing to climate change, are a major threat to sustaining irrigated rice production. Improving the rice adaptation to water-deficit is, therefore, a primary breeding target. The main goal of this dissertation is to study the morphological, anatomical, physiological and genetic basis for responses of a rice plant to water-deficit stress. To give leads into how water-deficit tolerant rice should behave, a comparative study were conducted, whereby representative rice genotypes was compared at the same moisture stress during the vegetative stage with genotypes of wheat, a dryland cereal wheat (Triticum aestivum L.) known to be more tolerant to water-deficit than rice. Under-water-deficit, rice genotypes (IR64 & Apo) developed thinner roots allowing rapid water-acquisition, whereas wheat followed a water-conserving strategy through developing thicker leaves and roots, and moderate tillering. Root anatomy such as root diameter, xylem and stele diameter and xylem number were more plastic in wheat than in rice under-water-deficit. The methodology and findings from those representative genotypes were then projected to a diverse panel of nearly 300 rice genotypes. Such a panel was previously constructed by the International Rice Research Institute as a potential means of discovery of novel beneficial alleles for diverse phenotypic traits and their plasticity, with 46K high-quality single nucleotide polymorphisms (SNPs). A genome-wide association study (GWAS) was undertaken to identify the genomic regions regulating the morphological, physiological and root anatomical traits in rice, based on a large-scale greenhouse phenotyping of these traits. The genetic basis of these traits was different in control and water-deficit stress (strong quantitative trait loci [QTL] × environment interaction), in line with novel loci detected for the plasticity of traits. Key a priori candidate genes near to these genetic loci were also identified. Rice grain yield is strongly affected by water-deficit stress coinciding with sensitive reproductive stage. Strong genotypic variability for grain yield as well as yield components and related traits were observed in the same rice indica diversity panel, under control and reproductive stage water-deficit stress in field conditions across two years. The GWAS analysis identified the core loci of rice genome governing the grain yield and related traits. Most of the genomic loci were specific to treatment and year, indicating strong QTL × environment interactions. To enable GWAS findings to be used for better designing of genotypes by breeding, an existing process-based crop model GECROS was used in a case study, where grain yield of the same indica diversity panel (267 rice genotypes) from the control treatment in one season was dissected into eight physiological parameters. Some parameters had a stronger effect on grain yield than other parameters. Using these parameters, the model showed the ability to predict the genotypic variation of rice diversity panel for grain yield under different field conditions. Further, the GWAS analysis was extended to model-input parameters on randomly chosen 213 genotypes as a training dataset. The SNP-based estimates of parameter values calculated from the additive allelic effect of the loci were used as input to the crop model GECROS. Although the SNP-based modelling approach demonstrated the ability to predict the genotypic variation in training datasets under different environments, the prediction accuracy was lower in the remaining 54 genotypes used as a testing dataset. In addition, the prediction accuracy of grain yield was also lower using either parameter or SNP-based GECROS model in completely new season. However, the model-based sensitivity analysis effectively identified the different SNPs between control and water-deficit environments. Virtual ideotypes designed based on pyramiding the SNPs identified by modelling had a higher yield than those based on SNPs for yield per se.</p

Evaluation of the ingestive behaviour of the dairy cow under two systems of rotation with slope

The ingestive behaviour of grazing animals is modulated by the vegetation characteristics, topography and the type of stocking method. This research was carried out in 2019, at the Rumipamba CADER-UCE. It aimed to evaluate the impact of two contrasting stocking methods of dairy cows grazing a pasture with an average of slope >8.5%. Four dairy cows were set to graze a 0.4 ha paddock for 5 days for continuous stocking methods, while for the electric fence methods the dairy cows were restricted to 0.2 ha and the fence was moved uphill every 3 hours, repeating this process four times a day. Cow were equipped with activity sensors for 12 h per day. The whole procedure was repeated 2 times after realizing an equalization cuts and both paddocks, a rest time of 30 days and a random reassignment of paddocks to one of the treatments. The cows showed a difference in terms of the percentage of grazing P=0.0072, being higher with the electric fence (55% of the measurement time). From rising-plate-meter estimates of available biomass along the grazing periods, we calculated despite similar forage allowances (electric fence = 48.06 kg DM/cow/d and continuous = 48.21 DM/cow/d) a higher forage intake was obtained in the electric fence treatment (17.5 kg DM/cow/d) compared the continuous stocking (15.7 kg DM/cow/d) (P=0.006). In terms of milk production animals grazing under the differences electrical fence stocking method tended (P=0.0985) to produce more milk (17.39 kg/d) than those grazing in the continuous system (15.16 kg/d) due to the influence of the slope (P=0.05), while for milk quality the protein content was higher for the electric fence (33.7 g/l) than the continuous method (30.5 g/l) (P=0.039). None of the other milk properties differed between methods (P>0.05)