Tunisia, being part of the secondary center of diversity for durum wheat, has rich unexploited landraces that are being continuously lost and replaced by high yielding modern cultivars. This study aimed to investigate the genetic diversity and population structure of 196 durum wheat lines issued from landraces collected from Tunisia using Diversity Array Technology sequencing (DArTseq) and to understand possible ways of introduction in comparing them to landraces from surrounding countries. A total of 16,148 polymorphic DArTseq markers covering equally the A and B genomes were effective to assess the genetic diversity and to classify the accessions. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish five distinct groups that matched well with the farmer’s variety nomenclature. Interestingly, Mahmoudi and Biskri landraces constitute the same gene pool while Jenah Zarzoura constitutes a completely different group. Analysis of molecular variance (AMOVA) showed that the genetic variation was among rather than within the landraces. DAPC analysis of the Tunisian, Mediterranean and West Asian landraces confirmed our previous population structure and showed a genetic similarity between the Tunisian and the North African landraces with the exception of Jenah Zarzoura being the most distant. The genomic characterization of the Tunisian collection will enhance their conservation and sustainable use.
Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30–69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.
Macadamia (Macadamia integrifolia Maiden & Betche, Macadamia tetraphylla L.A.S. Johnson and their hybrids) is grown commercially around the world for its high-quality edible kernel. Traditional breeding efforts involve crossing varieties to produce thousands of progeny seedlings for evaluation. Cultivar improvement for nut yield using component traits and genomics are options for macadamia breeding, but accurate knowledge of genetic diversity and structure of the breeding population is required. This study reports allelic diversity within and between families of 295 seedling offspring from 29 parents, population structure and the extent of linkage disequilibrium (LD) in the population. Genotyping generated 19,527 silicoDArT and 5329 SNP markers, and, after filtering, 16,171 silicoDArTs and 4113 SNPs were used for diversity analyses. LD decay was initially rapid at short distances, but low-level LD persisted for long distances, with an average r2 = 0.124 for SNPs within 1 kb of each other. The seedling population was relatively genetically diverse and very similar to that of the 29 parents. The diversity (HE = 0.255 for progeny and 0.250 for parents) among these individuals indicates the level of diversity at the wider population level in the breeding programme, though the population appears less diverse than other fruit crops. Macadamia progeny was moderately differentiated (FST = 0.401) and formed k = 3 distinct clusters, which represents M. integrifolia germplasm separating from two different hybrid groups. There was low to no relationship between heterozygosity and performance for nut yield among progeny. These findings will inform future genomic studies of the Australian macadamia breeding programme, such as genome-wide association studies and genomic selection, where knowledge and control of population structure are vital.
Island populations can represent genetically distinct and evolutionarily important lineages relative to mainland conspecifics. However, phenotypic divergence of island populations does not necessarily reflect genetic divergence, particularly for lineages inhabiting islands periodically connected during Pleistocene low sea stands. Marine barriers may also not be solely responsible for any divergence that is observed. Here, we investigated genetic divergence among and within the three phenotypically distinct subspecies of bare‐nosed wombats (Vombatus ursinus) in south‐east Australia that are presently—but were not historically—isolated by marine barriers. Using genome‐wide single nucleotide polymorphisms, we identified three genetically distinct groups (mainland Australia, Bass Strait island, and Tasmania) corresponding to the recognized subspecies. However, isolation by distance was observed in the Tasmanian population, indicating additional constraints on gene flow can contribute to divergence in the absence of marine barriers, and may also explain genetic structuring among fragmented mainland populations. We additionally confirm origins and quantify the genetic divergence of an island population 46 years after the introduction of 21 individuals from the Vulnerable Bass Strait subspecies. In the light of our findings, we make recommendations for the maintenance of genetic variation and fitness across the species range.
One hundred and nine accessions of spring barley seedlings were phenotyped under soil drought conditions. Chlorophyll fluorescence induction (OJIP) parameters, leaf water content, relative turgidity, net assimilation rate (PN), and water use efficiency (WUE) of plants were measured. All the tested lines were genotyped by means of DArT sequencing (DArTseq) technology. For association mapping a 11,780 polymorphic DArTseq and 4,725 DArTseq SNP markers were used. Our results revealed dissimilar patterns of the relationships between OJIP-parameters under control and drought conditions. A high level of correlation between parameters characterizing Photosystem’s II (PSII) energy trapping efficiency (Fv/Fm) and photochemical events downstream of PSII reaction center (e.g., Performance Index—PICSo) was observed only in the case of drought-treated plants. Generally, OJIP parameters were correlated with leaf water content (less in control). This correlation was weaker with WUE, and absent with PN. Under drought stress, 6,252 genotype × phenotype associations, which passed false discovery rate (FDR) verification, were found between all the studied phenotypic characteristics (23, including 19 OJIP parameters) and 2,721 markers. On the other hand, only 282 associations passed FDR test in the control. They comprised 22 phenotypic parameters and 205 markers. Probing for gene annotations of sequences was performed for markers associated with Fv/Fm for both drought and control, markers were associated with studied traits in both control and drought, as well as for markers associated with both OJIP and other physiological parameters in drought. Our work allowed us to conclude that drought treatment differentiates the studied lines through the revealing of relationships between water content and the damages to PSII reaction centers or different components of PSII energy transfer chain. Moreover, the former was not connected with net photosynthesis rate.
The understanding of black tea quality and percent relative water content (%RWC) traits in tea (Camellia sinensis) by a quantitative trait loci (QTL) approach can be useful in elucidation and identification of candidate genes underlying the QTL which has remained to be difficult. The objective of the study was to identify putative QTL controlling black tea quality and percent relative water traits in two tea populations and their F1 progeny. A total of 1,421 DArTseq markers derived from the linkage map identified 53 DArTseq markers to be linked to black tea quality and %RWC. All 53 DArTseq markers with unique best hits were identified in the tea genome. A total of 5,592 unigenes were assigned gene ontology (GO) terms, 56% comprised biological processes, cellular component (29%) and molecular functions (15%), respectively. A total of 84 unigenes in 15 LGs were assigned to 25 different Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways based on categories of secondary metabolite biosynthesis. The three major enzymes identified were transferases (38.9%), hydrolases (29%) and oxidoreductases (18.3%). The putative candidate proteins identified were involved in flavonoid biosynthesis, alkaloid biosynthesis, ATPase family proteins related to abiotic/biotic stress response. The functional annotation of putative QTL identified in this current study will shed more light on the proteins associated with caffeine and catechins biosynthesis and % RWC. This study may help breeders in selection of parents with desirable DArTseq markers for development of new tea cultivars with desirable traits.
Many shark species are at risk of overexploitation due to their high economic value, slow maturation, and low recruitment compared to most teleosts. However, there is insufficient knowledge about population structure at different spatial scales necessary to optimise fisheries models. We used single-nucleotide polymorphisms (SNPs) obtained through complexity-reduction genome sequencing to quantify the population structure of two highly mobile and commercially fished shark species: bronze whalers (Carcharhinus brachyurus) and dusky sharks (C. obscurus). We applied a comprehensive approach to test several population-structure hypotheses and signal consistency across methods and marker type. We found that C. obscurus was panmictic across Australia and Indonesia and across the Indian Ocean to South Africa based on neutral loci, whereas for C. brachyurus, the westernmost Australian samples appeared to be separate from the rest. The southernmost east Australian samples indicated some difference from the rest of Australia and New Zealand based on candidate loci for C. brachyurus, and potentially also C. obscurus; however, the lack of a reference genome makes the interpretation difficult. Despite similar patterns in both species, subtle and potentially important structure differences emphasise the importance of studying each target species independently rather than assuming similar patterns from closely related species with similar dispersal abilities, as well as considering different marker types in future studies. We found evidence of connectivity across the regions sampled, suggesting that the cumulative effects of regional fisheries and the potential for cross-jurisdictional fishery assessments and management should be considered for Australian, Indonesian, and New Zealand populations.
In this study, we investigated the genetic diversity and population structure of the core collection of hexaploid wheat accessions in the Japanese wheat gene bank NBRP-Wheat. The core collection, consisting of 188 accessions of Triticum aestivum, T. spelta, T. compactum, T. sphaerococcum, T. macha and T. vavilovii, was intensively genotyped by DArTseq markers and consisted of 20,186 SNPs and 60,077 present and absent variations (PAVs). Polymorphic markers were distributed in all chromosomes, with a tendency for smaller numbers on the D-genome chromosomes. We examined the population structure by Bayesian clustering and principal component analysis with a general linear model. Overall, the core collection was divided into seven clusters. Non-admixture accessions in each cluster indicated that the clusters reflect the geographic distribution of the accessions. Both structure analyses strongly suggested that the cluster consisting of T. spelta and T. macha is out-grouped from other hexaploid wheat accessions. We performed genome-wide association analysis pilot studies for nine quantitative and seven qualitative traits and found marker-trait associations for all traits but one, indicating that the current core collection will be useful for detecting uncharacterized QTLs associated with phenotypes of interest.
Here we present “Restore and Renew,” a replicable framework for gathering and interpreting evolutionary, ecological, and genomic data in support of restoration practices. In an era of rapid climatic change and continuous widespread clearing, revegetation projects need to focus on producing resilient and long‐term self‐sustaining populations. Restore and Renew expands current knowledge of genetic provenance via genome‐scan data, environmental niche modeling (ENM), and site‐specific climate information. The sampling strategy is to obtain leaf tissue representing the distributions of over 100 species commonly used in restoration. We apply generalized dissimilarity modeling to genome‐wide single nucleotide polymorphism datasets from hundreds of samples. Species‐specific local provenances are obtained using a model that represents observed patterns of genetic variation across the landscape. Climate modeling is implemented to interpret genetic provenance boundaries in the context of current and future climatic conditions at the specified site. Results are presented in an easy‐to‐use webtool ( www.restore‐and‐renew.org.au), where the user simply selects their site of interest and a target species to obtain the size and distribution of local genetic provenance. Although Restore and Renew is not prescriptive, it allows restoration practitioners to make informed decisions on where to source material from, to fulfill their restoration scenario of choice. Two examples, Westringia fruticosa and Acacia suaveolens, are presented to demonstrate how the analytical pipeline responds to different ecological and evolutionary patterns. The webtool has multiple applications for biodiversity management and will continue to evolve with new species and analytical/interpretative outputs.
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativumlandraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.