A collection of 100 wheat varieties representing more than 100 years of wheat-breeding history in Scandinavia was established in order to identify marker-trait associations for plant height (PH), grain yield (GY), and biomass potential for bioethanol production. The field-grown material showed variations in PH from 54 to 122 cm and in GY from 2 to 6.61 t ha(-1). The release of monomeric sugars was determined by high-throughput enzymatic treatment of ligno-cellulosic material and varied between 0.169 and 0.312 g/g dm for glucose (GLU) and 0.146 and 0.283 g/g dm for xylose (XYL). As expected, PH and GY showed to be highly influenced by genetic factors with repeatability (R) equal to 0.75 and 0.53, respectively, while this was reduced for GLU and XYL (R = 0.09 for both). The study of trait correlations showed how old, low-yielding, tall varieties released higher amounts of monomeric sugars after straw enzymatic hydrolysis, showing reduced recalcitrance to bioconversion compared to modern varieties. Ninety-three lines from the collection were genotyped with the DArTseq(®) genotypic platform and 5525 markers were used for genome-wide association mapping. Six quantitative trait loci (QTLs) for GY, PH, and GLU released from straw were mapped. One QTL for PH was previously reported, while the remaining QTLs constituted new genomic regions linked to trait variation. This paper is one of the first studies in wheat to identify QTLs that are important for bioethanol production based on a genome-wide association approach.
Tropical tuna fisheries are central to food security and economic development of many regions of the world. Contemporary population assessment and management generally assume these fisheries exploit a single mixed spawning population, within ocean basins. To date population genetics has lacked the required power to conclusively test this assumption. Here we demonstrate heterogeneous population structure among yellowfin tuna sampled at three locations across the Pacific Ocean (western, central, and eastern) via analysis of double digest restriction-site associated DNA using Next Generation Sequencing technology. The differences among locations are such that individuals sampled from one of the three regions examined can be assigned with close to 100% accuracy demonstrating the power of this approach for providing practical markers for fishery independent verification of catch provenance in a way not achieved by previous techniques. Given these results, an extended pan-tropical survey of yellowfin tuna using this approach will not only help combat the largest threat to sustainable fisheries (i.e. illegal, unreported, and unregulated fishing) but will also provide a basis to transform current monitoring, assessment, and management approaches for this globally significant species.
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P < 0.05) segregation distortion across all 11 chromosomes, and 513 (83.3 %) of these distorted loci showed distortion in favor of the elite watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.
The Magpie Fiddler ray, Trygonorrhina melaleuca Scott 1954, is presently South Australia’s (SA) rarest fish, represented by only three museum specimens collected near Adelaide over the past 60 years and listed as Endangered in the IUCN Red List of Threatened Species. However, there is some doubt as to whether the Magpie Fiddler Ray is a different species from the widespread and common Southern Fiddler Ray, Trygonorrhina dumerilii (Castelnau 1873), resulting in two very contrasting scenarios for marine conservation. If the Magpie Fiddler Ray is a black and white patterned variant of the Southern Fiddler Ray then it will be removed from the Red List and appear as a synonym of T. dumerilii. Conversely, if it proves to be a different species then it remains SA’s rarest fish species and highly data deficient. We analysed mtDNA and the largest ever nuclear gene dataset (>4,000 loci) applied to chondrichthyan species level systematics from the most recently collected Magpie Fiddler Ray specimens and a geographically representative selection of Southern Fiddler Rays to determine the species status of this enigmatic ray. We found that the Magpie Fiddler Rays share a mitochondrial haplotype with 23 Southern Fiddler Rays and are not differentiated from 35 Southern Fiddler Rays at more than 4000 SNPs derived from DArTseq data. The morphological trait values that are putatively diagnostic for the Magpie Fiddler Ray fall within the range of variation observed among Southern Fiddler Rays. Our analyses are consistent with the notion that the Magpie Fiddler Ray is a rare colour and pattern variant of the widespread and abundant Southern Fiddler Ray. We also identified two hybrids between the Eastern and Southern Fiddler Rays, only the third time that hybrids have been identified in nature in chondrichthyans. Our results provide critical guidance in the assessment of its conservation status and an ending to a 60 year old conundrum for marine conservation.
Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for example, temperature-dependent sex determination)1. Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles2. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene–environment interactions3. Most mechanistic models of transitions invoke a role for sex reversal3,4,5. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish6 and rarely in amphibians7,8. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change.
Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from
the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
Fire blight, caused by the Gram-negative bacterium Erwinia amylovora, is the most important bacterial disease affecting apple (Malus × domestica) and pear (Pyrus communis) production. The use of antibiotic treatment, though effective to some degree, is forbidden or strictly regulated in many European countries, and hence an alternative means of control is essential. The planting of fire blight-resistant cultivars seems to be a highly feasible strategy. In this study, we explored a segregating population derived from a cross between the wild apple species Malus fusca and the M. × domestica cultivar Idared. F1 progenies used for mapping were artificially inoculated with Erwinia amylovora strain Ea222_JKI at a concentration of 109 cfu/ml in three different years. The averages of percentage lesion length of all replicates of each genotype were used as numerical traits for statistical analysis. A Kruskal–Wallis analysis was used to determine marker–phenotype association and revealed a linkage group with Diversity Arrays Technology (DArT) markers significantly linked with fire blight. After locating the positions of the DArT markers on the Golden Delicious genome, simple sequence repeat (SSR) markers were developed from chromosome 10 to replace the DArT markers and to determine the quantitative trait locus (QTL) region. Multiple QTL mapping (MQM) revealed a strong QTL (Mfu10) on linkage group 10 of M. fusca explaining about 65.6 % of the phenotypic variation. This is the first report on a fire blight resistance QTL of M. fusca.
In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties.
A set of about 100 winter barley (Hordeum vulgare L.) cultivars, comprising diverse and economically important German barley elite germplasm released during the last six decades, was previously genotypically characterized by single nucleotide polymorphism (SNP) markers using the Illumina GoldenGate BeadArray Technology to detect associations with phenotypic data estimated in three-year field trials at 12 locations.