SNP markers retrieval for a non-model species: a practical approach

<p>Abstract</p> <p>Background</p> <p>SNP (Single Nucleotide Polymorphism) markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC) on 454 data from four lily genotypes and compared results with respect to SNP retrieval.</p> <p>Results</p> <p>CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs.</p> <p>Conclusion</p> <p>In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.</p

Small bowel Crohn’s disease: MR enteroclysis and capsule endoscopy compared to balloon-assisted enteroscopy

New modalities are available to visualize the small bowel in patients with Crohn’s disease (CD). The aim of this study was to compare the diagnostic yield of magnetic resonance enteroclysis (MRE) and capsule endoscopy (CE) to balloon-assisted enteroscopy (BAE) in patients with suspected or established CD of the small bowel. Consecutive, consenting patients first underwent MRE followed by CE and BAE. Patients with high-grade stenosis at MRE did not undergo CE. Reference standard for small bowel CD activity was a combination of BAE and an expert panel consensus diagnosis. Analysis included 38 patients, 27 (71%) females, mean age 36 (20–74) years, with suspected (n = 20) or established (n = 18) small bowel CD: 16 (42%) were diagnosed with active CD, and 13 (34%) by MRE with suspected high-grade stenosis, who consequently did not undergo CE. The reference standard defined high-grade stenosis in 10 (26%) patients. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value of MRE and CE for small bowel CD activity were 73 and 57%, 90 and 89%, 88 and 67%, and 78 and 84%, respectively. CE was complicated by capsule retention in one patient. MRE has a higher sensitivity and PPV than CE in small bowel CD. The use of CE is considerably limited by the high prevalence of stenotic lesions in these patients

Biotechnological advances in Lilium

Modern powerful techniques in plant biotechnology have been developed in lilies (Lilium spp., Liliaceae) to propagate, improve and make new phenotypes. Reliable in vitro culture methods are available to multiply lilies rapidly and shorten breeding programs. Lilium is also an ideal model plant to study in vitro pollination and embryo rescue methods. Although lilies are recalcitrant to genetic manipulation, superior genotypes are developed with improved flower colour and form, disease resistance and year round forcing ability. Different DNA molecular markers have been developed for rapid indirect selection, genetic diversity evaluation, mutation detection and construction of Lilium linkage map. Some disease resistance-QTLs are already mapped on the Lilium linkage map. This review presents latest information on in vitro propagation, genetic engineering and molecular advances made in lily.</p

The role of ornamentals in human life

The integration of flowers in daily human life has a long history and substantiates our appreciation for their delicacy and wide variation in possible shapes and colours. Since the very early civilizations flowers were used for medical purposes and above all have been part of important cultural and religious customs. Records of their use have been preserved over centuries in different parts of the world and in most if not all major religions flowers have a featuring role. Whereas in the past flower production for floral design was local and probably limited and restricted to wealthy and powerful people that could afford gardens for pleasure, nowadays floral production has become a knowledge and infrastructural intensive, highly specialised industry with trading networks on a global scale and floricultural exhibitions being organised all over the world. As with all intensive industry, concerns on environmental aspects including carbon footprints as well as the well-being of labourers have been raised and have led to certification programs that resulted in impressive reductions in energy and resources as well as environmental impact. It can be expected that given the global environmental and economic issues, ornamental production will have to even intensify these efforts substantially to provide flowers at low environmental costs for people to enjoy in and around their homes.</p

Genetic diversity and structure of Lilium pumilum DC. in southeast of Qinghai-Tibet plateau

Lilium pumilum DC. is a valuable species not only for its showy flowers but also for its edible and medicinal values. As one of the distribution areas of L. pumilum, Qinghai-Tibet plateau has unique environmental features which have high impact on the evolution of the species. No population genetic studies have been done for L. pumilum so far. To provide the first reference data for evolutionary study and understanding the influence of eco-geographic factors on the distribution of genetic variation in L. pumilum, interspecific simple sequence repeat markers were used to investigate genetic diversity and population structure of 28 populations sampled from southeast of Qinghai-Tibet plateau. Fifteen selected primers generated a total of 147 polymorphic bands. The genetic diversity was low within populations (average He = 0.173), but higher at the species level (He = 0.392). A clear population structure and high level of genetic differentiation (F ST = 0.518) were detected by unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. All clustering approaches supported a division of the 28 populations into 4 major groups for which analysis of molecular variance confirmed a significant variation among groups (34.3 %). These population genetic parameters suggest limited gene flow among populations and evidence for isolation by distance (r = 0.272, P < 0.0001) was found in this study. Altitude, AMT and AMP explained 9.5, 11.5 and 14.0 % of the total variance among populations indicating that eco-geographic factors have a significant effect. Considering the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve L. pumilum in Qinghai-Tibet plateau

Transcriptome analysis of Gerbera hybrid: including in silico confirmation of defence genes found

For the ornamental crop Gerbera hybrida, breeding at the moment is done using conventional methods. As this has drawbacks in breeding speed and efficiency, especially for complex traits like disease resistance, we set out to develop genomic resources. The leaf and flower bud transcriptomes of four parents, used to generate two gerbera populations, were sequenced using Illumina paired-end sequencing. In total, 36,770 contigs with an average length of 1397 bp were generated and these have been the starting point for SNP identification and annotation. The consensus contig sequences were used to map reads of individual parents, to identify genotype specific SNPs, and to assess the presence of common SNPs between genotypes.Comparison with the non-redundant protein database (nr) showed that 29,146 contigs gave BLAST hits. Of sequences with blast results, 73.3% obtained a clear gene ontology (GO) annotation. EST contigs coding for enzymes were found in Kyoto Encyclopedia of Genes and Genomes maps (KEGG). Through these annotated data and KEGG molecular interaction network, transcripts associated with the phenylpropanoid metabolism, other secondary metabolite biosynthesis pathways, phytohormone biosynthesis and signal transduction were analysed in more detail. Identifying genes involved in these processes could provide genetic and genomic resources for studying the mechanism of disease resistance in gerbera

Genetic diversity and structure of Lilium pumilum DC. in southeast of Qinghai-Tibet plateau

Lilium pumilum DC. is a valuable species not only for its showy flowers but also for its edible and medicinal values. As one of the distribution areas of L. pumilum, Qinghai-Tibet plateau has unique environmental features which have high impact on the evolution of the species. No population genetic studies have been done for L. pumilum so far. To provide the first reference data for evolutionary study and understanding the influence of eco-geographic factors on the distribution of genetic variation in L. pumilum, interspecific simple sequence repeat markers were used to investigate genetic diversity and population structure of 28 populations sampled from southeast of Qinghai-Tibet plateau. Fifteen selected primers generated a total of 147 polymorphic bands. The genetic diversity was low within populations (average He = 0.173), but higher at the species level (He = 0.392). A clear population structure and high level of genetic differentiation (F ST = 0.518) were detected by unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. All clustering approaches supported a division of the 28 populations into 4 major groups for which analysis of molecular variance confirmed a significant variation among groups (34.3 %). These population genetic parameters suggest limited gene flow among populations and evidence for isolation by distance (r = 0.272, P < 0.0001) was found in this study. Altitude, AMT and AMP explained 9.5, 11.5 and 14.0 % of the total variance among populations indicating that eco-geographic factors have a significant effect. Considering the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve L. pumilum in Qinghai-Tibet plateau.</p