Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa
Shahin, A. ; Kaauwen, M.P.W. van; Esselink, G. ; Bargsten, J.W. ; Tuyl, J.M. van; Visser, R.G.F. ; Arens, P. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
exploiting est databases - ssr-markers - insights - barley - maps - l. - identification - longiflorum - annotation - evolution
Background Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. Results Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. Conclusions Two transcriptome sets were built that are valuable resources for marker development, comparative genomic studies and candidate gene approaches. Next generation sequencing of leaf transcriptome is very effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative studies.
Diversity between and within farmers’ varieties of tomato from Eritrea
Asgedom, S. ; Vosman, B. ; Esselink, D. ; Struik, P.C. - \ 2011
African journal of biotechnology 10 (2011)12. - ISSN 1684-5315 - p. 2193 - 2200.
simple sequence repeat - ssr-markers - lycopersicon-esculentum - genetic-variation - polymorphic dna - identification - regions - plants - aflp - l.
Tomato yields in Eritrea are low (15 Mg/ha) compared with 19 Mg/ha in Africa and 27 Mg/ha worldwide. This is partly caused by poor quality of varieties used. This study analysed the diversity among and heterogeneity within farmers’ varieties of tomato from Eritrea and compared these varieties with other African and Italian varieties. Fifteen simple sequence repeat (SSR) markers were used for the genetic analysis. Genetic similarities among the varieties were calculated and an Unweighted Pair Group Method with Arithmetic Mean analysis was performed. Furthermore, individual plants of varieties were genotyped to evaluate uniformity within varieties. A high degree of diversity was observed among the Eritrean varieties. Thirteen out of the 15 SSRs were polymorphic, with 2 to 5 alleles per marker. The dendrogram showed two major types of varieties: San-Marzano and Marglob. Eritrean varieties were closely related to old Italian varieties in both types. Analysis of the within-variety variation showed that the Eritrean tomato genotypes were less uniform than the other varieties, probably because of deliberate mixing. A survey among farmers showed that some of them purposely mixed seeds to prolong the harvesting period, for yield stability and stress tolerance. Farmers value ‘new material’ as a source of influx
A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues
Marcel, T.C. ; Varshney, R.K. ; Barbieri, M. ; Jafary, H. ; Kock, M.J.D. de; Graner, A. ; Niks, R.E. - \ 2007
Theoretical and Applied Genetics 114 (2007)3. - ISSN 0040-5752 - p. 487 - 500.
powdery mildew resistance - quantitative trait loci - aflp markers - microsatellite markers - disease-resistance - ssr-markers - linkage map - genome - rice - cloning
A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin