Repeat Class Research Articles

Transposon Silencing of Small RNAs

Transposons and fragments of transposable elements make up approximately half of the human genome; mobilization of these elements can destabilize the genome and lead to disease-associated mutations. In 2003, miRNAs and siRNAs were known to silence target mRNAs, but small RNAs had not been directly linked to transposon control. In August of that year, Aravin et al. reported the developmental profile of Drosophila small RNAs by using conventional sequencing technology. These pioneering studies identified a novel class of repeat associated siRNAs and hypothesized that they control transposon activity and chromatin structure. It is now clear that these rasiRNAs bind to Piwi clade Argonaute proteins and that Piwi-interacting RNAs (piRNAs) have a conserved function in genome maintenance and germline development. This PaperPick refers to The Small RNA Profile during Drosophila melanogaster Development by A.A. Aravin, M. Lagos-Quintana, A. Yalcin, M. Zavolan, D. Marks, B. Snyder, T. Gaasterland, J. Meyer, and T. Tuschl, published in August 2003. Video Abstract Dr. Thomas Tuschl discusses the context for the work on small RNA profiling during Drosophila development and elaborates on our current understanding of some of the classes of small RNAs originally described by Aravin et al.

Survey and characterization of NBS-LRR (R) genes in Curcuma longa transcriptome.

Resistance genes are among the most important gene classes for plant breeding purposes being responsible for activation of plant defense mechanisms. Among them, the nucleotide binding site-leucine rich repeat (NBS-LRR) class R-genes are the most abundant and actively found in all types of plants. Insilico characterization of EST database resulted in the detection of 28 NBS types R-gene sequences in Curcuma longa. All the 28 sequences represented the NB-ARC domain, 21 of which were found to have highly conserved motif characteristics and categorized as regular NBS genes. The Open Reading Frames varied from 361 (CL.CON.3566) to 112 (CL.CON.1267) with an average of 279 amino acids. Most alignment occurred with monocots (67.8%) with emphasis on Oryza sativa and Zingiber sequences. All best alignments with dicots occurred with Arabidopsis thaliana, Populus trichocarpa and Medicago sativa. These detected NBS type Rgenes from Curcuma longa can be used as a valuable resource for molecular marker development, molecular mapping of R-genes, and identification of resistance gene analogs and functional and evolutionary characterization of NBS-LRR-encoding resistance genes in asexually reproducing plants.

Transcriptional repression of repeat-derived transcripts correlates with histone hypoacetylation at repetitive DNA elements in aged mice brain

In order to better characterize epigenetic alterations at repetitive DNA elements with aging, DNA methylation and histone marks at various repeat classes were investigated. Repetitive DNA elements were hypermethylated in the brains of old mice. Histone hypoacetylation and altered histone trimethylation at repetitive sequences were detected in brain tissues during aging. The expression of repeat-derived transcripts (RDTs) was then measured to explore any correlations with the observed epigenetic alterations. Large numbers of RDTs investigated were down-regulated along with age. Bisulfite sequencing revealed that CpG dinucleotide methylation patterns at the repeats of the RDT promoter region were mostly well maintained during aging. ChIP assay showed that histones were deacetylated at the promoter region of RDTs in aged mice brain. The observations indicate that the transcriptional repression of RDTs appears to be related to histone hypoacetylation, but not to DNA hypermethylation at repeat DNA elements in the brains of aged mice.

Two classes of BRC repeats in BRCA2 promote RAD51 nucleoprotein filament function by distinct mechanisms

The human tumor suppressor protein BRCA2 plays a key role in recombinational DNA repair. BRCA2 recruits RAD51 to sites of DNA damage through interaction with eight conserved motifs of approximately 35 amino acids, the BRC repeats; however, the specific function of each repeat remains unclear. Here, we investigated the function of the individual BRC repeats by systematically analyzing their effects on RAD51 activities. Our results reveal the existence of two categories of BRC repeats that display unique functional characteristics. One group, comprising BRC1, -2, -3, and -4, binds to free RAD51 with high affinity. The second group, comprising BRC5, -6, -7, and -8, binds to free RAD51 with low affinity but binds to the RAD51-ssDNA filament with high affinity. Each member of the first group reduces the ATPase activity of RAD51, whereas none of the BRC repeats of the second group affects this activity. Thus, through different mechanisms, both types of BRC repeats bind to and stabilize the RAD51 nucleoprotein filament on ssDNA. In addition, members of the first group limit binding of RAD51 to duplex DNA, where members of the second group do not. Only the first group enhances DNA strand exchange by RAD51. Our results suggest that the two groups of BRC repeats have differentially evolved to ensure efficient formation of a nascent RAD51 filament on ssDNA by promoting its nucleation and growth, respectively. We propose that the BRC repeats cooperate in a partially redundant but reinforcing manner to ensure a high probability of RAD51 filament formation.

Stability, denaturation and refolding of Mycobacterium tuberculosis MfpA, a DNA mimicking protein that confers antibiotic resistance

MfpA from Mycobacterium tuberculosis is a founding member of the pentapeptide repeat class of proteins (PRP) that is believed to confer bacterial resistance to the drug fluoroquinolone by mimicking the size, shape and surface charge of duplex DNA. We show that phenylalanine side chain stacking stabilizes the N-terminus of MfpA's pentapeptide thus extending the DNA mimicry analogy. The Lumry–Eyring model was applied to multiple spectral measures of MfpA denaturation revealing that the MfpA dimer dissociates to monomers which undergo a structural transition that leads to aggregation. MfpA retains high secondary and tertiary structure content under denaturing conditions. Dimerization stabilizes MfpA's pentapeptide repeat fold. The high Arrhenius activation energy of the barrier to aggregate formation rationalizes its stability. The mechanism of MfpA denaturation and refolding is a ‘double funnel’ energy landscape where the ‘native’ and ‘aggregate’ funnels are separated by the high barrier that is not overcome during in vitro refolding.

Genetic variation within and between winter wheat genotypes from Turkey, Kazakhstan, and Europe as determined by nucleotide-binding-site profiling

The genetic diversity within wheat breeding programs across Turkey and Kazakhstan was compared with a selection of European cultivars that represented the genetic diversity across eight European countries and six decades of wheat breeding. To focus the measure of genetic diversity on that relevant to disease-resistant phenotypes, nucleotide-binding-site (NBS) profiling was used to detect polymorphisms associated with the NBS motifs found within the NBS--leucine-rich repeat (LRR) class of resistance (R) genes. Cereal-specific NBS primers, designed specifically to the conserved NBS motifs found within cereal R-genes, provided distinct NBS profiles. Although the genetic diversity associated with NBS motifs was only slightly higher within the Eastern wheat genotypes, the NBS profiles produced by Eastern and European wheat lines differed considerably. Structure analysis divided the wheat genotypes into four groups, which compared well with the origin of the wheat genotypes. The highest levels of genetic diversity were seen for the wheat genotypes from the Genetic Resource Collection held in Ankara, Turkey, as wheat genotypes within breeding programs were genetically more similar. The wheat genotypes from Kazakhstan were the most similar to the European cultivars, reflecting the significant number of eastern European cultivars used in the breeding program in Kazakhstan. In general, the NBS profiles suggested that NBS-LRR R-gene usage in winter wheat breeding in Turkey and Kazakhstan differed from that deployed in European cultivars.

Trans-Repression of Gene Activity Upstream of T-DNA Tagged RLK902 Links Arabidopsis Root Growth Inhibition and Downy Mildew Resistance

Receptor-like kinases (RLKs) constitute a large family of signal perception molecules in Arabidopsis. The largest group of RLKs is the leucine-rich repeat (LRR) class that has been described to function in development and defense. Of these, CLAVATA1 (CLV1) and ERECTA (ER) receptors function in maintaining shoot meristem homeostasis and organ growth, but LRR RLKs with similar function in the root remain unknown. For the interaction of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis the involvement of LRR RLKs has not been demonstrated. A set of homozygous T-DNA insertion lines mutated in LRR RLKs was investigated to assess the potential role of these receptors in root meristem maintenance and compatibility. One mutant line, rlk902, was discovered that showed both reduced root growth and resistance to downy mildew in a recessive manner. The phenotypes of this mutated line could not be rescued by complementation, but are nevertheless linked to the T-DNA insertion. Microarray studies showed that gene expression spanning a region of approximately 84 kb upstream of the mutated gene was downregulated. The results suggest T-DNA mediated trans-repression of multiple genes upstream of the RLK902 locus links both phenotypes.

Arabidopsis NDR1 Is an Integrin-Like Protein with a Role in Fluid Loss and Plasma Membrane-Cell Wall Adhesion

Arabidopsis (Arabidopsis thaliana) NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1), a plasma membrane-localized protein, plays an essential role in resistance mediated by the coiled-coil-nucleotide-binding site-leucine-rich repeat class of resistance (R) proteins, which includes RESISTANCE TO PSEUDOMONAS SYRINGAE2 (RPS2), RESISTANCE TO PSEUDOMONAS SYRINGAE PV MACULICOLA1, and RPS5. Infection with Pseudomonas syringae pv tomato DC3000 expressing the bacterial effector proteins AvrRpt2, AvrB, and AvrPphB activates resistance by the aforementioned R proteins. Whereas the genetic requirement for NDR1 in plant disease resistance signaling has been detailed, our study focuses on determining a global, physiological role for NDR1. Through the use of homology modeling and structure threading, NDR1 was predicted to have a high degree of structural similarity to Arabidopsis LATE EMBRYOGENESIS ABUNDANT14, a protein implicated in abiotic stress responses. Specific protein motifs also point to a degree of homology with mammalian integrins, well-characterized proteins involved in adhesion and signaling. This structural homology led us to examine a physiological role for NDR1 in preventing fluid loss and maintaining cell integrity through plasma membrane-cell wall adhesions. Our results show a substantial alteration in induced (i.e. pathogen-inoculated) electrolyte leakage and a compromised pathogen-associated molecular pattern-triggered immune response in ndr1-1 mutant plants. As an extension of these analyses, using a combination of genetic and cell biology-based approaches, we have identified a role for NDR1 in mediating plasma membrane-cell wall adhesions. Taken together, our data point to a broad role for NDR1 both in mediating primary cellular functions in Arabidopsis through maintaining the integrity of the cell wall-plasma membrane connection and as a key signaling component of these responses during pathogen infection.

Isolation of resistance gene analogs from grapevine resistant and susceptible to downy mildew and anthracnose

Downy mildew and anthracnose are major diseases of the grapevine ( Vitis spp.) cultivars grown in Thailand. Due to the deleterious effects of fungicides frequently used for disease management in grapevine, disease resistance genes have been sought after with the ultimate goal of developing new cultivars with improved disease resistance levels. In this study, nucleotide-binding site (NBS)-leucine rich repeat (LRR) class of resistance gene analogs (RGAs) were cloned by PCR amplification using degenerate primers specific to P-loop and GLPL, conserved regions of NBS. Ninety-one clones containing putative RGA sequences were obtained from a downy mildew and anthracnose resistant hybrid ‘NY88.0507.01’ and a susceptible cultivar ‘Black Queen’. These cloned sequences were subdivided into 14 groups based on their nucleotide sequence similarity of 90% or greater. BLASTx of fourteen selected clones showed the highest amino acid sequence similarity with known NBS-LRR proteins or putative resistance (R) protein candidates. Multiple alignments of these representative RGAs with 5 known R proteins revealed conserved P-loop, kinase-2, RNBS and GLPL motifs which are typical components of the NBS-LRR proteins. Four RGAs had at least 40% identity with known R proteins. Phylogenetic analysis demonstrated that the representative RGAs from both resistant and susceptible grapevines dispersed along the phylogram on the two major branches of either TIR ( Drosophila Toll and mammalian Interleukin- 1 Receptor) or non-TIR type of the NBS-LRR proteins.

Development of <i>Pinus koraiensis</i> SSR Primers Based on EST-SSR Information Technology

A total 408 SSRs were distributed in 18,181 ESTs sequences in Pinaceae in NCBI (National Center for Biotechnology Information) searched by SSRIT software, accounting for 2.24% of the whole EST sequences. We designed 132 pairs of EST-SSR primers by primer3. Of the designed 132 pairs, 29 pairs were able to produce an amplification product in the 10 Pinus koraiensis DNA samples, but only five primers in the 29 pairs exhibited polymorphism. Dinucleotide repeats were the most common repeat class. The repeated primitives of dinucleotide were 10, accounting for 52.73% of the whole repeated primitives; the repeat numbers were 87. The second most common repeat class was trinucleotide. The repeated primitives of trinucleotide were 27, accounting for 42.27% of the whole repeated primitives, and repeat numbers were 78.

Nucleocytoplasmic distribution is required for activation of resistance by the potato NB-LRR receptor Rx1 and is balanced by its functional domains.

The Rx1 protein, as many resistance proteins of the nucleotide binding-leucine-rich repeat (NB-LRR) class, is predicted to be cytoplasmic because it lacks discernable nuclear targeting signals. Here, we demonstrate that Rx1, which confers extreme resistance to Potato virus X, is located both in the nucleus and cytoplasm. Manipulating the nucleocytoplasmic distribution of Rx1 or its elicitor revealed that Rx1 is activated in the cytoplasm and cannot be activated in the nucleus. The coiled coil (CC) domain was found to be required for accumulation of Rx1 in the nucleus, whereas the LRR domain promoted the localization in the cytoplasm. Analyses of structural subdomains of the CC domain revealed no autonomous signals responsible for active nuclear import. Fluorescence recovery after photobleaching and nuclear fractionation indicated that the CC domain binds transiently to large complexes in the nucleus. Disruption of the Rx1 resistance function and protein conformation by mutating the ATP binding phosphate binding loop in the NB domain, or by silencing the cochaperone SGT1, impaired the accumulation of Rx1 protein in the nucleus, while Rx1 versions lacking the LRR domain were not affected in this respect. Our results support a model in which interdomain interactions and folding states determine the nucleocytoplasmic distribution of Rx1.

Effect of sporophytic PIRL9 genotype on post-meiotic expression of the Arabidopsis pirl1;pirl9 mutant pollen phenotype

Plant intracellular ras-group-related leucine-rich repeat proteins (PIRLs) are a novel class of plant leucine-rich repeat (LRR) proteins structurally related to animal ras-group LRRs involved in cell signaling and gene regulation. Gene knockout analysis has shown that two members of the Arabidopsis thaliana PIRL gene family, PIRL1 and PIRL9, are redundant and essential for pollen development and viability: pirl1;pirl9 microspores produced by pirl1/PIRL1;pirl9 plants consistently abort just before pollen mitosis I. qrt1 tetrad analysis demonstrated that the genes become essential after meiosis, during anther stage 10. In this study, we characterized the phenotype of pirl1;pirl9 pollen produced by plants heterozygous for pirl9 (pirl1;pirl9/PIRL9). Alexander's staining, scanning electron microscopy, and fluorescence microscopy indicated that pirl1;pirl9 double mutants produced by pirl9 heterozygotes have a less severe phenotype and more variable morphology than pirl1;pirl9 pollen from pirl1/PIRL1;pirl9 plants. Mutant pollen underwent developmental arrest with variable timing, often progressing beyond pollen mitosis I and arresting at the binucleate stage. Thus, although the pirl1 and pirl9 mutations act post-meiosis, the timing and expressivity of the pirl1;pirl9 pollen phenotype depends on the pirl9 genotype of the parent plant. These results suggest a continued requirement for PIRL1 and PIRL9 beyond the initiation of pollen mitosis. Furthermore, they reveal a modest but novel sporophytic effect in which parent plant genotype influences a mutant phenotype expressed in the haploid generation.

Isolation, Characterization and Phylogenetic Analysis of Nucleotide Binding Site-encoding Disease-resistance Gene Analogues from European Aspen (Populus tremula)

Abstract The majority of verified plant disease resistance genes (R genes) isolated to date was of the nucleotide binding site-leucine rich repeat (NBS-LRR) class. The conservation between different NBS-LRR R genes opens the avenue for the use of PCR based strategies in isolating and cloning other R gene family members or analogs (resistance gene analogue, RGA) using degenerate primers for these conserved regions. In this study, to better understand the R gene in European aspen (Populus tremula), a perennial tree, we used degenerate primers to amplify RGA sequences from European aspen. Cloning and sequence characterization identified 37 European aspen RGAs, which could be phylogenetically classified into seven subfamilies. Deduced amino acid sequences of European aspen RGAs showed strong identity, ranging from 30.41 to 46.63%, to toll interleukin receptor (TIR) R gene subfamily. BLAST searches with reference to the genomic sequence of P. trichocarpa found 209 highly homologous regions distributed in 28 genomic loci, suggesting the abundance and divergence of NBS-encoding R genes in European aspen genome. Although, numerous studies have reported that plant R genes are under diversifying selection for specificity to evolving pathogens, non-synonymous to synonymous nucleotide substitution (dN/dS) ratio were <1 for NBS domains of European aspen RGA, showing the evidence of purifying selection in this perennial tree. In further analysis, many intergenic exchanges were also detected among these RGAs, indicating a probable role in homogenising NBS domains. The present study permits insights into the origin, diversification, evolution and function of NBS-LRR R genes in perennial species like European aspen and will be useful for further R gene isolation and exploitation.

Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains

The interspersed repeat content of mammalian genomes has been best characterized in human, mouse and cow. In this study, we carried out de novo identification of repeated elements in the equine genome and identified previously unknown elements present at low copy number. The equine genome contains typical eutherian mammal repeats, but also has a significant number of hybrid repeats in addition to clade-specific Long Interspersed Nuclear Elements (LINE). Equus caballus clade specific LINE 1 (L1) repeats can be classified into approximately five subfamilies, three of which have undergone significant expansion. There are 1115 full-length copies of these equine L1, but of the 103 presumptive active copies, 93 fall within a single subfamily, indicating a rapid recent expansion of this subfamily. We also analysed both interspersed and simple sequence repeats (SSR) genome-wide, finding that some repeat classes are spatially correlated with each other as well as with G+C content and gene density. Based on these spatial correlations, we have confirmed that recently-described ancestral vs. clade-specific genome territories can be defined by their repeat content. The clade-specific Short Interspersed Nuclear Element correlations were scattered over the genome and appear to have been extensively remodelled. In contrast, territories enriched for ancestral repeats tended to be contiguous domains. To determine if the latter territories were evolutionarily conserved, we compared these results with a similar analysis of the human genome, and observed similar ancestral repeat enriched domains. These results indicate that ancestral, evolutionarily conserved mammalian genome territories can be identified on the basis of repeat content alone. Interspersed repeats of different ages appear to be analogous to geologic strata, allowing identification of ancient vs. newly remodelled regions of mammalian genomes.

R gene-controlled host specificity in the legume–rhizobia symbiosis

Leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. An intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. It is widely believed that the host specificity is determined by specific recognition of bacterially derived Nod factors by the cognate host receptor(s). Here we describe the positional cloning of two soybean genes Rj2 and Rfg1 that restrict nodulation with specific strains of Bradyrhizobium japonicum and Sinorhizobium fredii, respectively. We show that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. The involvement of host R genes in the control of genotype-specific infection and nodulation reveals a common recognition mechanism underlying symbiotic and pathogenic host-bacteria interactions and suggests the existence of their cognate avirulence genes derived from rhizobia. This study suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors.

RLK7, a leucine-rich repeat receptor-like kinase, is required for proper germination speed and tolerance to oxidative stress in Arabidopsis thaliana

The leucine-rich repeat class of receptor-like kinase (LRR-RLKs) encoding genes represents the largest family of putative receptor genes in the Arabidopsis thaliana genome. However, very little is known about the range of biological process that they control. We present in this paper the functional characterization of RLK7 that has all the structural features of a receptor-like kinase of the plant-specific LRR type. To this end, we identified and characterized three independent T-DNA insertion mutants, constructed lines carrying truncated versions of this putative receptor, one lacking the cytoplasmic kinase domain (RLK7Δkin) and the other one lacking 14 LRR repeats (RLK7ΔLRR) and generated RLK7 overexpressing lines. We thus provide evidences that RLK7 is involved in the control of germination speed and the tolerance to oxidant stress. First, consistent with the expression kinetics of the RLK7 gene in the seeds, we found that all three mutants showed a delay in germination, whereas the overexpressors, RLK7Δkin and RLK7ΔLRR lines displayed a phenotype of more precocious germination. Second, a non-hypothesis driven proteomic approach revealed that in the seedlings of the three T-DNA insertion lines, four enzymes directly or indirectly involved in reactive oxygen species detoxification, were significantly less abundant. Consistent with this finding, the three mutants were less tolerant than the wild type to a hydrogen peroxide treatment, whereas the overexpressors, RLK7Δkin and RLK7ΔLRR lines presented the opposite phenotype.

PIRL1 and PIRL9, encoding members of a novel plant-specific family of leucine-rich repeat proteins, are essential for differentiation of microspores into pollen

Plant intracellular Ras-group-related leucine-rich repeat proteins (PIRLs) are a plant-specific class of leucine-rich repeat (LRR) proteins related to animal and fungal LRRs that take part in developmental signaling and gene regulation. As part of a systematic functional study of the Arabidopsis thaliana PIRL gene family, T-DNA knockout mutants defective in the closely related PIRL1 and PIRL9 genes were identified and characterized. Pirl1 and pirl9 single mutants displayed normal transmission and did not exhibit an obvious developmental phenotype. To investigate the possibility of functional redundancy, crosses to generate double mutants were carried out; however, pirl1;pirl9 plants were not recovered. Reciprocal crosses between wild type and pirl1/PIRL1;pirl9 plants, which produce 50% pirl1;pirl9 gametophytes, indicated male-specific transmission failure of the double-mutant allele combination. Scanning electron microscopy and viability staining showed that approximately half of the pollen produced by pirl1/PIRL1;pirl9 plants was inviable and severely malformed. Tetrad analyses with qrt1 indicated that pollen defects segregated with the double-mutant allele combination, thus demonstrating that PIRL1 and PIRL9 function after meiosis. Pollen development was characterized with bright field, fluorescence, and transmission electron microscopy. Pirl1;pirl9 mutants stopped growing as microspores, failed to initiate vacuolar fission, aborted, and underwent cytoplasmic degeneration. Development consistently arrested at the late microspore stage, just prior to pollen mitosis I. Thus, PIRL1 and PIRL9 have redundant roles essential at a key transition point early in pollen development. Together, these results define a functional context for these two members of this distinct class of plant LRR genes.

Structure of a thyroid hormone receptor DNA-binding domain homodimer bound to an inverted palindrome DNA response element.

Thyroid hormone receptor (TR), as a member of the nuclear hormone receptor family, can recognize and bind different classes of DNA response element targets as either a monomer, a homooligomer, or a heterooligomer. We report here the first crystal structure of a homodimer TR DNA-binding domain (DBD) in complex with an inverted repeat class of thyroid response element (TRE). The structure shows a nearly symmetric structure of the TR DBD assembled on the F2 TRE where the base recognition contacts in the homodimer DNA complex are conserved relative to the previously published structure of a TR-9-cis-retinoic acid receptor heterodimer DNA complex. The new structure also reveals that the T-box region of the DBD can function as a structural hinge that enables a large degree of flexibility in the position of the C-terminal extension helix that connects the DBD to the ligand-binding domain. Although the isolated TR DBDs exist as monomers in solution, we have measured highly cooperative binding of the two TR DBD subunits onto the inverted repeat DNA sequence. This suggests that elements of the DBD can influence the specific TR oligomerization at target genes, and it is not just interactions between the ligand-binding domains that are responsible for TR oligomerization at target genes. Mutational analysis shows that intersubunit contacts at the DBD C terminus account for some, but not all, of the cooperative homodimer TR binding to the inverted repeat class TRE.

Characterization of novel microsatellite markers in Musa acuminata subsp. burmannicoides, var. Calcutta 4

BackgroundBanana is a nutritionally important crop across tropical and sub-tropical countries in sub-Saharan Africa, Central and South America and Asia. Although cultivars have evolved from diploid, triploid and tetraploid wild Asian species of Musa acuminata (A genome) and Musa balbisiana (B genome), many of today's commercial cultivars are sterile triploids or diploids, with fruit developing via parthenocarpy. As a result of restricted genetic variation, improvement has been limited, resulting in a crop frequently lacking resistance to pests and disease. Considering the importance of molecular tools to facilitate development of disease resistant genotypes, the objectives of this study were to develop polymorphic microsatellite markers from BAC clone sequences for M. acuminata subsp. burmannicoides, var. Calcutta 4. This wild diploid species is used as a donor cultivar in breeding programs as a source of resistance to diverse biotic stresses.FindingsMicrosatellite sequences were identified from five Calcutta 4 BAC consensi datasets. Specific primers were designed for 41 loci. Isolated di-nucleotide repeat motifs were the most abundant, followed by tri-nucleotides. From 33 tested loci, 20 displayed polymorphism when screened across 21 diploid M. acuminata accessions, contrasting in resistance to Sigatoka diseases. The number of alleles per SSR locus ranged from two to four, with a total of 56. Six repeat classes were identified, with di-nucleotides the most abundant. Expected heterozygosity values for polymorphic markers ranged from 0.31 to 0.75.ConclusionsThis is the first report identifying polymorphic microsatellite markers from M. acuminata subsp. burmannicoides, var. Calcutta 4 across accessions contrasting in resistance to Sigatoka diseases. These BAC-derived polymorphic microsatellite markers are a useful resource for banana, applicable for genetic map development, germplasm characterization, evolutionary studies and marker assisted selection for traits.

Immigrant and Native Children in Germany

Resident foreign citizens in Germany, a country that cannot deny its character as a country of immigration, number around 6.7 million out of Germany’s total population of 82.4 million inhabitants. Relative to the native population, the age structure among people with migration background is shifted considerably younger. The share of children living with parents who have a migration background is quite large: More than 1 million children under 17 years of age are foreign citizens. This paper draws a portrait of immigrant children in comparison to native children. Data being analysed for this purpose make clear that children with migration background are disadvantaged in most sectors of life: Large shares of these children grow up in households with difficult financial straits and under less than optimal housing conditions. Young children with migration background face disadvantages in preschool and many are held back due to limited German language proficiency. Children and youth in foreign-born families tend to start school later and repeat classes more often. Children with migration background are not adequately supplied with health care, mainly because they and their parents less often participate in early diagnosis and preventive care. Youth with migration background are more involved in violent crimes.