Ty1-copia Retrotransposons Research Articles

Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion and overexpression of PvIND.

Fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris), the principal global grain legume staple, two main production categories are distinguished by fibre deposition in pods: dry beans, with fibrous, stringy pods; and stringless snap/green beans, with reduced fibre deposition, which frequently revert to the ancestral stringy state. Here, we identify genetic and developmental patterns associated with pod fibre deposition. Transcriptional, anatomical, epigenetic and genetic regulation of pod strings were explored through RNA-seq, RT-qPCR, fluorescence microscopy, bisulfite sequencing and whole-genome sequencing. Overexpression of the INDEHISCENT ('PvIND') orthologue was observed in stringless types compared with isogenic stringy lines, associated with overspecification of weak dehiscence-zone cells throughout the pod vascular sheath. No differences in DNA methylation were correlated with this phenotype. Nonstringy varieties showed a tandemly direct duplicated PvIND and a Ty1-copia retrotransposon inserted between the two repeats. These sequence features are lost during pod reversion and are predictive of pod phenotype in diverse materials, supporting their role in PvIND overexpression and reversible string phenotype. Our results give insight into reversible gain-of-function mutations and possible genetic solutions to the reversion problem, of considerable economic value for green bean production.

Diversity Chromosome Evolution of Ty1-copia Retrotransposons in Pennisetum purpureum Revealed by FISH

Pennisetum purpureum is a potential species for biofuel production. Characterization and chromosomal distribution of retrotransposons could enhance the comprehension of the role and dynamics of the repetitive elements in plants. In this study, a phylogenetic tree was constructed according to the conserved reverse transcriptase sequences and revealed that these Ty1-copia retrotransposons had a typical structure. Analysis showed that the total Ty1-copia retrotransposons had a significant component, as high as 5.12 × 103 copy numbers in P. purpureum. Then, the chromosomal pattern of four known lineages were also analyzed with the Pennisetum glaucum genome, which suggested that the Sire/Maximus lineage had the highest copy number and followed by Tork/Angela, Tork/TAR, Retrofit/Ale. Additionally, the chromosomal distribution of total Ty1-copia retrotransposons was detected by fluorescence in situ hybridization (FISH) to be a dispersed pattern with weak clustering, mostly near the centromeric regions of P. purpureum chromosomes; interestingly, there were four obvious signals in the subterminal chromosomes. These results suggested that there occurred differential dynamic evolution directions of Ty1-copia retrotransposons within P. purpureum. Furthermore, co-localization of Ty1-copia, 5S rDNA, and 35S rDNA indicated that two chromosome 2 and four chromosome 4 were identified. Concurrently, subterminal signals of Ty1-copia-type retrotransposons were located on four other homologous chromosomes. Altogether, these results shed light on the diversification of Ty1-copia retrotransposons and have the significance for generation of valid chromosomal markers in retrotransposon families.

Identifying new variation at the J locus, previously identified as e6, in long juvenile \u2018Paranagoiana\u2019 soybean

Key messageA previously identified soybean maturity locus, E6, is discovered to be J, with the long juvenile allele in Paranagoiana now deemed j−x.Soybean grown at latitudes of ~20° or lower can produce lower grain yields due to the short days. This limitation can be overcome by using the long juvenile trait (LJ) which delays flowering under short day conditions. Two LJ loci have been mapped to the same location on Gm04, J and E6. The objective of this research was to investigate the e6 allele in ‘Paranagoiana’ and determine if E6 and J are the same locus or linked loci. KASP markers showed that e6 lines did not have the j−1 allele of LJ PI 159925. A population fixed for E1 but segregating for E6, with e6 introgressed from Paranagoiana, showed single gene control for flowering and maturity under short days. Sequencing Glyma.04G050200, the J gene, with long amplification Taq found that the e6 line ‘Paranagoiana’ contains a Ty1-copia retrotransposon of ~10,000 bp, inserted within exon 4. PCR amplification of the cDNA of Glyma.04G050200 also showed differences between the mRNA sequences (presence of insertion in j−x). Hence, we conclude that the loci E6 and J are one locus and deem this new variation found in Paranagoiana as j−x.

Sequence Evolution, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in the Saccharum spontaneum Genome

Saccharum spontaneum is a wild germplasm resource of the genus Saccharum that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in S. spontaneum. A total of 44 Ty1-copia reverse transcriptase subclones isolated from S. spontaneum showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the S. spontaneum genome.

Supernumerary B Chromosomes and Plant Genome Changes: A Snapshot of Wild Populations of Aegilops speltoides Tausch (Poaceae, Triticeae).

In various eukaryotes, supernumerary B chromosomes (Bs) are an optional genomic component that affect their integrity and functioning. In the present study, the impact of Bs on the current changes in the genome of goatgrass, Aegilops speltoides, was addressed. Individual plants from contrasting populations with and without Bs were explored using fluorescence in situ hybridization. In parallel, abundances of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons (TEs), and the species-specific Spelt1 tandem repeat (TR) in vegetative and generative spike tissues were estimated by real-time quantitative PCR. The results revealed: (i) ectopic associations between Bs and the regular A chromosomes, and (ii) cell-specific rearrangements of Bs in both mitosis and microgametogenesis. Further, the copy numbers of TEs and TR varied significantly between (iii) genotypes and (iv) different spike tissues in the same plant(s). Finally, (v) in plants with and without Bs from different populations, genomic abundances and/or copy number dynamics of TEs and TR were similar. These findings indicate that fluctuations in TE and TR copy numbers are associated with DNA damage and repair processes during cell proliferation and differentiation, and ectopic recombination is one of the mechanisms by which Bs play a role in genome changes.

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

Screening diversity and distribution of Copia retrotransposons reveals a specific amplification of BARE1 elements in genomes of the polyploid Hordeum murinum complex.

We explored diversity, distribution and evolutionary dynamics of Ty1-Copia retrotransposons in the genomes of the Hordeum murinum polyploid complex and related taxa. Phylogenetic and fluorescent in situ hybridization (FISH) analyses of reverse transcriptase sequences identified four Copia families in these genomes: the predominant BARE1 (including three groups or subfamilies, A, B and C), and the less represented RIRE1, IKYA and TAR-1. Within the BARE1 family, BARE1-A elements and a subgroup of BARE1-B elements (named B1) have proliferated in the allopolyploid members of the H. murinum complex (H. murinum and H. leporinum), and in their extant diploid progenitor, subsp. glaucum. Moreover, we found a specific amplification of BARE1-B elements within each Hordeum species surveyed. The low occurrence of RIRE1, IKYA and TAR-1 elements in the allopolyploid cytotypes suggests that they are either weakly represented or highly degenerated in their diploid progenitors. The results demonstrate that BARE1-A and BARE1-B1 Copia elements are particularly well represented in the genomes of the H. murinum complex and constitute its genomic hallmark. No BARE1-A and -B1 homologs were detected in the reference barley genome. The similar distribution of RT-Copia probes across chromosomes of diploid, tetraploid and hexaploid taxa of the murinum complex shows no evidence of proliferation following polyploidization.

An improved and robust method to efficiently deplete repetitive elements from complex plant genomes

Genome size and complexity often present major challenges to genome-based approaches in crop plants and other agricultural species. For instance, repetitive sequences comprise 80% to 90% of the genome of hexaploid wheat, which has a haploid genome size of approximately 17 Gb. In this study, we developed an improved design and procedure for short-read library preparation that uses a modified adaptor and duplex-specific nuclease (DSN) for the efficient elimination of highly repeated sequence elements within genomes. The improved adapter, which has a hairpin-like form for stability, was constructed from truncated sequences adjacent to the original Illumina TruSeq adapter and can be converted to a full-length adapter structure during PCR amplification. Using the hairpin-structured adaptor, we prepared randomly sheared genomic libraries from rice and diploid, tetraploid, and hexaploid wheat cultivars and evaluated the efficiency of DSN for the enzymatic depletion of repetitive elements. According to real-time quantitative PCR analysis, the relative abundances of 18S and 25S ribosomal DNA decreased respectively to 1.15% and 3.54% in rice and 1.70%–1.95% and 14.71%–20.01% in the three wheat cultivars. Whole-genome sequencing analysis of a diploid wheat cultivar, KU104-1, indicated that DSN treatment with the designed hairpin-structured adapter dramatically reduced highly repetitive elements, such as Ty1-Copia and Ty3-Gypsy retrotransposons and DNA transposons, within the genome, while sequencing reads derived from low-copy genes and protein coding sequences increased more than 50%. Our new procedure should be useful not only for wheat genomes but also for other agricultural plant species with relatively large and complex genomes.

Estimation of nuclear genome size and characterization of Ty1-copia like LTR retrotransposon in Mesua ferrea L.

Mesua ferrea L. is a multipurpose versatile tree that is well known as a prospective feedstock biodiesel plant. The potentiality of M. ferrea as a sustainable source of feedstock for biodiesel industry is dependent on an extensive knowledge of the genome structure of the plant. However, to date, there has been no genomic research aimed at the exploitation of the biotechnological potential of this species. Flow cytometry with propidium iodide as the DNA stain was used to estimate the nuclear DNA content of Mesua and the 2C value is estimated to be 1.40 ± 0.02 pg. Somatic chromosome count from root-tip cells is found to be 2n = 30 corresponding to the diploid level (n = 15). Fold variation in genome size (1.14) is observed among the plants collected from different geographic locations in Assam and is attributed to reverse transcriptase-RNase H (RT-RH) domains of the Ty1-copia retrotransposons. Dot blot analysis revealed that Ty1-copia accounts for 2.5% of total haploid nuclear genome of Mesua and phylogenetic analyses showed that the RT-RH sequences are heterogeneous and resolved into 3 distinct groups. These results contribute to our understanding about genome organization of Mesua and will provide valuable information for its utilization in future.

Intraspecific and intraorganismal copy number dynamics of retrotransposons and tandem repeat in Aegilops speltoides Tausch (Poaceae, Triticeae).

Transposable elements (TE) and tandem repeats (TR) compose the largest fraction of the plant genome. The abundance and repatterning of repetitive DNA underlie intrapopulation polymorphisms and intraspecific diversification; however, the dynamics of repetitive elements in ontogenesis is not fully understood. Here, we addressed the genotype-specific and tissue-specific abundances and dynamics of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons and species-specific Spelt1 tandem repeat in wild diploid goatgrass, Aegilops speltoides Tausch. Copy numbers of TEs and TR were estimated by real-time quantitative PCR in vegetative and generative tissues in original plants from contrasting allopatric populations and artificial intraspecific hybrids. The results showed that between leaves and somatic spike tissues as well as in progressive microsporogenesis of individual genotypes, the copy numbers of three TEs correlatively oscillated between 2- to 4-fold and the TR copy numbers fluctuated by 18- to 440-fold. Inter-individual and intraorganismal TEs and TR copy number dynamics demonstrate large-scale parallelism with extensive chromosomal rearrangements that were detected using fluorescent in situ hybridization in parental and hybrid genotypes. The data obtained indicate that tissue-specific differences in the abundance and pattern of repetitive sequences emerge during cell proliferation and differentiation in ontogenesis and reflect the reorganization of individual genomes in changing environments, especially in small peripheral population(s) under the influence of rapid climatic changes.

Mapping and Characterization of the fefe Gene That Controls Iron Uptake in Melon (Cucumis melo L.)

Iron (Fe) deficiency in plants limits crop growth and productivity. Molecular mechanisms that plants use to sense and respond to Fe deficiency by coordinated expression of Fe-uptake genes are not fully understood. The C940-fe chlorotic melon (Cucumis melo) mutant known as fefe is unable to upregulate Fe-uptake genes, however, the FeFe gene had not been identified. In this study, we used two F2 mapping populations to map and identify the FeFe gene as bHLH38, a homolog of subgroup Ib bHLH genes from Arabidopsis thaliana that are involved in transcriptional regulation of Fe-uptake genes in partnership with the FIT gene. A Ty1-copia type retrotransposon insertion of 5.056 kb within bHLH38 is responsible for the defect in bHLH38 in fefe, based on sequencing and expression analysis. This retrotransposon insertion results in multiple non-functional transcripts expected to result in an altered and truncated protein sequence. Hairy root transformation of fefe plants using wild-type bHLH38 resulted in functional complementation of the chlorotic fefe phenotype. Using a yeast-2-hybrid assay, the transcription factor Fit interacted with the wild-type bHLH38 protein, but did not interact with the fefe bHLH38 protein, suggesting that heterodimer formation of Fit/bHLH38 to regulate Fe-uptake genes does not occur in fefe roots. The second subgroup Ib bHLH gene in the melon genome is not functionally redundant to bHLH38, in contrast to Arabidopsis where four subgroup Ib bHLH genes are functionally redundant. Whereas the Arabidopsis bHLH transcript levels are upregulated by Fe deficiency, melon bHLH38 was not regulated at the transcript level. Thus, the fefe mutant may provide a platform for studying bHLH38 genes and proteins from other plant species.

Characterization, Genomic Organization, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in Erianthus arundinaceus.

Erianthus arundinaceus is an important wild species of the genus Saccharum with many valuable traits. However, the composition and structure of its genome are largely unknown, which have hindered its utilization in sugarcane breeding and evolutionary research. Retrotransposons constitute an appreciable fraction of plant genomes and may have played a significant role in the evolution and sequence organization of genomes. In the current study, we investigate the phylogenetic diversity and genomic abundance of Ty1-copia retrotransposons for the first time and inspect their chromosomal distribution patterns in E. arundinaceus. In total, 70 Ty1-copia reverse transcriptase (RT) sequences with significant levels of heterogeneity were obtained. The phylogenetic analysis revealed these Ty1-copia retrotransposons were classified into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Retrofit/Ale, and Sire/Maximus). Dot-blot analysis showed estimated the total copy number of Ty1-copia retrotransposons to be about 4.5 × 103 in the E. arundinaceus genome, indicating they were a significant component. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons from the four lineages had strikingly similar patterns of chromosomal enrichment, being exclusively enriched in the subterminal heterochromatic regions of most E. arundinaceus chromosomes. This is the first clear evidence of the presence of Ty1-copia retrotransposons in the subterminal heterochromatin of E. arundinaceus. Altogether, these results promote the understanding of the diversification of Ty1-copia retrotransposons and shed light on their chromosomal distribution patterns in E. arundinaceus.

Cloning and analysis of reverse transcriptases from Ty1-copia retrotransposons in Camellia sinensis

ABSTRACTAs mobile genetic elements, the diversity and activity of the Tyl-copia retrotransposons are key contributors to genome organisation and evolution, which have been investigated in many plants but little in the tea plant, Camellia sinensis. We selected a total of 12 varieties of tea plant distributed across a large geographical area and sequenced the reverse transcriptase (RT) sequences of Ty1-copia retrotransposons using degenerate primers. The sequences that were widespread among tea varieties, were approximately 260 bp in length and exhibited high heterogeneity among tea plants. The RT sequences from tea plants were similar to other known Ty1-copia retrotransposon RT sequences. Phylogenetic analysis showed that tea RT sequences were closely related to those from woody plants, such as pear, poplar and apple. In contrast, they were more distantly related to RT sequences from herbaceous plants, such as tomato and rice. Activity assay revealed that Ty1-copia retrotransposons are transcriptionally active during the normal development of tea plants. These results will support further research on Ty1-copia retrotransposons in C. sinensis.

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.

BackgroundInitial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions.ResultsQuantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression.ConclusionsWe demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3337-3) contains supplementary material, which is available to authorized users.

Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris).

BackgroundSugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included. Therefore, to fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me2).ResultsChIP-Seq analysis revealed that active centromeres containing CenH3 consist of the satellite pBV and the Ty3-gypsy retrotransposon Beetle7, while heterochromatin marked by H3K9me2 exhibits heterogeneity in repeat composition. H3K9me2 was mainly associated with the satellite family pEV, the Ty1-copia retrotransposon family Cotzilla and the DNA transposon superfamily of the En/Spm type. In members of the section Beta within the genus Beta, immunostaining using the CenH3 antibody was successful, indicating that orthologous CenH3 proteins are present in closely related species within this section.ConclusionsThe identification of repetitive genome portions by ChIP-Seq experiments complemented the sugar beet reference sequence by providing insights into the repeat composition of poorly characterized CenH3-chromatin and H3K9me2-heterochromatin. Therefore, our work provides the basis for future research and application concerning the sugar beet centromere and repeat-rich heterochromatic regions characterized by the presence of H3K9me2.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0805-5) contains supplementary material, which is available to authorized users.

Activation of Ty1-copia Group Retrotransposons of Dendrobium officinale under Abiotic Stress Conditions

By using universal primer Ty1-copia retrotransposon reverse transcriptase (RT), the conserved reverse transcriptase domain of about 260 bp, which was induced by cold stress and osmotic stress, was amplified by RTPCR from the Dendrobium officinale in this study, indicating that the retrotransposon could be activated by stress conditions. The amplicons were recovered and cloned for sequencing and analyzing by related bioinformatics software. 78 Ty1-copia like retrotransposon RTs transcriptionally activated were obtained with high heterogeneity. The length of these sequences varied from 245 to 265 bp, all the sequences were rich in AT and homology ranged from 42.9% to 99.2%. The same to Ty1-copia like retrotransposon RT of genome, different cis-acting regulatory elements induced by stress conditions and the starting transcription signals, corresponding to CAAT box, TATA box conserved sequences and some other regulatory elements. The cis-acting regulatory elements induced by stress conditions of reverse transcriptase transcriptionally activated of Ty1-copia retrotransposons were significantly increased than Ty1-copia like retrotransposon RT of genome. When translated into amino acids, some sequences presented stop codon mutation or/and frameshift mutation, and all sequences presented mutation in conserved sequence SLYGKQ. Four categories were identified through phylogenic analysis after alignment analyses of their amino acid sequences, and with Ty1-copia like retrotransposon RT of genome having low homology, which indicated that reverse transcriptase transcriptionally activated of Ty1-copia retrotransposons, which induced under stress conditions, had significantly differences with Ty1-copia like retrotransposon RT of genome.

Identification of Gene Related to Hard Bunch Phenotype in Oil Palm (Elaeis guineensis Jacq.)

<p>ABSTRACT</p><p>Molecular genetic analysis of hard bunch phenomenon in oil palm was done in order to elucidate the role of genetic factor underlying hard bunch in oil palm plantation. The aim of this study was to identify the AFLP primer combination that co-segregates with hard bunch phenotype related gene in oil palm. Molecular analysis was done by bulk segregant analysis approach. DNA was isolated from leaves of the normal and hard bunch palm. DNA from ten individual palms from each category were pooled and used as a template. A total of 56 AFLP primer combinations were selected for selection of polymorphic primer, and as a result it was found that 22 AFLP primer combinations (39.28%) were polymorphic. A total of 48 individual of palm DNA containing 24 individual for each group were further genotyped by those 22 polymorphic markers. Of these, one AFLP primer combination (E-ACC/M-CTG) was obtained as a co-segregated marker that distinguished the hard bunch DNA from the normal one. Based on the analysis of the target sequence aligned to the oil palm DNA sequences available in database, we found that our sequence has similarity with Ty-1 copia retrotransposon. This sequence distribute in all 16 linkage group of oil palm genome.</p><p>Keywords: abnormal fruits, AFLP, oil palm, Ty-1 copia retrotransposon</p>

Diversity and evolution of Ty1-copia retroelements within Chalcidoidea by reverse transcriptase domain analysis.

Ty1-copia retrotransposons are widespread and diverse in insects. Some features of their hosts, such as mating and genetic systems, are predicted to influence the spread of selfish genetic elements like Ty1-copia. Using part of the reverse transcriptase gene as a reference, we experimentally surveyed Ty1-copia elements in eight species of fig wasps (Hymenoptera: Chalcidoidea), and performed an in silico analysis of six available genomes of chalcid wasps. Contrary to initial expectations that selfish elements such as Ty1-copia would be purged from the genomes of these species because of inbreeding and haplodiploidy, almost all of these wasps harbour an abundance of diverse Ty1-copia elements. Phylogenetic analyses suggest that the families of Ty1-copia elements found in these species have had a long association with their chalcid hosts. These results suggest an evolutionary scenario in which there was ancestral polymorphism followed by some taxa-specific events including stochastic loss and further diversification. Furthermore, estimating natural selection within the internal and terminal portions of the Ty1-copia phylogenies demonstrated that the elements are under strong evolutionary constraints for their long-term survival, but evolve like pseudogenes in the short term, accompanied by the rise and fall of parasitic elements in the history of wasp lineage.

Development and application S-SAP molecular markers for the identification of apple (Malus × domestica Borkh.) sports

SummaryApple (Malus _ domestica Borkh.) is a widely-cultivated, economically important fruit crop with nutritional and medicinal value. Apple has emerged as a model horticultural crop in the post-genomic era. Apple sport resources are important, develop gradually in the apple industry, and provide genetic diversity. In this study, we have successfully developed a sequence-specific amplification polymorphism (S-SAP) marker system based on Ty1-copia retrotransposons in the apple genome. Among the 34 primer combinations used to develop the S-SAP marker system, two primer combinations produced profiles with clear and different peak patterns. Based on these primer combinations, 15 apple sport accessions (four ‘Gala’, six ‘Fuji’, and five ‘Delicious’) were grouped into three clusters based on a genetic variation coefficient value of 0.78. In addition, 27 ‘Delicious’ apple sport accessions were also selected to perform S-SAP marker analysis using the same two primer combinations. The results showed that all ‘Delicious’ apple sport accessions tested were clearly distinguished. The S-SAP data shared many consistencies with known relationships among apple sport accessions. The available evidence showed that these S-SAP markers had a high level of polymorphism in these apple accessions, which could be applied efficiently to determine genetic diversity, systematic evolution, and for variety identification.

Development of Ty1-copia retrotransposon-based SSAP molecular markers for the study of genetic diversity in peach

Sequence-specific amplified polymorphism (SSAP) technology is a novel, anchored PCR approach derived from AFLP, which amplifies the region between a transposon insertion and an adjacent restriction site and have higher levels of polymorphism. In the current study, we developed 16 SSAP markers based on the long terminal repeat (LTR) sequences of Ty1-copia retrotransposons in the peach and used them for DNA profiling of 52 individual peaches: 44 peach cultivars and 8 ornamental peaches. These primer combinations produced a total of 1,553 fragments and 1,517 polymorphic bands with a polymorphism percentage of 97.7%. Furthermore, the Shannon's information index of each primer combination ranged from 0.1593 to 0.4456. Neighbor-joining analyses revealed two main genetic clusters, corresponding to the fruit flesh types: (A-1) MF (melting flesh) with clingstone and ornamental peaches; (A-2) MF with freestone and NMF (non-melting flesh) with clingstone. Finally, cluster analyses revealed that all ornamental peaches are closely related to the MF with clingstone peach cultivars. The application of these primer combinations identified using SSAP will facilitate future cultivar identification and germplasm management in peaches.