Isolation and chromosomal distribution of a novel Ty1-copia-like sequence from Secale, which enables identification of wheat-Secale africanum introgression lines

Identification of P genome chromosomes in Agropyron cristatum and wheat-A. cristatum derivative lines by FISH

Agropyron cristatum (L.) Gaertn. (P genome) is cultivated as pasture fodder and can provide many desirable genes for wheat improvement. With the development of genomics and fluorescence in situ hybridization (FISH) technology, probes for identifying plant chromosomes were also developed. However, there are few reports on A. cristatum chromosomes. Here, FISH with the repeated sequences pAcTRT1 and pAcpCR2 enabled the identification of all diploid A. cristatum chromosomes. An integrated idiogram of A. cristatum chromosomes was constructed based on the FISH patterns of five diploid A. cristatum individuals. Structural polymorphisms of homologous chromosomes were observed not only among different individuals but also within individuals. Moreover, seventeen wheat-A. cristatum introgression lines containing different P genome chromosomes were identified with pAcTRT1 and pAcpCR2 probes. The arrangement of chromosomes in diploid A. cristatum was determined by identifying correspondence between the P chromosomes in these genetically identified introgression lines and diploid A. cristatum chromosomes. The two probes were also effective for discriminating all chromosomes of tetraploid A. cristatum, and the differences between two tetraploid A. cristatum accessions were similar to the polymorphisms among individuals of diploid A. cristatum. Collectively, the results provide an effective means for chromosome identification and phylogenetic studies of P genome chromosomes.

Isolation of two new retrotransposon sequences and development of molecular and cytological markers for Dasypyrum villosum (L.)

Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.

Isolation and application of P genome-specific DNA sequences of Agropyron Gaertn. in Triticeae

Different types of P genome sequences and markers were developed, which could be used to analyze the evolution of P genome in Triticeae and identify precisely wheat- A. cristatum introgression lines. P genome of Agropyron Gaertn. plays an important role in Triticeae and could provide many desirable genes conferring high yield, disease resistance, and stress tolerance for wheat genetic improvement. Therefore, it is significant to develop specific sequences and functional markers of P genome. In this study, 126 sequences were isolated from the degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) products of microdissected chromosome 6PS. Forty-eight sequences were identified as P genome-specific sequences by dot-blot hybridization and DNA sequences analysis. Among these sequences, 22 displayed the characteristics of retrotransposons, nine and one displayed the characteristics of DNA transposons and tandem repetitive sequence, respectively. Fourteen of 48 sequences were determined to distribute on different regions of P genome chromosomes by fluorescence in situ hybridization, and the distributing regions were as following: all over P genome chromosomes, centromeres, pericentromeric regions, distal regions, and terminal regions. We compared the P genome sequences with other genome sequences of Triticeae and found that the similar sequences of the P genome sequences were widespread in Triticeae, but differentiation occurred to various extents. Additionally, thirty-four molecular markers were developed from the P genome sequences, which could be used for analyzing the evolutionary relationship among 16 genomes of 18 species in Triticeae and identifying P genome chromatin in wheat-A. cristatum introgression lines. These results will not only facilitate the study of structure and evolution of P genome chromosomes, but also provide a rapid detecting tool for effective utilization of desirable genes of P genome in wheat improvement.

Characterization of wheat – Secale africanum introgression lines reveals evolutionary aspects of chromosome 1R in rye

Wild Secale species, Secale africanum Stapf., serve as a valuable source for increasing the diversity of cultivated rye (Secale cereale L.) and provide novel genes for wheat improvement. New wheat – S. africanum chromosome 1Rafr addition, 1Rafr(1D) substitution, 1BL.1RafrS and 1DS.1RafrL translocation, and 1RafrL monotelocentric addition lines were identified by chromosome banding and in situ hybridization. Disease resistance screening revealed that chromosome 1RafrS carries resistance gene(s) to new stripe rust races. Twenty-nine molecular markers were localized on S. africanum chromosome 1Rafr by the wheat – S. africanum introgression lines. Twenty markers can also identically amplify other reported wheat – S. cereale chromosome 1R derivative lines, indicating that there is high conservation between the wild and cultivated Secale chromosome 1R. Nine markers displayed polymorphic amplification between S. africanum and S. cereale chromosome 1Rafr derivatives. The comparison of the nucleotide sequences of these polymorphic markers suggested that gene duplication and sequence divergence may have occurred among Secale species during its evolution and domestication.

Diversity and evolution of four dispersed repetitive DNA sequences in the genus Secale

We present the first characterization of 360 sequences in six species of the genus Secale of both cultivated and wild accessions. These include four distinct kinds of dispersed repetitive DNA sequences named pSc20H, pSc119.1, pSaO5(411), and pSaD15(940) belonging to the Revolver family. During the evolution of the genus Secale from wild to cultivated accessions, the pSaO5(411)-like sequences became shorter mainly because of the deletion of a trinucleotide tandem repeating unit, the pSc20H-like sequences displayed apparent homogenization in cultivated rye, and the second intron of Revolver became longer. In addition, the pSc20H-, pSc119.1-, and pSaO5(411)-like sequences cloned from wild rye and cultivated rye could be divided into two large clades. No single case of the four kinds of repetitive elements has been inherited by each Secale accession from a lone ancestor. It is reasonable to consider the vertical transmission of the four repetitive elements during the evolution of the genus Secale. The pSc20H- and pSaO5(411)-like sequences showed evolutionary elimination at specific chromosomal locations from wild species to cultivated species. These cases imply that different repetitive DNA sequences have played different roles in the chromosome development and genomic evolution of rye. The present study adds important information to the investigations dealing with characterization of dispersed repetitive elements in wild and cultivated rye.

Isolation and characterization of Ty1-copia group of LTRs in genome of three species of Datura: D. innoxia, D. stramonium and D. metel

Retrotransposons (RT) constitute a major fraction of plant genome. They are implicated in evolution and sequence organization. These elements have been proposed to have major role in evolution and variation in genome size. The sequence information of these RT regions in terms of divergence and conservation could be utilized for determining the interrelationship among various copia retrotransposons within the genome. In order to assess the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequence was amplified from genomes of three medicinally important Datura species: D. innoxia, D. stramonium and D. metel using the primers derived from two conserved domains of RT region. A total of twenty one independent amplicons from RT regions were cloned, sequenced and compared. The intra-family divergence at amino acid level ranged from 4 to 52 %. Though intra-family RT sequences are conserved, no two sequences are identical. Southern blot hybridization suggested that Ty1-copia-like retrotransposons are dispersed throughout the Datura genome. The results indicate a high degree of heterogeneity among the Ty1-copia group of retroelements in Datura species.