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The standard A chromosome transcripts of rye and wheat are strongly and differently affected by additional rye B chromosomes

ABSTRACT: In this study we evaluate the impact of Bs on the transcriptome of the host genome; comparative analysis of rye with and without Bs was conducted. In addition, a wheat - rye B chromosome addition line was used to evaluate the effect of a B chromosome, which was added to a foreign host species. To ensure the comparability of the transcriptomes, we selected in both species anthers undergoing the first pollen mitosis for comparative RNA-seq.Our comparative RNA-seq analyses revealed that the presence of rye B chromosomes modulates the gene activity of the standard A chromosome complement of the natural host species rye and the alien host wheat. Thus, B encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes.

ORGANISM(S): Triticum aestivum (wheat) Hordeum vulgare (barley)

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PROVIDER: S-BSST1711 | biostudies-other |

SECONDARY ACCESSION(S): PRJEB46034

REPOSITORIES: biostudies-other

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Identification of genome-specific transcripts in wheat-rye translocation lines.

Project description:Studying gene expression in wheat-rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [1]; Devos et al., 1995 [2]; Lee et al., 2010 [3]; Lee et al., 2013 [4]). To overcome limitations of current gene expression studies on wheat-rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat-rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.

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Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

2015-02-24 | GSE58678 | GEO

Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

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Oligonucleotide Probes for ND-FISH Analysis to Identify Rye and Wheat Chromosomes.

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Rye Wheat Hydrids GBS

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Ultrastructure and Dynamics of Synaptonemal Complex Components During Meiotic Pairing and Synapsis of Standard (A) and Accessory (B) Rye Chromosomes.

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Cytogenetic and molecular identification of small-segment chromosome translocation lines from wheat-rye substitution lines to create wheat germplasm with beneficial traits.

Project description:Intergeneric crop plant hybrid lines with small-segment chromosome translocations are very useful in plant genetic research and breeding. In this study, to create small-segment chromosome translocations with beneficial agronomic characters, the progeny of wheat-rye substitution lines 5R/5A and 6R/6A were selected from generations F2 to F5 for rye-specific characteristics. A PCR primer and specific simple sequence repeat marker for rye were used in F5 populations to detect rye chromatin and to amplify a specific chromosome band in six translocation lines (06-6-5, 06-6-6, 06-6-9, 6-26-1, 7-23, and 7-33). Fragment pSc119.1 cloned from 7-33 had 99% homology with the big ear gene sequence (GenBank AF512607.1) in wheat. The six lines were further characterized via pollen mother cell meiosis analysis for genetic stability, and chromosome C-banding and genomic in situ hybridization for rye chromatin. The results show that line 7-33 was still within the 5R/5A substitution lines and possessed the big ear gene. The other lines all contained small-segment rye chromosome translocations. The results indicated that substitution line hybridization is an effective method for creating small-segment chromosome translocations with useful agronomic traits. Trials for these six wheat-rye translocation lines are justified because they possess many important stably-inherited agronomic characters, including disease resistance and improved yield.

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Characterization of chromosome constitution in three wheat - Thinopyrum intermedium amphiploids revealed frequent rearrangement of alien and wheat chromosomes.

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