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GBS-based genomic characterization of a wheat–Thinopyrum 3J(3D) chromosome substitution line (GLA3)

ABSTRACT: A wheat–Thinopyrum chromosome substitution line (GLA3) was characterized at the genomic level using genotyping-by-sequencing (GBS). In the GLA3 line, a Thinopyrum-derived group 3 chromosome (3J) replaces wheat chromosome 3D. To confirm the chromosomal composition, identify the homoeologous relationships of the alien chromosome, and detect potential chromosomal rearrangements or deletions, GBS read coverage analysis was performed. Short reads from the GLA3 introgression line were aligned to the wheat (Triticum aestivum IWGSC RefSeq v2.1) and Thinopyrum intermedium (v3.1) reference genomes, revealing the absence of chromosome 3D and the presence of Thinopyrum group 3 chromatin predominantly of J-genome origin.

INSTRUMENT(S): NextSeq 2000

ORGANISM(S): Triticum aestivum

SUBMITTER: Balázs Kalapos

PROVIDER: E-MTAB-17093 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity. Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx

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GBS-based genomic characterization of a wheat–Thinopyrum 3J(3D) chromosome substitution line (GLA3)

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