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ABSTRACT: Homoeologous group-1 wheat-rye 1RS translocation lines

PROVIDER: PRJNA947142 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23929243_1.fastq.gz	Fastqsanger.gz
	SRR23929243_2.fastq.gz	Fastqsanger.gz
	SRR23929244_1.fastq.gz	Fastqsanger.gz
	SRR23929244_2.fastq.gz	Fastqsanger.gz
	SRR23929245_1.fastq.gz	Fastqsanger.gz

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Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression

Project description:Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely-cultivated allohexaploid wheat variety carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.

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Project description:Transcriptome of rye, 1BL.1RS translocation and non-translocation under cold

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Project description:Five RNA samples were used. The RNA source material was from wheat cytogenetic stocks from Dr. Adam Lukaszewski, University of California, Riverside. The lines used for this study are Pavon, Pavon Dt1BL, 1RS.1BL, 1B+5 and T-1 wheat samples. whole seedling minus starchy endosperm. Equal portions of RNA from unstressed and 48 hr drought-stressed seedling were combined to make one RNA sample. The person who produced the RNA was Prasanna R. Bhat in the TJ Close lab at University of California, Riverside. Everything downstream of RNA production was done at the UC Irvine DNA and Protein Microarray Facility (Denis Heck, manager) by Sriti Misra. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Prasanna Bhat. The equivalent experiment is TA10 at PLEXdb.] genetic line: Pavon(2-replications); genetic line: Pavon Dt1BL(2-replications); genetic line: 1RS.1BL(2-replications); genetic line: T-1(2-replications); genetic line: 1B+5(2-replications)

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Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes

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