Durum wheat (Triticum turgidum L. ssp. durum) originates from BBAA wild tetraploid emmer, later evolving to domesticated emmer and then to primitive tetraploid wheat, durum wheat landraces and ultimately durum wheat cultivars. Tetraploid wheats are the donor of the A and B genomes of hexaploid bread wheat (DDAABB), representing therefore a valuable source of genetic variability and beneficial alleles suitable for enhancing both durum and bread wheat resilience to abiotic stresses and disease resistance. Herein, we report preliminary results as regard to the International collaborative project aiming at generating chromosome-level assemblies for 40 tetraploid wheat genomes representative of the whole genetic diversity, from wild emmer to modern cultivars. The sequenced genomes were selected from the 3,186 genotypes assembled in the Global Durum wheat Genomic Resource (GDGR). The expanded catalogue of sequence variation obtained from each of the wild emmer wheat (WEW), domesticated emmer wheat (DEW), turgidum wheat landraces (TWL) and durum wheat cultivars (DWC) groups will allow investigating and exploiting the genetic diversity within tetraploid wheats, for evolutionary studies and future pre-breeding programs. To demonstrate the utility of the pangenome and provide insights into the effects of structural variation and allelic diversity related to crop adaptation and breeding, we’ll present two loci involved in disease resistance and spike development, ultimately linked to grain yield, as case studies. For de-novo annotation of pan-genomes and studying the diversity within the pantranscriptomes, short- and long-read RNA-sequencing datasets were produced from multiple tissues from ten core accessions. A particular focus on differential gene expression during kernel development allowed to categorize transcripts as core (transcribed in all genotypes), shell (expressed in 2-9 genotypes) or cloud (unique to a single genotypes). Preliminary functional characterization of core and dispensable genes pointed out genotype-specific expression of genes involved in carbohydrate metabolism, hormone signalling and transcriptional regulation. Gene co-expression network analysis is in progress towards the identification of genotypespecific expression profiles associated to kernel development. Finally, association between transcript abundance variation and gene copy number and/or structural rearrangements will be investigated and presented.
Forestan, C., Ens, J., Farooq, M.A., Bozzoli, M., Colombo, M., Mazzucotelli, E., et al. (2025). THE TETRAPLOID WHEAT PAN-GENOME AND PAN-TRANSCRIPTOME, A FUNCTIONAL RESOURCE FOR THE WHOLE WHEAT COMMUNITY.
THE TETRAPLOID WHEAT PAN-GENOME AND PAN-TRANSCRIPTOME, A FUNCTIONAL RESOURCE FOR THE WHOLE WHEAT COMMUNITY
FORESTAN C.;FAROOQ M. A.;BOZZOLI M.;COLOMBO M.;PANCALDI L.;CAPPUCCI C.;SALVI S.;TUBEROSA R.;MACCAFERRI M.
2025
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) originates from BBAA wild tetraploid emmer, later evolving to domesticated emmer and then to primitive tetraploid wheat, durum wheat landraces and ultimately durum wheat cultivars. Tetraploid wheats are the donor of the A and B genomes of hexaploid bread wheat (DDAABB), representing therefore a valuable source of genetic variability and beneficial alleles suitable for enhancing both durum and bread wheat resilience to abiotic stresses and disease resistance. Herein, we report preliminary results as regard to the International collaborative project aiming at generating chromosome-level assemblies for 40 tetraploid wheat genomes representative of the whole genetic diversity, from wild emmer to modern cultivars. The sequenced genomes were selected from the 3,186 genotypes assembled in the Global Durum wheat Genomic Resource (GDGR). The expanded catalogue of sequence variation obtained from each of the wild emmer wheat (WEW), domesticated emmer wheat (DEW), turgidum wheat landraces (TWL) and durum wheat cultivars (DWC) groups will allow investigating and exploiting the genetic diversity within tetraploid wheats, for evolutionary studies and future pre-breeding programs. To demonstrate the utility of the pangenome and provide insights into the effects of structural variation and allelic diversity related to crop adaptation and breeding, we’ll present two loci involved in disease resistance and spike development, ultimately linked to grain yield, as case studies. For de-novo annotation of pan-genomes and studying the diversity within the pantranscriptomes, short- and long-read RNA-sequencing datasets were produced from multiple tissues from ten core accessions. A particular focus on differential gene expression during kernel development allowed to categorize transcripts as core (transcribed in all genotypes), shell (expressed in 2-9 genotypes) or cloud (unique to a single genotypes). Preliminary functional characterization of core and dispensable genes pointed out genotype-specific expression of genes involved in carbohydrate metabolism, hormone signalling and transcriptional regulation. Gene co-expression network analysis is in progress towards the identification of genotypespecific expression profiles associated to kernel development. Finally, association between transcript abundance variation and gene copy number and/or structural rearrangements will be investigated and presented.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
