The release of several wheat reference genome sequences lays the basis for accelerating wheat improvement. However, additional effort is require to capture/exploit native variability. Triticum turgidum genetic resources provide a rich diversity reservoir, valuable for both durum and common wheat. We collected iSelect 90K wheat SNP data for 1,856 accessions from 11 tetraploid wheat taxa, including wild and domesticated emmer wheat (WEW and DEW), durum landraces (DWL) and modern durum cultivars (DWC), known as Global Tetraploid wheat Collection (GTC). Infinium raw data were processed under a unique pipeline and over 23,000 SNPs were anchored to Svevo genome. WEW and DEW were highly structured while DWL showed high admixture already at low k values. WEW germplasm was split into North-Eastern and Southern Levant Fertile Crescent populations (WEW-NE and WEW-SL, respectively) and many subpopulations. DEW and DWL showed two similar but independent radial dispersal patterns including six main populations each following North/South and Fertile Crescent to Mediterranean basin and Greece-to-Balkans (Western), Iran-to-Transcaucasia and Oman-to-India, Ethiopia (Eastern) spread. Domestication bottlenecks and haplotype transmission rate were traced for the three main transitions (WEW-to-DEW early domestication, DEW-to-DWL and DWL-to-DWC evolution under domestication). WEW had the highest, evenly distributed diversity, thus providing the reference for assessing diversity reductions. Diversity reduction index (DRI), Fst, haplotype-based XP-EHH, hapFLK and XP-CLR metrics served to produce a selection/demography signal map. In total, 104 pericentromeric (average size of 107.7 Mb) and 350 non-pericentromeric (average size of 11.4 Mb) signal clusters were identified. Numerous strong diversity depletions characterized the WEW-to-DEW transition, for 2Gb in total. These signals progressively consolidated through domestication and breeding and novel signals were found, affecting up to 5Gb in DWC. WEW-to-DEW signals involved extended pericentromeric regions tagged by DRI and Fst while DEW-to-DWL and DWL-to-DWC were mostly associated to numerous XP-EHH and XP-CLR signals. Nevertheless, DEW-to-DWL-specific strong signals were observed in chromosomes 1A, 1B, 2B, 3B, 7A, 7B. Genome-wide haplo-blocks were transmitted from WEW-NE and WEW-SL to DEW with a 0.65/0.35 overall inheritance ratio. Based on haplo-block transmission rate in selected key-regions, durum wheat (DWL) most probably originated from the Southern-levant and SL-to-Europe DEW. Modern durum originated mostly from the North-African and Transcaucasian DWL. Ethiopian germplasm, T.turanicum and T.carthlicum were the most differentiated with minimal contribution to modern durum. Our results show the usefulness of the GTC to elucidate the evolutionary patterns associated to loci, haplotype blocks and causative sequence variants for traits of breeding interest.

SVEVO DURUM WHEAT GENOME SEQUENCE AS A FRAMEWORK TO INVESTIGATE TETRAPLOID WHEAT (TRITICUM TURGIDUM SSPS.) EVOLUTION AND DIVERSITY

Marco Maccaferri
;
Sara Milner;Danara Ormanbekova;Simona Corneti;Silvio Salvi;Roberto Tuberosa
;
2019

Abstract

The release of several wheat reference genome sequences lays the basis for accelerating wheat improvement. However, additional effort is require to capture/exploit native variability. Triticum turgidum genetic resources provide a rich diversity reservoir, valuable for both durum and common wheat. We collected iSelect 90K wheat SNP data for 1,856 accessions from 11 tetraploid wheat taxa, including wild and domesticated emmer wheat (WEW and DEW), durum landraces (DWL) and modern durum cultivars (DWC), known as Global Tetraploid wheat Collection (GTC). Infinium raw data were processed under a unique pipeline and over 23,000 SNPs were anchored to Svevo genome. WEW and DEW were highly structured while DWL showed high admixture already at low k values. WEW germplasm was split into North-Eastern and Southern Levant Fertile Crescent populations (WEW-NE and WEW-SL, respectively) and many subpopulations. DEW and DWL showed two similar but independent radial dispersal patterns including six main populations each following North/South and Fertile Crescent to Mediterranean basin and Greece-to-Balkans (Western), Iran-to-Transcaucasia and Oman-to-India, Ethiopia (Eastern) spread. Domestication bottlenecks and haplotype transmission rate were traced for the three main transitions (WEW-to-DEW early domestication, DEW-to-DWL and DWL-to-DWC evolution under domestication). WEW had the highest, evenly distributed diversity, thus providing the reference for assessing diversity reductions. Diversity reduction index (DRI), Fst, haplotype-based XP-EHH, hapFLK and XP-CLR metrics served to produce a selection/demography signal map. In total, 104 pericentromeric (average size of 107.7 Mb) and 350 non-pericentromeric (average size of 11.4 Mb) signal clusters were identified. Numerous strong diversity depletions characterized the WEW-to-DEW transition, for 2Gb in total. These signals progressively consolidated through domestication and breeding and novel signals were found, affecting up to 5Gb in DWC. WEW-to-DEW signals involved extended pericentromeric regions tagged by DRI and Fst while DEW-to-DWL and DWL-to-DWC were mostly associated to numerous XP-EHH and XP-CLR signals. Nevertheless, DEW-to-DWL-specific strong signals were observed in chromosomes 1A, 1B, 2B, 3B, 7A, 7B. Genome-wide haplo-blocks were transmitted from WEW-NE and WEW-SL to DEW with a 0.65/0.35 overall inheritance ratio. Based on haplo-block transmission rate in selected key-regions, durum wheat (DWL) most probably originated from the Southern-levant and SL-to-Europe DEW. Modern durum originated mostly from the North-African and Transcaucasian DWL. Ethiopian germplasm, T.turanicum and T.carthlicum were the most differentiated with minimal contribution to modern durum. Our results show the usefulness of the GTC to elucidate the evolutionary patterns associated to loci, haplotype blocks and causative sequence variants for traits of breeding interest.
IWC, 1st International Wheat Congress, program and online Author's presentations
1
1
Marco Maccaferri,Elisabetta Mazzucotelli,Raj K. Pasam, Anna M. Mastrangelo, Reem Joukhadar, Francesca Desiderio, Sara Milner, Danara Ormanbekova, Simona Corneti, Silvio Salvi, Roberto Tuberosa,Neil S. Harris, Gabriella Sonnante, Benjamin Kilian, Hakan Ozkan, Pasquale De Vita, Daniela Marone, Domenica Nigro, Agata Gadaleta, Mike Pumphrey, Weizhen Liu, Michela Janni, Domenico De Paola, Krysta Wiebe, John M. Clarke, Ron Knox, Assaf Distelfeld, Aldo Ceriotti, Nicola Pecchioni, Curtis J. Pozniak, Steven S. Xu, Shiaoman Chao, Matthew J. Hayden, Luigi Cattivelli
File in questo prodotto:
Eventuali allegati, non sono esposti

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/731514
 Attenzione

Attenzione! I dati visualizzati non sono stati sottoposti a validazione da parte dell'ateneo

Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact