Abstract
Wild emmer wheat ( Triticum turgidum subsp. dicoccoides , WEW) was one of the first crops domesticated in the Neolithic revolution that shifted humanity to agrarian societies. Understanding its population genomics has both evolutionary significance and direct relevance to wheat improvement. Leveraging whole-genome sequencing (WGS) data from 291 accessions (~ 9.5x coverage), we identified 3.4 million high-quality SNPs for population genomics, evolutionary analysis, and genome-wide association studies (GWAS) of seedling-stage resistance to five races each of the stem, leaf, and stripe rust pathogens. Phylogenetic, principal component, and population structure analyses revealed three distinct WEW subgroups: the Northern Population (NP), Southern Levant (SL), and a highly differentiated judaicum subgroup consisting of accessions near the Sea of Galilee. Diversity and pairwise F ST analyses highlighted varying divergence among these subpopulations. The SL accessions exhibited higher resistance to all races of the three rust pathogens compared to the judaicum and NP. The SL accessions also exhibited the highest frequency of resistance to all rust pathogens, whereas NP lacked stem rust resistance but retained resistance to some leaf and stripe rust races. GWAS identified 27, 26, and 41 significant loci associated with stem, leaf, and stripe rust resistance, respectively, most of which were novel. A major resistance hotspot was identified on chromosome 1BS (~ 50–100 Mb), associated with multiple races of different rust pathogens, suggesting the presence of shared or tightly linked resistance factors in the region. The most significant loci explained up to 73% of the phenotypic variation, with some conferring race-specific and others multi-race resistance. Notably, several accessions exhibited broad-spectrum resistance, including lines resistant to all stripe rust races, others resistant to multiple leaf and stem rust races, and a subset combining resistance to multiple rust species, representing valuable germplasm for breeding durable resistance. This study provides a comprehensive genomic and phenotypic characterization of WEW, uncovering its population structure and identifying valuable genetic resources for rust resistance. The identified loci and resistant accessions offer key opportunities for the targeted introgression of novel resistance genes into cultivated wheat, contributing to durable and sustainable global wheat production.
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Claims 14
Claim · model-written summary
Whole-genome sequencing of 291 wild emmer wheat accessions yielded 3.4 million high-quality SNPs.
- Taxon
- wild emmer wheat
Triticum dicoccoidest0 - Outcome
- high-quality SNPse1
- Value
- 3.4 millione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we identified 3.4 million high-quality SNPs”
t0“wild emmer wheat”
Claim · model-written summary
Phylogenetic, principal component and population structure analyses revealed three distinct wild emmer subgroups: Northern Population, Southern Levant and a differentiated judaicum subgroup.
Verbatim
e1“revealed three distinct WEW subgroups: the Northern Population (NP), Southern Levant (SL), and a highly differentiated judaicum subgroup consisting of accessions near the Sea of Galilee”
Claim · model-written summary
Diversity and pairwise FST analyses showed varying divergence among the wild emmer subpopulations.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Outcome
- varying divergencee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Diversity and pairwise F ST analyses highlighted varying divergence among these subpopulations”
t0“wild emmer wheat”
Claim · model-written summary
SL accessions showed higher seedling resistance to all races of the three rust pathogens than the judaicum and NP subgroups.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Material
- SL accessionse1
- Interactor
- rust pathogense1pathogen
- Outcome
- resistancee1
- Direction
- highere1
- Comparator
- judaicum and NPe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The SL accessions exhibited higher resistance to all races of the three rust pathogens compared to the judaicum and NP”
t0“wild emmer wheat”
Claim · model-written summary
SL accessions had the highest frequency of resistance to all rust pathogens.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Interactor
- rust pathogense1pathogen
- Outcome
- highest frequency of resistancee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The SL accessions also exhibited the highest frequency of resistance to all rust pathogens”
t0“wild emmer wheat”
Claim · model-written summary
NP accessions lacked stem rust resistance.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Interactor
- stem ruste1pathogen
- Outcome
- lacked stem rust resistancee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“NP lacked stem rust resistance”
t0“wild emmer wheat”
Claim · model-written summary
NP accessions retained resistance to some leaf and stripe rust races.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Interactor
- leaf and stripe ruste1pathogen
- Outcome
- retained resistance to some leaf and stripe rust racese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“retained resistance to some leaf and stripe rust races”
t0“wild emmer wheat”
Claim · model-written summary
GWAS identified 27 significant loci associated with stem rust resistance in wild emmer wheat.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Outcome
- significant loci associated with stem, leaf, and stripe rust resistancee1
- Value
- 27e1
- Qualifier
- steme1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“GWAS identified 27, 26, and 41 significant loci associated with stem, leaf, and stripe rust resistance, respectively”
t0“wild emmer wheat”
Claim · model-written summary
GWAS identified 26 significant loci associated with leaf rust resistance in wild emmer wheat.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Outcome
- significant loci associated with stem, leaf, and stripe rust resistancee1
- Value
- 26e1
- Qualifier
- leafe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“GWAS identified 27, 26, and 41 significant loci associated with stem, leaf, and stripe rust resistance, respectively”
t0“wild emmer wheat”
Claim · model-written summary
GWAS identified 41 significant loci associated with stripe rust resistance in wild emmer wheat.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Outcome
- significant loci associated with stem, leaf, and stripe rust resistancee1
- Value
- 41e1
- Qualifier
- stripee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“GWAS identified 27, 26, and 41 significant loci associated with stem, leaf, and stripe rust resistance, respectively”
t0“wild emmer wheat”
Claim · model-written summary
A major resistance hotspot on chromosome 1BS (about 50-100 Mb) was associated with multiple races of different rust pathogens.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Interactor
- rust pathogense1pathogen
- Gene
- chromosome 1BSe1
- Outcome
- major resistance hotspote1
- Value
- ~ 50–100 Mbe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“A major resistance hotspot was identified on chromosome 1BS (~ 50–100 Mb), associated with multiple races of different rust pathogens”
t0“wild emmer wheat”
Claim · model-written summary
The most significant loci explained up to 73% of the phenotypic variation.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Gene
- most significant locie1
- Outcome
- phenotypic variatione1
- Value
- 73%e1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The most significant loci explained up to 73% of the phenotypic variation”
t0“wild emmer wheat”
Claim · model-written summary
Several wild emmer accessions exhibited broad-spectrum rust resistance.
- Taxon
- wild emmer wheatTriticum dicoccoidest0
- Outcome
- broad-spectrum resistancee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“several accessions exhibited broad-spectrum resistance”
t0“wild emmer wheat”
Claim · model-written summary
The identified loci and resistant accessions offer opportunities for targeted introgression of novel resistance genes into cultivated wheat.
- Taxon
- cultivated wheat
Triticum aestivume1 - Outcome
- targeted introgression of novel resistance genese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The identified loci and resistant accessions offer key opportunities for the targeted introgression of novel resistance genes into cultivated wheat”