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Durum wheat genome highlights past domesticationsignatures and future improvement targets
Gabriella Sonnante
Istituto di Bioscienze e Biorisorse - CNR
Conferenza DiSBA – CNR 12-13 dicembre 2019
Durum wheat (or “pasta” wheat) is an important food crop in
the world, with an estimated annual global production of 36
million t.
Turkey and Canada are the largest producing countries, with
estimated 2 million ha each, followed by Algeria, Italy and
India, each cultivating over 1.5 million ha. Before war, Syria
belonged to this group of large producers.
A very large amount of genetic diversity exists in durum
wheat germplasm, and that diversity also extends to the
many traditional ways of consuming durum, including
special dishes that represent the national identities for
some Mediterranean countries: pasta, couscous,
bourghul, freekeh, gofio, particular breads, etc.
Durum wheat (Triticum turgidum ssp. durum)
Human driven teraploid wheat evolution
WILD EMMER WHEAT
Domestication
DOMESTICATED EMMER WHEAT
Continued evolution under Domestication
DURUM WHEAT LANDRACES DOMESTICATED EMMER WHEAT
MODERN DURUM WHEAT CULTIVARS
Breeding improvement
DURUM WHEAT LANDRACES
- Fully assembled genome of the modern cv. Svevo
- Genome-wide account of modifications imposed by thousands of years of empirical selection and breeding
- comparing the Svevo genome with the assembled genome of Wild Emmer Wheat accession Zavitan
- through a survey of the genetic diversity and selection signatures in a Global Tetraploid Wheat Collection
consisting of 1,856 accessions
- Efficient, genome-enabled dissection of the Cdu-B1 locus. A region bearing a signature of historic selection co-locates
with Cdu-B1, a quantitative trait locus (QTL) spanning 0.7 cM on chromosome 5B known to control cadmium
(Cd) accumulation in the grain
Durum wheat genome
# Library type Insert sizeSequencing
InstrumentRead length
Minimal
Coverage
1 PCR-free paired end library 450-460bp HiSeq 2500 PE 250bp X123
2 PCR-free paired end library 700- 800bp HiSeqX PE 150-160bp X38
3 Mate pair library 2-4kbp HiSeqX PE 150-160bp X39
4 Mate pair library 5-7kbp HiSeqX PE 150-160bp X41
5 Mate pair library 8-10kbp HiSeqX PE 150-160bp X38
Detailed sequencing data
Sequencing output
3.35 terabases (Tb) of data
279 × coverage (estimated genome size of 12 Gb)
Contigs Scaffolds
Total number of sequences 474,837 129,464
Assembly size (bp) 10,299,203,836 10,450,113,204
Gaps size (bp) 0 149,190,797
Gaps % 0.00 1.42
N50-length (bp) 56,196 5,972,063
N50-number of sequences 54,378 493
N90-length (bp) 13,008 1,085,649
N90-number of sequences 194,738 2,019
Maximal length (bp) 475,246 54,262,061
Detailed assembly results – (DenovoMAGIC2-NRGene)
Chromosome Sequence length Number of scaffolds
chr1A 585,266,722 126
chr1B 681,112,512 248
chr2A 775,448,786 167
chr2B 790,338,525 247
chr3A 746,673,839 190
chr3B 836,514,780 275
chr4A 736,872,137 241
chr4B 676,292,951 197
chr5A 669,155,517 155
chr5B 701,372,996 247
chr6A 615,672,275 140
chr6B 698,614,761 257
chr7A 728,031,845 198
chr7B 722,970,987 250
chrUn 498,719,471 126,526
Summary statistics of the durum wheat pseudomolecules (two
Hi-C libraries)
Scaffolds ordered and oriented using Svevo x Zavitan genetic map.
Conformation capture sequencing (Hi-C) resulted in 14
pseudomolecules (chromosomes) and a group of unassigned
scaffolds.
Pseudomolecules encompass 93.5% of the assembled sequence,
90% of the scaffolds oriented
Material File in public repository Tissue Reference
T. durum (Td) cv. Svevo This study 57 treatments seedling /adult plants - 9 RNA Pools This study
Td cv. Svevo This study Grains at 5 levels of developments This study
Td cv. Senatore Cappelli This study Grains at 5 levels of developments This study
Ta cv. Chinese Spring Illumina/PacBio reads PRJEB15048 Leaf; Root; Seedling; Seed; Stem; Spike Clavijo et al, 2016
Td cv. Kronos Bioproject PRJNA191054 young roots; young shoots; spike; grain Krasileva et al. 2013
Ta cv. Chinese Spring RNA-Seq (acc. number ERP004714) grain; leaf; root; spike; stem Pingault et al. 2015
Td cv. Altar84; Capeiti8; Claudio; Cresco; Edmore; Kofa; Meridiano;
Neodur; Saragolla; Strongfield; ValnovaThis study anther+ovary; root; leaf
Td cv. Svevo This study anther+ovary; root; leaf; seed_anthesis; seed_milk
T. turgidum dicoccoides “Zavitan” accession WEW: BioProject PRJNA310175Leaf; root; flag leaf; developing spikes; glumes;
flowers; grainsAvni et al. 2017
Two wild emmer, two landraces, two durum cultivars SRA (acc. N: SRR2084071 etc.) Glumes Zou et al 2015
RNA seq
Annotation
- Genes/Proteins (High Confidence; Low Confidence)- Gene Functions- Repeat Elements- microRNAs (from sRNA libraries)- Long non-coding RNAs- NLR gene family (Nucleotide Leucin-Rich Repeat Domain)- CpG islands- Prolamin proteins (Glutenins, Gliadins, Avenin-like)- Identification of pseudogenes- Orthologous gene family analysis- Genome-wide atlas of putative functional variants (SNPs-indels) between WEW and Durum wheat. In total, 597 variants.
Svevo (DW) – Zavitan (WEW) – Strong overall synteny
66,559 – 67,182 – Total High Confidence gene number
Similar chromosome structure and Transposable Element composition
Structural, functional and conserved synteny landscape of
the DW genome
a - Chromosome name and size (arms differentiated by gray shading)
b - Density of WEW High Confidence (HC) gene models
c - Links connecting homologous genes between WEW and DW
d - Density of DW HC gene models
e - Location of published QTLs
f - k-mer frequencies
g - Long terminal repeat (LTR)-retrotransposon density
h - DNA transposon frequency
i - Mean expression of HC genes calculated
Links in center connect homoeologous genes between subgenomes;
blue links between homoeologous chromosomes and
green links between large translocated regions.
Germplasm structure and phylogenetic relationships
Global Tetraploid Wheat Collection
- 1,856 accessions (non-redundant, filtered. Originally 2,558)
four main germplasm groups involved in tetraploid wheat domestication history and breeding:
Wild Emmer Wheat (WEW), Domesticated Emmer Wheat (DEW),
Durum Wheat Landraces (DWL), Durum Wheat Cultivars (DWC)
- 17,340 SNPs (90K SNP Infinium assay - unique, non –redundant, single Mendelian markers, genetically and
physically mapped) used for:
- Genetic Diversity
- Population Structure
- Identification of Selection Signature
DEW
DEW-ETH
DWL-ETH
DWLDWL DWL
DWL
DWC
DWCDEW
WEW-SL
DWL
DWL-ETH
DEW-ETH
DWC
WEW-SL
WEW-NE
Global Tetraploid Wheat Collection – Population Structure
Admixture analysis
Wild Emmer Wheat
WEW from North-Eastern Fertile
Crescent (WEW-NE)
Turkey-Karakadag pop 1
Turkey-Karakadag pop 2
Turkey-Karakadag pop 3
Turkey-Karakadag pop 4
Iran-NW (Kermanshaha) / Iraq
Admixed accession
WEW from Southern Levant
Fertile Crescent (WEW-SL)
Israel Northern pop 1
Israel Northern pop 2
Israel central pop 3
Jordan
Syria
Turkey-Gaziantep (admixed NE-SL)
Lebanon
k=2*
k=3
k=4
k=5
k=6
k=7
k=8
k=9
k=10
k=11
k=12
Domesticated Emmer Wheat DEW
populations (K=6*)
Turkey to TransCaucasia
Turkey to Balkans
Southern Europe
Southern Levant to Europe 1
Southern Levant to Europe 2
India-Oman-Ethiopia
k=2
k=3
k=4
k=5
k=6*
k=7
k=8
k=9
k=10
k=11
k=12
k=13
k=14
k=15
k=16
k=17
k=18
k=19
k=20
Durum Wheat Landraces
Southern Levant to North Africa
Greece to Balkans
Turkey to Trans Caucasia
Turkey to whole Fertile Crescent
T. turanicum subpopulation
India-Oman-Ethiopia
k=2
k=3
k=4
k=5
k=6*
k=7
k=8
k=9
k=10
k=11
k=12
Durum Wheat Cultivars DWC populations (K=5*)
ICARDA and Italian breeding for dry-land areas
Core Italian breeding
Core CIMMYT-70 wide adaptation and ICARDA
breeding for temperate areas
Core CIMMYT-80 high yielding potential
North American-French breeding
k=2
k=3
k=4
k=5*
Average rate of
diversity reduction
from WEW to DWC:
32.6% (SNP-based),
espec. In peri-
centromeric
recombination depleted region
SNP-based
diversity index
for the main
germplasm
groups in the
Global
Tetraploid
Wheat Collection
DRI: Diversity reduction index Fst: Single site divergence index XP-EHH: Cross population haplotype homozygosity
XP-CLR: Multilocus test for allele frequency differentiation hapFLK: Haplotype-based differentiation test
Total 454 selection signals identified by at least 1 metrics Cross-
population
selection index
metrics for the
comparison between DWL
and DWC
VRN-A1
tough-glumesQTL
DRI: Diversity reduction index Fst: Single site divergence index XP-EHH: Cross population haplotype homozygosity
XP-CLR: Multilocus test for allele frequency differentiation hapFLK: Haplotype-based differentiation test
Cross-
population
selection index
metrics for the
comparison between DWL
and DWC
Cross-
population
selection index
metrics for the
comparison
between DEWand DWL
Disease resistanceYellow pigment (Psy-1)
Glu-A1
Grain proteincontent QTLsWEW to DEWDEW to DWL
a) The Cdu-B1 locus was mapped in three bi- parentalpopulations (G9586, 8962-TL and Svevo × Zavitan) to beon chromosome 5B [QTL accounts >80% of thephenotypic variation in Cd concentration].
b) High-throughput sequencing of exomes refined theCdu-B1 locus by identifying additional polymorphismassociated with low (blue) and high (black) Cdaccumulation; positions of markers from the originalmapping populations are indicated
c) Alignment of Cdu-B1 between Svevo and Zavitanidentified a region of increased sequence variation. Thisregion contains a variable gene that encodes a metaltransporter, HMA3-B1 (blue)
Functional analyses demonstrated that the alleleTdHMA3-B1b (but not TdHMA3-B1a) is responsible forCd accumulation
4.3 Mbp Fine Mapping (8982-TL)
7.2 Mbp Weibe et al. 2010 (G9586)
Genome Alignment (Svevo vs. Zavitan)
Cdu-B1 Variable Region
High Cd
Haplotypes
Low Cd
Haplotypes
90k (G9586)
90k (Svevo x Zavitan)
SNPs and
InDels
per kbp
Genes
Using the Svevo genome to identify a candidate gene associated with differences in cadmium (Cd) accumulation in the grain of durum wheat
TdHMA3-B1a
TdHMA3-B1b
https://www.interomics.eu/durum-wheat-genome
https://www.interomics.eu/durum-wheat-genome-intranet
D. Nigro
A. Gadaleta
University of
Bari, Italy
R. Tuberosa
M. Maccaferri
D. Ormanbekova
E. Frascaroli
S. Corneti
S. Salvi
University of
Bologna, Italy
H. Budak
S. Biyiklioglu
Montana
State
University
USA
A.T.O. Melo
I. Hale
University
New
Hampshire
USA
K.F.X. Mayer
S.O. Twardziok
H. Gundlach
M. Spannagl
T. Lux
V.M. Prade
Helmholtz
Zentrum
München,
Germany
B. Kilian Global Crop
Diversity Trust,
Germany
N. Stein
S.G. Milner
M. Mascher
A. Himmelbach
Leibniz Institute
Plant Genetics,
Germany
N. Pecchioni
P. De Vita
D. Marone
A.M. Mastrangelo
CREA
Foggia, Italy
L. Cattivelli
E. Mica
C. Marè
E. Mazzucotelli
P. Bagnaresi
P. Faccioli
F. Desiderio
C. Crosatti
CREA
Fiorenzuola
d’Arda, Italy
S.S. Xu
S. Chao
J.D. Faris
E.T. Schafer
Agricult. Res.
Center, USA
Washington
State
University
USA
M. Pumphery
L. Milanesi
A. Manconi
M. Gnocchi
M. Moscatelli
CNR-ITB
Segrate, Italy
CNR-IBBA
Milano, Italy
A. Ceriotti
A. Stella
P. Cozzi
M. Lauria
B. Lazzari
G. Sonnante CNR-IBBR
Bari, Italy
A. Distelfed
R. Avni
J. Deek
Tel Aviv
University,
Israel
R.K. Pasam
R. Joukhadar
M.J. Hayden
Agriculture
Victoria,
Australia
C.J. Pozniak
K. Wiebe
J. Ens
R.P. MacLachlan
J.M. Clarke
S. Walkowiak
A. Sharpe
C. S. Koh
University of
Saskatchewan,
Canada
R. Knox Swift Current Res.
Develop. Centre
Canada
N. S. Harris
K.Y.H. Liang
G.J. Taylor
University
of Alberta,
Canada
H. Özkan Çukurova
University,
Turkey
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