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Durum wheat genome reveals the signature of 10,000 years of selection

Marco Maccaferri, Neil S. Harris, Sven O. Twardziok, Raj K. Pasam, Heidrun Gundlach, Manuel Spannagl, Danara Ormanbekova, Thomas Lux, Verena Prade, Sara Milner, Axel Himmelbach, Martin Mascher, Paolo Bagnaresi, Primetta Faccioli, Paolo Cozzi, Massimiliano Lauria, Barbara Lazzari, Alessandra Stella, Andrea Manconi, Matteo Gnocchi, Marco Moscatelli, Raz Avni, Jasline Deek, Sezgi Biyiklioglu, Elisabetta Frascaroli, Simona Corneti, Silvio Salvi, Gabriella Sonnante, Francesca Desiderio, Caterina Marè, Cristina Crosatti, Erica Mica, Hakan Ozkan, Benjamin Kilian, Pasquale De Vita, Daniela Marone, Reem Joukhadar, Elisabetta Mazzucotelli, Domenica Nigro, Agata Gadaleta, Shiaoman Chao, Justin Faris, Arthur T. O. Melo, Mike Pumphrey, Nicola Pecchioni, Luciano Milanesi, Krysta Wiebe, Jennifer Ens, Ron P. MacLachlan, John M. Clarke, Andrew G. Sharpe, Kevin Koh, Kevin Y. H. Liang, Gregory J. Taylor, Ron Knox, Hikmet Budak, Anna M. Mastrangelo, Steven S. Xu, Nils Stein, Iago Hale, Assaf Distelfeld, Matthew J. Hayden, Roberto Tuberosa, Sean Walkowiak, Klaus F. X. Mayer, Aldo Ceriotti, Curtis J. Pozniak, Luigi Cattivelli

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Svevo, the first high-quality durum wheat genome being assembled and annotated

• Svevo (1996): CIMMYT line × Zenit

• High protein content and high yellow pigment

• Quality reference for Italian durum wheat 1996-2010

• Parent of many recent Italian durum wheat cultivars

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Durum wheat genome annotation

Annotation of the assembled genome implemented with extensive transcriptome data and curated reference protein sets identified 66,559 High Confidence genes, 774 miRNA coding loci and 8.4 Gb (82%) of transposons and their deteriorated remnants.

High Confidence genes: loci that contained an complete transcript with evidence of expression and coding sequence with annotated start and stop codon and significant match to reference protein sequence (query coverage >90% and subject coverage >90% and e-value <10-10).

https://www.interomics.eu/durum-wheat-genome GrainGenes (https://wheat.pw.usda.gov/GG3/jbrowse_Durum_Svevo)

Maccaferri, et al, 2019, Nature Genetics

All available markers and about 2,105 QTLs/MTAs have been projected onto the durum wheat genome

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1. The sequence allows the exact estimation of genetic vs. physical relationship

Highly-recombinogenic regions: average recombination rate of 1.8 Mb/cM (18HC genes/cM), approx 22% of the genome 42% HC genes, 60% QTLs

Recombination-depleted centromeric regions: average recombination rate of 107 Mb/cM (350HC genes/cM), approx 44% of the genome 23% HC gene, 10% QTLs

SvxZ

v-G

BS

(cM

)

Chromosome 1A

Physical distance (Mb)

Ge

net

ic d

ista

nce

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2. An insight in the tetraploid wheat evolution

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Durum wheat domestication and selection: from wild emmer to elite cultivars

Wild emmer (T. turgidum subsp. dicoccoides) is the progenitor of all tetraploid wheats.

Cultivated emmer wheat (Triticum turgidum subsp. dicoccum) was domesticated from wild emmer in the Near-Eastern Fertile Crescent ~10,000 years BP, via selection of plants carrying mutations on the two genes conferring the non-brittle rachis phenotype.

Plant breeding has selected cultivars first from landraces and then applying genetic knowledge (elite cultivars).

1

2

3

Durum wheat (T. turgidum L. subsp. durum) landraces subsequently evolved from cultivated emmer through a process of selection for free-threshing naked forms. The first durum wheat dates ~6,500–7,500 years BP, but durum became established as a prominent crop only ~1,500-2,000 years ago.

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The durum wheat genome reveals signatures of domestication, empirical selection and breeding

Markers anchored onto

the genome are used to analyze the

genetic diversity

90K iSelect genotyping was applied to a Global Tetraploid Collection of 1,852 accessions made of wild and cultivated emmer, landraces of T. turgidum subspecies (durum, turanicum, polonicum, carthlicum, turgidum) and cultivars sampled from all major cultivation areas worldwide

A genome wide comparison of the genetic diversity between subpopulations allows the identification of regions that have been fixed during domestication and breeding (selective sweep signatures)

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T. dicoccoides

T. dicoccum

T. durum modern cultivars

T. durum modern landraces

T. turanicum

T. carthlicum

T carthlicum

Phylogenetic NJ tree

T turanicum

Du

rum

lan

dra

ces

17,614 anchored SNP

filtered for Mendelian

segregation,

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Genetic diversity along the genome

WEW: Wild Emmer Wheat DEW: Domesticated Emmer Wheat DWL: Durum Wheat Landraces DWC: Durum Wheat Cultivar

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Domestication and selection have limited genetic diversity, but this loss of diversity is not homogeneous along the genome

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Identification of selection signatures

• Analyses performed with 5 different indexes: Diversity reduction index (DRI), divergence index (Fst), cross population Extended Haplotype Homozigosity (XP-EHH), multilocus test for allele frequency differentiation (XP-CLR) and haplotype-based differentiation test (hapFLK)

• Data have been projected on the genome together with the position of all known QTLs and genes

• On the right the example for the transition between Wild Emmer Wheat and Domesticated Emmer Wheat

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*TaGW2-A - Grain weight

*Q-5B - Domestication

WEW vs. DEW

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DEW vs. DWL

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C

DWL vs. DWC

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3. Genome sequence and germplasm resources to improve cultivated durum

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Cdu-B1: a locus controlling grain Cadmium accumulation

• Cadmium (Cd) accumulation represents a potential threat for human health and in durum wheat some genotypes accumulate Cd in grain at levels that exceed the limits

• A single major locus, Cdu-B1, controls grain Cd concentration, being Svevo high and Zavitan low Cd accumulator Zavitan is a wild emmer accession for which the genome sequence is also available (Avni et al, Science 2017)

• Cdu-B1 has been localized to a 0.14 cM interval on chromosome 5B corresponding to an interval of 4.3 Mb, 19 genes, one candidate: TdHMA3-B1

Curtis Pozniak

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5A Near perfect colinearity for the CduB1 interval

between Svevo and Zavitan

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• TdHMA3-B1 codes for a metal transporter

• A 17 bp duplication in high-Cd accumulator Svevo generates a premature stop codon and thus a non-functional TdHMA3-B1 protein

• The duplication is fully associated with the Cd phenotypes

• Expression of TdHMA3-B1 from the low-Cd accumulator Zavitan in yeast produced a protein localized at the tonoplast that complemented the Cd-sensitive phenotype of the ycf1 mutant

Wild emmer

Durum wheat

Cdu-B1: a locus controlling grain Cadmium accumulation

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Population structure and HMA3-B1a/b allele frequency

WEW DEW DW Ethiopian landraces

DW Western (Medit.) landraces DW Eastern (Transcaucasian to Russian) landraces

DW elite cultivars

a) b) a) b) c) d) e) f) a) b) a) b) c) d) e) c) f) g) a*) b*) T.

cart

hl

icu

m

T.tu

ran

icu

m

green = HMA3-B1a, functional allele, red = HMA3-B1b, non functional allele

Clustering based on FINESTRUCTURE

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Population structure and HMA3-B1a/b allele frequency

WEW DEW DW Ethiopian landraces

DW Western (Medit.) landraces DW Eastern (Transcaucasian to Russian) landraces

DW elite cultivars

a) b) a) b) c) d) e) f) a) b) a) b) c) d) e) c) f) g) a*) b*)

T. c

art

hlic

um

T. t

ura

nic

um

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Conclusions

• We provide a high quality assembly of the genome of the durum wheat cultivar Svevo, a contribution to the wheat pangenome analysis.

• We demonstrate that the genome sequence of durum wheat (and of the wild emmer) is an essential tool for durum wheat breeding allowing genome wide investigation of the modifications associated with breeding as well as the isolation of relevant agronomic loci.