Durum wheat genome highlights past domestication signatures and future improvement targets

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

doi:10.1038/s41588-019-0381-3

Cited by 532 publications

(542 citation statements)

References 47 publications

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“…The average gene density of Chandler v2.0 was 19.28 genes per 100 kb, with higher gene content in the proximity of telomeric regions ( Figure 2 ), consistent with other plant genomes (Maccaferri et al 2019; Linsmith et al 2019). In addition, 92% (37,102) of the predicted gene models of Chandler v2.0 was supported by expression data, and 97% showed high similarity with a protein-coding transcript from either the J. regia RefSeq v1 gene set or a protein from the wider NCBI RefSeq plant database ( Supplemental Table S7 ), highlighting the accuracy and robustness of the Chandler v2.0 genome annotation.…”

Section: Resultssupporting

confidence: 83%

“…The recent introduction of long-read sequencing technologies and long-range scaffolding methods has enabled chromosome-scale assembly for multiple plant species, including highly heterozygous tree crops such as almond ( Prunus dulcis ; (Sánchez-Pérez et al 2019) and kiwifruit ( Actinidia eriantha ; (Tang et al 2019). The availability of genomes with fully assembled chromosomes provides foundations for understanding plant domestication and evolution (Jarvis et al 2017; Maccaferri et al 2019; Sánchez-Pérez et al 2019), the mechanisms governing important traits (e.g. flower color and scent; (Raymond et al 2018), as well as the impact of epigenetic modifications on phenotypic variability (Daccord et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Marrano

Britton

Zaini

et al. 2019

Preprint

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27The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements 28 in the characterization of walnut genetic and functional variation. However, it is highly 29 fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to 30 fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly 31 of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-32 read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the 33 previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the 34 full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences 35 at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 36 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of 37 the new protein-coding genes (90%) are full-length, which represents a significant improvement 38 compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new 39 chromosome-level genome on different areas of walnut research. By studying the proteome 40 changes occurring during catkin development, we observed that the virtual proteome obtained 41 from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the 42 identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale 43 genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously 44 undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic 45 regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler 46 v2.0 is a valuable resource to understand and explore walnut biology better.47 48Persian walnut (Juglans regia L.) is among the top three most-consumed nuts in the world, and 50 over the last ten years, its global production increased by 37% (International Nut and Dried Fruit 51

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Section: Resultssupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Marrano

Britton

Zaini

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…The evolutionary history of bread wheat is relatively well understood and the genomes of many of the descendants of the wheat ancestors have been sequenced (Jia et al ., ; Ling et al ., , ; Luo et al ., ; G. Zhao et al ., ). The genome sequences of pasta wheat and the closely related wild emmer have also been determined (Avni et al ., ; Maccaferri et al ., ). This offers the opportunity to study the phylogenetic intricacies of MIKC‐type MADS‐box gene evolution in this important group of cereals in great detail.…”

Section: Discussionmentioning

confidence: 97%

“…Zhao et al, 2017). The genome sequences of pasta wheat and the closely related wild emmer have also been determined (Avni et al, 2017;Maccaferri et al, 2019). This offers the opportunity to study the phylogenetic intricacies of MIKC-type MADS-box gene evolution in this important group of cereals in great detail.…”

Section: Dynamic Evolution Of Mikc-type Mads-box Genes In Distal Telomentioning

confidence: 99%

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

et al. 2019

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Summary Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine‐tuning important traits is of great importance. MADS‐box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC‐type MADS‐box genes. Homoeolog retention is significantly above the average genome‐wide retention rate for wheat genes, indicating that many MIKC‐type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily‐specific expression pattern, indicating broad conservation of function of MIKC‐type genes during wheat evolution. We also found extensive expansion of some MIKC‐type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC‐type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC‐type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.

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“…At present, our understanding of genetics and molecular basis of STBresistance in durum wheat is limited. However, this situation may improve with the recent studies on Ethiopian durum wheat landraces (Kidane et al, 2017), Tunisian landraces (Aouini, 2018), and the publication of the fully assembled durum wheat genome (Maccaferri et al, 2019). Karisto, Fakhfakh, Cultivar mixtures for STB control Kouki, Mikaberidze, Yahyaoui Similarly, cultivar mixtures for controlling STB have been studied in bread wheat but not in durum wheat (Mundt et al, 1995;Mille & Jouan, 1997;Cowger & Mundt, 2002;Mille et al, 2006;Gigot et al, 2013;Vidal et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Improved control of Septoria tritici blotch in durum wheat using cultivar mixtures

M’Barek

Karisto

Abdedayem

et al. 2019

Preprint

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AbstractMixtures of cultivars with contrasting levels of resistance can suppress infectious diseases in wheat, as demonstrated in numerous field experiments. Most studies focused on airborne pathogens in bread wheat, while splash-dispersed pathogens have received less attention, and no studies have been conducted in durum wheat. We conducted a two-year field experiment in Tunisia, to evaluate the performance of cultivar mixtures with varying proportions of resistance (0–100%) in controlling the polycyclic, splash-dispersed disease Septoria tritici blotch (STB) in durum wheat. To measure STB severity, we used a high-throughput method based on digital image analysis of 3074 infected leaves collected from 42 and 40 experimental plots during the first and second years, respectively. This allowed us to quantify pathogen reproduction on wheat leaves and to acquire a large dataset that exceeds previous studies with respect to accuracy and precision. Our analyses show that introducing only 25% of a disease-resistant cultivar into a pure stand of a susceptible cultivar provides a substantial reduction of almost 50% in disease severity compared to the susceptible pure stand. However, comprising the resistant component of two cultivars instead of one did not further improve disease control, contrary to predictions of epidemiological theory. Susceptible cultivars can be agronomically superior to resistant cultivars or be better accepted by growers for other reasons. Hence, if mixtures with only a moderate proportion of the resistant cultivar provide a similar degree of disease control as resistant pure stands, as our analysis indicates, such mixtures are more likely to be accepted by growers.

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Durum wheat genome highlights past domestication signatures and future improvement targets

Cited by 532 publications

References 47 publications

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Improved control of Septoria tritici blotch in durum wheat using cultivar mixtures

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