The transcriptional landscape of polyploid wheat

Ramírez-González, Ricardo H.; Borrill, Philippa; Lang, Daniel; Harrington, Sophie A; Brinton, Jemima; Venturini, Luca; Davey, Mark W.; Jacobs, John; Ex, Fred van; Pasha, Asher; Khedikar, Yogendra; Robinson, Stephen J.; Cory, Aron T.; Florio, Tobin; Concia, Lorenzo; Juéry, Caroline; Schoonbeek, Henk‐jan; Steuernagel, Burkhard; Xiang, Daoquan; Ridout, Christopher J.; Chalhoub, Boulos; Mayer, Klaus; Benhamed, Moussa; Latrasse, David; Bendahmane, Abdelhafid; Wulff, Brande B. H.; Appels, R.; Tiwari, Vijay K.; Datla, Raju; Choulet, Frédéric; Pozniak, Curtis; Provart, Nicholas J.; Sharpe, Andrew; Paux, Etienne; Spannagl, Manuel; Bräutigam, Andrea; Uauy, Cristóbal

doi:10.1126/science.aar6089

Cited by 712 publications

(861 citation statements)

References 88 publications

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“…S1a–d). In some cases, where Ultrafast bootstraps and SH‐aLRT were not high enough to support a clade (> 90 and 75, respectively), synteny and previous classifications were considered (Ramírez‐González et al ., ). Thirty‐eight genes belonging to the FLC ‐, Bsister and AGL17 ‐subclades could not be assigned to a category, because their homoeolog status could not definitely be determined (Tables ; Fig.…”

Section: Methodsmentioning

confidence: 97%

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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Section: Methodsmentioning

confidence: 97%

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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“…This enthusiasm is tempered by the subtle phenotypes observed in wheat, compared to diploid species, and the inherent difficulties of working in the polyploid system. However, the combination of tools and resources being generated, such as expression atlases and networks (IWGSC ; Ramírez‐González et al ), sequenced mutants (Krasileva et al ) and gene‐editing technologies (Zhang et al ), should position the community in the best possible place to start understanding the genes and pathways that control grain size and weight.…”

Section: Challenges and Opportunitiesmentioning

confidence: 99%

A reductionist approach to dissecting grain weight and yield in wheat

Brinton

Uauy

2019

JIPB

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122

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Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub‐components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on‐farm yield.

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“…For example, the IWGSC () established that there is no dominance between the subgenomes of wheat at the transcriptional level and there is little regulation of genes between the three genomes. More recent work has shown coordination of homoeologs, potentially allowing for the development of new functions for homoeologs (Ramírez‐González et al ).…”

Section: Applicationsmentioning

confidence: 99%

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

Haas

Schreiber

Mascher

2019

JIPB

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Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre‐dates the era of next‐generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole‐genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.

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The transcriptional landscape of polyploid wheat

Cited by 712 publications

References 88 publications

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

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

A reductionist approach to dissecting grain weight and yield in wheat

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

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