Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

VanBuren, Robert; Wai, Ching Man; Wang, Xuewen; Pardo, Jeremy; Yocca, Alan E.; Wang, Hao; Chaluvadi, Srinivasa R.; Han, Guomin; Bryant, Douglas W.; Edger, Patrick P.; Messing, Joachim; Sorrells, Mark E.; Mockler, Todd C.; Bennetzen, Jeffrey L.; Michael, Todd P.

doi:10.1038/s41467-020-14724-z

Cited by 134 publications

(133 citation statements)

References 78 publications

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“…Only one previous study has conducted genome-wide comparisons between a desiccation-sensitive and -tolerant angiosperm (13), and no such systems are currently available for the grasses. We assembled a draft genome of the desiccation-tolerant grass E. nindensis and compared it to the recently sequenced E. tef genome (18) to distinguish genetic elements associated with desiccation tolerance from those more broadly linked with drought response. Similar to most (∼90%) of chloridoid grasses, E. nindensis and E. tef are polyploid, and they have the same karotype (2n = 4× = 40) (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Chromosome-scale genome assemblies of the Chloridoideae grasses E. tef (desiccation sensitive) and Oropetium thomaeum (desiccation tolerant) were recently completed (17,18). Here, we sequenced the desiccation-tolerant grass Eragrostis nindensis and performed detailed comparative genomics within Chloridoideae and across the grass family to search for patterns of convergence in the evolution of desiccation tolerance.…”

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confidence: 99%

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Intertwined signatures of desiccation and drought tolerance in grasses

Pardo

Wai

Chay

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Grasses are among the most resilient plants, and some can survive prolonged desiccation in semiarid regions with seasonal rainfall. However, the genetic elements that distinguish grasses that are sensitive versus tolerant to extreme drying are largely unknown. Here, we leveraged comparative genomic approaches with the desiccation-tolerant grass Eragrostis nindensis and the related desiccation-sensitive cereal Eragrostis tef to identify changes underlying desiccation tolerance. These analyses were extended across C4 grasses and cereals to identify broader evolutionary conservation and divergence. Across diverse genomic datasets, we identified changes in chromatin architecture, methylation, gene duplications, and expression dynamics related to desiccation in E. nindensis. It was previously hypothesized that transcriptional rewiring of seed desiccation pathways confers vegetative desiccation tolerance. Here, we demonstrate that the majority of seeddehydration-related genes showed similar expression patterns in leaves of both desiccation-tolerant and -sensitive species. However, we identified a small set of seed-related orthologs with expression specific to desiccation-tolerant species. This supports a broad role for seed-related genes, where many are involved in typical drought responses, with only a small subset of crucial genes specifically induced in desiccation-tolerant plants.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Intertwined signatures of desiccation and drought tolerance in grasses

Pardo

Wai

Chay

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…Here, we established a set of genomic resources that allowed us to comprehensively assess the genetic variation found in fonio, a cereal crop that holds great promises for agriculture in marginal environments. The analysis of fl-LTR-RT revealed two sub-genome specific transposon clusters that experienced a peak of activity around 1.1 - 1.5 MYA, indicating that the two fonio sub-genomes hybridized after this period 41 . The Ks analysis estimated that the two sub-genomes diverged prior to these transposon bursts ∼ 3 MYA, suggesting that fonio is an allotetraploid species.…”

Section: Discussionmentioning

confidence: 99%

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Abrouk

Ahmed

Cubry

et al. 2020

Preprint

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33Sustainable food production in the context of climate change necessitates diversification of 34 agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria 35 exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we 36 established high-quality genomic resources to facilitate fonio improvement through molecular 37 breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 38 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population 39 structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic 40 factors. Two genes associated with seed size and shattering showed signatures of selection. Most 41 known domestication genes from other cereal models however have not experienced strong 42 selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and 43 dry environments. 44 45 agriculture 1-3 . The Food and Agriculture Organization of the United Nations (FAO) stated that arid 50 and semi-arid regions are the most vulnerable environments to increasing uncertainties in regional 51 and global food production 4 . In most countries of Africa and the Middle East, agricultural 52 productivity will decline in the near future 4 , because of climate change, land degradation, and 53 groundwater depletion 5 . Agricultural selection, from the early steps of domestication to modern-54 day crop breeding, has resulted in a marked decrease in agrobiodiversity 6,7 . Today, three cereal 55 4 crops alone, bread wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa) account 56 for more than half of the globally consumed calories 8 . 57Many of today's major cereal crops, including rice and maize, originated in relatively humid 58 tropical and sub-tropical regions 9,10 . Although plant breeding has adapted the major cereal crops 59 to a wide range of climates and cultivation practices, there is limited genetic diversity within these 60 few plant species for cultivation in the most extreme environments. On the other hand, crop wild 61 relatives and orphan crops are often adapted to extreme environments and their utility to unlock 62 marginal lands for agriculture has recently regained interest 2,6,[11][12][13][14] . Current technological advances 63 in genomics and genome editing provide an opportunity to rapidly domesticate wild relatives and 64 to improve orphan crops 15,16 . De novo domestication of wild species or rapid improvement of semi-65 domesticated crops can be achieved in less than a decade by targeting a few key genes 6 . 66White fonio (Digitaria exilis (Kippist) Stapf) (Fig. 1) is an indigenous African millet species with 67 a great potential for agriculture in marginal environments 17,18 . Fonio is cultivated under a large 68 range of environmental conditions, from a tropical monsoon climate in western Guinea to a hot, 69 arid desert climate (BWh) in the Sahel zone. Some extra-early matur...

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“…The genetic diversity in teff was also discovered by using a range of molecular markers [4] and its genome has been sequenced [9]. Great genetic diversity in yield, lodging index, and stem strength related traits was recorded in teff [10,11].…”

Section: Introductionmentioning

confidence: 99%

“…Phenotypic variability in teff was recorded in-grain yield, grain color and size, days to panicle emergence, days to maturity (21 to 81 and 50 to 140, respectively), number of grains/plant (9000-90,000), plant height (20-156 cm), number of tillers/plant , and culm diameter (1.2-5 mm) [10,11].…”

Section: Introductionmentioning

confidence: 99%

In-Depth Field Characterization of Teff [Eragrostis tef (Zucc.) Trotter] Variation: From Agronomic to Sensory Traits

et al. 2020

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Teff is an important food crop that serves to prepare Injera-flat-bread. It is cultivated worldwide and is particularly susceptible to lodging. A diverse collection of teff [Eragrostis tef (Zucc.) Trotter] populations was characterized for a wide range of traits, ranging from agronomic to final Injera sensory parameters, under well-irrigated Mediterranean spring conditions. The populations tested were collected from single plants presenting lodging resistance at the site of collection and their traits were characterized herein. An early type of lodging was observed, which was most likely triggered by a fast and sharp inflorescence weight increase. Other populations were ‘strong’ enough to carry the inflorescence during most of the grain-filling period, up to a point where strong lodging occurred and plants where totally bent to the ground. Three mixed color seed populations were established from a single plant. These were separated into ‘white’ and ‘brown’ seeds and were characterized separately under field conditions. The newly ‘brown’ populations appear to be the result of a rather recent non-self (external) airborne fertilization from a dark pollen donor. Some of these hybrids were found to be promising in terms of Injera sensory traits. The population of these studies might serve as breeding material. Integration between a wide range of parameters and the correlations obtained between agronomic and sensory traits might improve our ability to breed towards a “real world” better end-product.

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Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Cited by 134 publications

References 78 publications

Intertwined signatures of desiccation and drought tolerance in grasses

Intertwined signatures of desiccation and drought tolerance in grasses

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

In-Depth Field Characterization of Teff [Eragrostis tef (Zucc.) Trotter] Variation: From Agronomic to Sensory Traits

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