Triticum population sequencing provides insights into wheat adaptation

Zhou, Yao; Zhao, Xuebo; Li, Yiwen; Xu, Jun; Bi, Aoyue; Kang, Lipeng; Xu, Daxing; Chen, Haofeng; Wang, Ying; Wang, Yuange; Liu, Sanyang; Jiao, Chengzhi; Lü, Hongfeng; Wang, Jing; Yin, Changbin; Jiao, Yuling; Lü, Fei

doi:10.1038/s41588-020-00722-w

Cited by 246 publications

(318 citation statements)

References 79 publications

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“…Moreover, LD-based maps are representative of a whole population and less susceptible to individual specific variation, for example introgressions which are known to prevent local formation of CO between the introgressed chromatid and the native chromatid. Introgressions from wild relative species are frequent in bread wheat species, representing from 4 to 32% of bread wheat genome (Zhou et al 2020). The limitation of LD-based maps relies on the fact that they can be affected by evolutionary patterns, which in turn can hinder their usefulness to study the evolution of recombination rate.…”

Section: Ld-based Recombination Maps Correlate Well With the Biparentmentioning

confidence: 99%

“…These introgressions repress recombination (Worland et al 1988) and this resulted in a poor correlation between CsRe genetic map and our LD-based maps for genomic region 7DR3 in our analysis. It was recently shown that natural or artificial introgressions of wheat wild-relatives DNA contributed to up to 710 Mb and 1580 Mb in wheat landraces and varieties respectively (Cheng et al 2019), and represent from 4 to 32% of bread wheat varieties genome (Zhou et al 2020). A similar analysis used exome capture to evaluate introgression in 890 hexaploid and tetraploid wheats (He et al 2019).…”

Section: Evolution Of the Recombination Landscape In Bread Wheatmentioning

confidence: 99%

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Evolution of recombination landscapes in diverging populations of bread wheat

Déserts

Bouchet

Sourdille

et al. 2021

Preprint

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Reciprocal exchanges of DNA (crossovers) that occur during meiosis are mandatory to ensure the production of fertile gametes in sexually reproducing species. They also contribute to shuffle parental alleles into new combinations thereby fuelling genetic variation and evolution. However, due to biological constraints, the recombination landscape is highly heterogenous along the genome which limits the range of allelic combinations and the adaptability of populations. An approach to better understand the constraints on the recombination process is to study how it evolved in the past. In this work we tackled this question by constructing recombination profiles in four diverging bread wheat (Triticum aestivum L.) populations established from 371 landraces genotyped at 200,062 SNPs. We used linkage disequilibrium (LD) patterns to estimate in each population the past distribution of recombination along the genome and characterize its fine-scale heterogeneity. At the megabase scale, recombination rates derived from LD patterns were consistent with family-based estimates obtained from a population of 406 recombinant inbred lines. Among the four populations, recombination landscapes were significantly positively correlated between each other and shared a statistically significant proportion of highly recombinant intervals. However, this comparison also highlighted that the similarity in recombination landscapes between populations was significantly decreasing with their genetic differentiation in most regions of the genome. This observation was found to be robust to SNP ascertainment and demography and suggests a relatively rapid evolution of factors determining the fine-scale localization of recombination in bread wheat.

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Section: Ld-based Recombination Maps Correlate Well With the Biparentmentioning

confidence: 99%

Section: Evolution Of the Recombination Landscape In Bread Wheatmentioning

confidence: 99%

Evolution of recombination landscapes in diverging populations of bread wheat

Déserts

Bouchet

Sourdille

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…S2). These separate lineages were also observed in the phylogenetic analysis based on RNA-seq-based polymorphisms [34] and whole-genome polymorphisms in wild einkorn [36]. The habitats of L1 accessions were southern Turkey, northern Iraq, and Iran, which correspond to the Fertile Crescent.…”

Section: Discussionmentioning

confidence: 61%

Phenotypic effects of Am genomes in nascent synthetic hexaploids derived from interspecific crosses between durum and wild einkorn wheat

Michikawa

Okada

Ikeda

et al. 2020

Preprint

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Background Allopolyploid speciation is a major evolutionary process in wheat (Triticum spp.) and the related Aegilops species. The generation of synthetic polyploids by interspecific crosses artificially reproduces the allopolyploidization of wheat and its relatives. These synthetic polyploids allow breeders to introduce agriculturally important traits into durum and common wheat cultivars. This study aimed to evaluate genetic and phenotypic diversity in wild einkorn (Triticum monococcum ssp. aegilopoides) accessions, to generate a set of synthetic hexaploid lines containing the various Am genomes from wild einkorn, and to reveal their agronomic characteristics.Results We examined the genetic diversity of 43 wild einkorn accessions using simple sequence repeat markers covering all the chromosomes and revealed two genetically divergent lineages, L1 and L2. The genetic divergence between these lineages was linked to their phenotypic divergence and the climate of their habitats. L1 accessions were characterized by early flowering, fewer spikes, large spikelets, and low-density spikelets compared to L2 accessions. These trait differences could have resulted from adaptation to their different habitats. We then developed 42 synthetic lines containing the AABBAmAm genome through interspecific crosses between T. turgidum cv. Langdon (AABB genome) as the female parent and the wild einkorn accessions (AmAm genome) as the male parents. Two of the 42 AABBAmAm synthetic lines exhibited hybrid dwarfism. Phenotypic variation, especially for days to flowering and spikelet-related traits, in the synthetic lines was significantly correlated with that in their wild einkorn parents. The phenotypic divergence between L1 and L2 accessions also reflected phenotypic differences among the synthetic lines. Furthermore, the AABBAmAm synthetic lines had longer spikelets and grains, long awns, high plant heights, soft grains, and late flowering, which are distinct from other synthetic hexaploid wheat lines such as AABBAA and AABBDD. Conclusions Wild einkorn genetically and phenotypically diverged into two lineages. The phenotypic variations in the synthetic lines reflected the divergence among wild einkorn. Utilization of various Am genomes of wild einkorn resulted in wide phenotypic diversity in the AABBAmAm synthetic hexaploids and provides promising new breeding materials for wheat.

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“…Wheat (Triticum aestivum L.) is the most-extensively cultivated staple crop (~ 17% of the total cultivated area) in the world 1 . It serves as a leading food for human consumption as an essential source of starch, proteins, vitamins, dietary ber, and phytochemicals 2 .…”

Section: Read Full License Introductionmentioning

confidence: 99%

High-quality genome assembly-based and functional analyses reveal the pathogenesis mechanisms and evolutionary landscape of wheat sharp eyespot Rhizoctonia cerealis

Lü

Guo

Zhang

et al. 2021

Preprint

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Wheat (Triticum aestivum) is one of the most important staple crops. The necrotrophic binucleate fungus Rhizoctonia cerealis is the causal agent for the devastating disease wheat sharp eyespot and additional diseases of other agricultural crops and bioenergy plants. In this study, we present the first high-quality genome assembly of R. cerealis Rc207, a highly aggressive strain isolated from wheat. The genome encodes expand and diverse sets of virulence-related proteins, especially secreted effectors, carbohydrate-active enzymes (CAZymes), metalloproteases, Cytochrome P450 (CYP450), and secondary metabolite-associated enzymes. Many of these genes, in particular those encoding secretory proteins and CYP450, showed markedly up-regulation during infection in wheat. Of 831 candidate secretory effectors, ten up-regulated secretory proteins, such as CAZymes, metalloproteases and antigens, were functionally validated as virulence factors required for the fungal infection in wheat. Further intra-species and inter-species comparative genomics analyses showed that repeat sequences, accounting for 17.87% of the genome, are the major driving force for the genome evolution, and frequently intraspecific gene duplication contributes to expansion of pathogenicity-related gene families. This is the first genome-scale investigation elucidating the pathogenesis mechanisms and evolutionary landscape of R. cerealis. Our results provide essential tools for further development of effective disease control strategies.

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Triticum population sequencing provides insights into wheat adaptation

Cited by 246 publications

References 79 publications

Evolution of recombination landscapes in diverging populations of bread wheat

Evolution of recombination landscapes in diverging populations of bread wheat

Phenotypic effects of Am genomes in nascent synthetic hexaploids derived from interspecific crosses between durum and wild einkorn wheat

High-quality genome assembly-based and functional analyses reveal the pathogenesis mechanisms and evolutionary landscape of wheat sharp eyespot Rhizoctonia cerealis

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