A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement

Zhang, Xu; Wang, Haiyan; Sun, Haojie; Li, Yingbo; Feng, Yilong; Jiao, Chengzhi; Li, Mengli; Song, Xinying; Wang, Tong; Wang, Zongkuan; Yuan, Chunxia; Sun, Li; Lu, Ruiju; Zhang, Wenli; Xiao, Jin; Wang, Xiue

doi:10.1016/j.molp.2022.12.021

Cited by 19 publications

(15 citation statements)

References 114 publications

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“…For chromosomal distribution, SnRK2-V genes were mapped to the corresponding chromosomes according to the completed genomic sequence of H. villosa in our previous study [ 36 ]. Ten SnRK2-V genes were identified and they were distributed unevenly on chromosomes.…”

Section: Resultsmentioning

confidence: 99%

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Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat

Liu,

Wei,

et al. 2024

BMC Genomics

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Background The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat. Results To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance. Conclusion Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.

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Section: Resultsmentioning

confidence: 99%

“…Moreover, analysis of chromosome location indicated that the SnRK2-V genes were distributed on the chromosome 1, 2, 3, 4 and 5. This indicates that SnRK2-V genes were formed before the differentiation of Triticeae species [ 36 – 39 ].…”

Section: Discussionmentioning

confidence: 99%

Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat

Liu,

Wei,

et al. 2024

BMC Genomics

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“…The CC domains of some MLA haplotypes present in D. villosum can be assigned to MLA subfamily 1, while others are assigned to MLA subfamily 2 ( Fig. S7 ), indicating that the differentiation of the CC domain occurred prior to the speciation of barley and Dasypyrum villosum , i.e., approximately 14.9 Mya, which predates the divergence of wheat and barley 8 Mya (77). Notably, we did not identify SCS6 homologs in other grass species, suggesting that SCS6 is likely a Hordeum -specific innovation.…”

Section: Resultsmentioning

confidence: 99%

“…MLA subfamilies 1 and 2 are mainly distinguished by their polymorphic CC domains (e.g., 65% identity and 81% similarity for MLA6 and SCS6 CC domains;(63)). The CC domains of some MLA haplotypes present in D. villosum can be assigned to MLA subfamily 1, while others are assigned to MLA subfamily 2 (Fig.S7), indicating that the differentiation of the CC domain occurred prior to the speciation of barley and Dasypyrum villosum, i.e., approximately 14.9 Mya, which predates the divergence of wheat and barley 8 Mya(77). Notably, we did not identify SCS6 homologs in other grass species, suggesting that SCS6 is likely a Hordeum-specific innovation.We performed statistical analysis on the coding sequences ofScs6 variants, MLA subfamily 2 members from barley, and other Mla subfamily 2 members in the Triticeae to identify sites under positive selection.…”

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confidence: 99%

A barley MLA receptor is targeted by a non-ribosomal peptide effector of the necrotrophic spot blotch fungus for disease susceptibility

Leng,

Kümmel,

Zhao

et al. 2023

Preprint

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The evolutionary history of plant interactions with necrotrophic pathogens that feed on dying host cells and their virulence mechanisms remains fragmentary. We have isolated the barley geneScs6, which is required for the necrotrophic fungusBipolaris sorokinianaisolate ND90Pr to cause spot blotch disease.Scs6is located at the disease resistance gene locusMildew locus a(Mla) and encodes an intracellular nucleotide-binding leucine-rich repeat receptor (NLR). In transgenic barley,Scs6is sufficient to confer susceptibility to ND90Pr in accessions naturally lacking the receptor, resulting in infection-associated host cell death. Expression ofScs6in evolutionarily distantNicotiana benthamianareconstitutes a cell death response to an uncharacterized non-ribosomal peptide effector produced by ND90Pr-specific non-ribosomal peptide synthetases (NRPSs) encoded at theVHv1virulence locus. Our data suggest that the heat-resistant effector directly activates the SCS6 receptor.Scs6is an allelic variant of functionally diversifiedMlaresistance genes each conferring strain-specific immunity to barley powdery mildew isolates with a matching proteinaceous pathogen effector. Domain swaps between MLA and SCS6 NLRs and expression of the resulting hybrid proteins inN. benthamianareveal that the SCS6 leucine-rich repeat domain is a specificity determinant for the NRPS-derived effector to activate the receptor.Scs6evolved after the divergence of barley from wheat and is maintained in several wild barley populations with an incidence of 8%, suggesting a beneficial function for the host. Evolution of thebona fideimmune receptor SCS6 targeted by the NRPS-derived effector was key for the emergence of strain-specific spot blotch disease in domesticated barley.

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“…The fully utilization and exploitation of wild genetic resources will benefit to the improvement of existing wheat varieties. A chromosome-scale genome assembly of Dasypyrum villosum detected two reciprocal translocation events and provided broad-spectrum disease resistance resources for wheat improvement (Zhang et al, 2023). By backcrossing the FHB-resistance Thinopyrum elongatum lines with the main F I G U R E 1 Five integrated components and their interdependences accounting for genomics-assisted breeding (GAB).…”

Section: Germplasm Collection and Characterizationmentioning

confidence: 99%

Genomics‐assisted breeding: The next‐generation wheat breeding era

Sun

Cheng

et al. 2023

Plant Breeding

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Common wheat provides approximately 20% of the total dietary calorie intake of human beings. Recent technological advances in whole‐genome sequencing and their application in wheat and its progenitor species provide new opportunities to uncover the genetic variation of wheat traits and to accelerate the traditional breeding (TB) strategies in the context of genomics‐assisted breeding (GAB). Integration of TB, marker‐assisted selection (MAS) and genomic selection (GS) with high‐density SNP markers is expected to accelerate the breeding process and to further enhance genetic gain. With the assistance of the next‐ or third‐generation sequencing technologies and high‐throughput phenotyping platforms, GAB can now realistically be considered in the following area: (i) genome sequencing and high‐quality assembly to uncover new variations, (ii) whole‐genome sequence‐based association studies, (iii) gene function (or functional gene) identification and (iv) integration of whole genomic breeding information, utilizing multi‐omics data and different breeding strategies. We argue that GAB is becoming the preferred strategy in pursuit of new wheat cultivars with superior traits on high yielding, high nutritional quality, climate‐resilience and so on.

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A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement

Cited by 19 publications

References 114 publications

Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat

Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat

A barley MLA receptor is targeted by a non-ribosomal peptide effector of the necrotrophic spot blotch fungus for disease susceptibility

Genomics‐assisted breeding: The next‐generation wheat breeding era

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