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Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV

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A novel rare allele of the barley host factor gene eIF4E for BaMMV/BaYMV infection was identified in an Iranian landrace that showed broad resistance to barley yellow mosaic virus disease, and molecular markers facilitating efficient selection were developed.

Abstract

The soil-borne yellow mosaic virus disease caused by different strains of barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) is a major threat to winter barley (Hordeum vulgare) production in Europe and East Asia. However, the exploration of resistant germplasm or casual genes for barley breeding is rather limited in relation to the rapid diversification of viral strains. Here, we identified an Iranian barley landrace ‘HOR3298,’ which represented complete resistance to BaYMV and BaMMV. In contrast to rym4 and rym5, which act as the predominant source in Europe and East Asia for breeding resistant cultivars over decades and which have been overcome by several virulent isolates, this landrace showed broad-spectrum resistance to multiple isolates of BaYMV/BaMMV in the fields of Germany and China. By employment of bulked segregant RNA sequencing, test for allelism, and haplotype analysis, a recessive resistance gene in ‘HOR3298’ was genetically mapped coincident with the host factor eukaryotic translation initiation factor 4E (eIF4E, causal gene of rym4 and rym5). The eIF4EHOR3298 allele encoded for a novel haplotype that contained an exclusive nucleotide mutation (G565A) in the coding sequence. The easily handled markers were developed based on the exclusively rare variation, providing precise selection of this allele. Thus, this work provided a novel reliable resistance source and the feasible marker-assisted selection assays that can be used in breeding for barley yellow mosaic virus disease resistance in cultivated barley.

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Acknowledgements

We gratefully acknowledge IPK Genebank and National Crop Genebank of China for kindly providing the barley accessions, Prof. Nils Stein (IPK-Gatersleben, Germany) for productive discussion, Prof. Rugen Xu (Yangzhou University, China) for providing BaYMV/BaMMV carrying soil, Ms. Haiying Guan (CAAS), Ms. Mary Ziems (IPK), Ms. Jelena Perovic (IPK) and Ms. Dörte Grau (JKI) for excellent technical support. This work was financially supported by National Key R&D Program of China (2018YFD1000702, 2018YFD1000700) to P. Yang and J. Liu, Fundamental Research Funds for Central Non-Profit of Institute of Crop Sciences of CAAS (S2018YC01, S2018PY04) and Agricultural Science and Technology Innovation Program of CAAS to P. Yang, and part of the collaborative project ‘‘Plant KBBE II-ViReCrop’’ by a Grant (FKZ 0315708) of the German Ministry of Education and Research (BMBF) to F. Ordon.

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Access to the BSR-seq reads data: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514114.

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Suppl. Fig. 1

Snapshot of multiple alignment of eIF4EHOR3298 and other eIF4E haplotypes (TIFF 1608 kb)

Suppl. Fig. 2

The developed dCAPS marker (A) and KASP marker (B), which could be used for selection of the eIF4EHOR3298 allele in both homozygotes and heterozygotes. The allele discrimination of KASP marker was called after 35 cycles of amplification (JPEG 770 kb)

Suppl. Table 1

The primers used in this study (PDF 185 kb)

Suppl. Table 2

The diversity panel of 498 Chinese barley landraces/historical cultivars (PDF 402 kb)

Suppl. Table 3

Output of the BSR-seq in resistant and susceptible bulks of F2 segregants derived from ‘HOR3298’ x ‘W757/612’ (PDF 96 kb)

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Shi, L., Jiang, C., He, Q. et al. Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV. Theor Appl Genet 132, 1777–1788 (2019). https://doi.org/10.1007/s00122-019-03314-3

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