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Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.

Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF - PLoS ONE (2012)

Bottom Line: We generated an F(6:7) recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2) population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance.Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium.Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China.

ABSTRACT
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25 °C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F(6:7) recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2) population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.

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Genetic map of BSMV Bsr1 resistance within the distal region of Bd21 chromosome 3.(a)Cartoon of the short arm of Bd21 chromosome 3 (Chr3S). The white region shows 705 kb of distal region of Chr 3 encompassing the fine mapping region. (b)Genetic map of the 705Kb region of chromosome 3. Markers are shown on the right with map distances on the left. The furthest flanking markers that were previously assigned to the Brachypodium Chr 3 are indicated by dashed lines. The Bsr1 locus is indicated in red. The six markers located within the predicted Bd21 locus served as anchors to establish co-linearity between the Bsr1 genetic map and the physical map of Bd21. (c) Physical map of the Bsr1 interval. Annotated genes are indicated by arrows and candidate genes are indicated in green. Approximate locations (bp) are shown on the left.
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pone-0038333-g003: Genetic map of BSMV Bsr1 resistance within the distal region of Bd21 chromosome 3.(a)Cartoon of the short arm of Bd21 chromosome 3 (Chr3S). The white region shows 705 kb of distal region of Chr 3 encompassing the fine mapping region. (b)Genetic map of the 705Kb region of chromosome 3. Markers are shown on the right with map distances on the left. The furthest flanking markers that were previously assigned to the Brachypodium Chr 3 are indicated by dashed lines. The Bsr1 locus is indicated in red. The six markers located within the predicted Bd21 locus served as anchors to establish co-linearity between the Bsr1 genetic map and the physical map of Bd21. (c) Physical map of the Bsr1 interval. Annotated genes are indicated by arrows and candidate genes are indicated in green. Approximate locations (bp) are shown on the left.

Mentions: To refine the map position of Bsr1, six Indel markers and eight CAPS makers were developed based on whole genome resequencing data from the DOE Joint Genome Institute (Table 4). These markers were used to create a new genetic linkage map for the distal 700 kb of chromosome 3 and indicated that Bsr1 lies in a 0.7 cM interval between the XCAPS-5 and XCAPS-12 markers and co-segregates with the XCAPS-9 and XCAPs-11 markers (Figure 3). The genetic order of the markers in this region was consistent with their physical locations on Chr 3, indicating that the genome assembly is correct in this region. Thus, Bsr1 lies within an ∼23 kb genomic region that contains five gene models, Bradi3g00730, Bradi3g00740, Bradi3g00750, Bradi3g00757 and Bradi3g00767. BLAST and protein domain analysis of these gene models revealed that Bradi3g00730 is similar to a MADS-box transcription factor containing a SRF-TF domain; Bradi3g00757 has homology to a resistance gene whose putative product contains an NB-ARC domain and an LRR domain; Bradi3g00767 is related to an antifreeze protein; and Bradi3g00740 and Bradi3g00750, have no predicted function.


Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.

Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF - PLoS ONE (2012)

Genetic map of BSMV Bsr1 resistance within the distal region of Bd21 chromosome 3.(a)Cartoon of the short arm of Bd21 chromosome 3 (Chr3S). The white region shows 705 kb of distal region of Chr 3 encompassing the fine mapping region. (b)Genetic map of the 705Kb region of chromosome 3. Markers are shown on the right with map distances on the left. The furthest flanking markers that were previously assigned to the Brachypodium Chr 3 are indicated by dashed lines. The Bsr1 locus is indicated in red. The six markers located within the predicted Bd21 locus served as anchors to establish co-linearity between the Bsr1 genetic map and the physical map of Bd21. (c) Physical map of the Bsr1 interval. Annotated genes are indicated by arrows and candidate genes are indicated in green. Approximate locations (bp) are shown on the left.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3366947&req=5

pone-0038333-g003: Genetic map of BSMV Bsr1 resistance within the distal region of Bd21 chromosome 3.(a)Cartoon of the short arm of Bd21 chromosome 3 (Chr3S). The white region shows 705 kb of distal region of Chr 3 encompassing the fine mapping region. (b)Genetic map of the 705Kb region of chromosome 3. Markers are shown on the right with map distances on the left. The furthest flanking markers that were previously assigned to the Brachypodium Chr 3 are indicated by dashed lines. The Bsr1 locus is indicated in red. The six markers located within the predicted Bd21 locus served as anchors to establish co-linearity between the Bsr1 genetic map and the physical map of Bd21. (c) Physical map of the Bsr1 interval. Annotated genes are indicated by arrows and candidate genes are indicated in green. Approximate locations (bp) are shown on the left.
Mentions: To refine the map position of Bsr1, six Indel markers and eight CAPS makers were developed based on whole genome resequencing data from the DOE Joint Genome Institute (Table 4). These markers were used to create a new genetic linkage map for the distal 700 kb of chromosome 3 and indicated that Bsr1 lies in a 0.7 cM interval between the XCAPS-5 and XCAPS-12 markers and co-segregates with the XCAPS-9 and XCAPs-11 markers (Figure 3). The genetic order of the markers in this region was consistent with their physical locations on Chr 3, indicating that the genome assembly is correct in this region. Thus, Bsr1 lies within an ∼23 kb genomic region that contains five gene models, Bradi3g00730, Bradi3g00740, Bradi3g00750, Bradi3g00757 and Bradi3g00767. BLAST and protein domain analysis of these gene models revealed that Bradi3g00730 is similar to a MADS-box transcription factor containing a SRF-TF domain; Bradi3g00757 has homology to a resistance gene whose putative product contains an NB-ARC domain and an LRR domain; Bradi3g00767 is related to an antifreeze protein; and Bradi3g00740 and Bradi3g00750, have no predicted function.

Bottom Line: We generated an F(6:7) recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2) population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance.Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium.Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China.

ABSTRACT
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25 °C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F(6:7) recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2) population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.

Show MeSH
Related in: MedlinePlus