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Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize.

Tao Y, Jiang L, Liu Q, Zhang Y, Zhang R, Ingvardsen CR, Frei UK, Wang B, Lai J, Lübberstedt T, Xu M - BMC Plant Biol. (2013)

Bottom Line: The combined results assigned the Scmv1 locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence.A presence/absence variation (PAV) in the Scmv1 region and two polymorphic sites around the Zmtrx-h gene were significantly associated with SCMV resistance.These results pave the way towards cloning of Scmv1 and facilitate marker-assisted selection for potyvirus resistance in maize.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, People's Republic of China. mxu@cau.edu.cn.

ABSTRACT

Background: Sugarcane mosaic virus (SCMV) disease causes substantial losses of grain yield and forage biomass in susceptible maize cultivars. Maize resistance to SCMV is associated with two dominant genes, Scmv1 and Scmv2, which are located on the short arm of chromosome 6 and near the centromere region of chromosome 3, respectively. We combined both linkage and association mapping to identify positional candidate genes for Scmv1.

Results: Scmv1 was fine-mapped in a segregating population derived from near-isogenic lines and further validated and fine-mapped using two recombinant inbred line populations. The combined results assigned the Scmv1 locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence. None of three predicted genes that are possibly involved in the disease resistance response are similar to receptor-like resistance genes. Candidate gene-based association mapping was conducted using a panel of 94 inbred lines with variable resistance to SCMV. A presence/absence variation (PAV) in the Scmv1 region and two polymorphic sites around the Zmtrx-h gene were significantly associated with SCMV resistance.

Conclusion: Combined linkage and association mapping pinpoints Zmtrx-h as the most likely positional candidate gene for Scmv1. These results pave the way towards cloning of Scmv1 and facilitate marker-assisted selection for potyvirus resistance in maize.

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Gene structure and LD pattern of the Scmv1 region across 94 maize inbred lines. All polymorphic sites with MAF ≥ 0.05 were used. In the gene diagram, filled black boxes represent exons, and open boxes indicate the UTRs. Dash-dot boxes mark the regions sequenced in this study. Polymorphic sties 1 to 5 are from the sequenced PCR product R1-2, 6 to 13 from A6, 14 to 20 from O1, 21 to 22 from 7–5, 23 to 25 from 2652F, and 26 to 30 from IDP11. The polymorphic sites and their locations on the gene diagram are connected by Dash-dot lines.
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Figure 4: Gene structure and LD pattern of the Scmv1 region across 94 maize inbred lines. All polymorphic sites with MAF ≥ 0.05 were used. In the gene diagram, filled black boxes represent exons, and open boxes indicate the UTRs. Dash-dot boxes mark the regions sequenced in this study. Polymorphic sties 1 to 5 are from the sequenced PCR product R1-2, 6 to 13 from A6, 14 to 20 from O1, 21 to 22 from 7–5, 23 to 25 from 2652F, and 26 to 30 from IDP11. The polymorphic sites and their locations on the gene diagram are connected by Dash-dot lines.

Mentions: To verify the candidate region and possibly refine the analysis by identifying quantitative trait nucleotide polymorphisms, we conducted an association mapping study using a panel of 94 inbred lines (Additional file 2), which were divided into six subgroups based on 70 SSR markers (Additional file 3). Multiple sequence alignment analysis identified 30 polymorphisms in six informative amplicons. Linkage disequilibrium (LD) analysis revealed lower r2 between these polymorphisms (Figure 4), with 91.03% of the r2 < 0.20. Two (single nucleotide polymorphism) SNP sites, S454 and S126, separately located on the 3′-end and intron of Zmtrx-h were significantly associated with SCMV resistance (P < 0.05; Table 4 and Additional file 4). Nonetheless, a low r2 value of 0.01 indicated two independent functional variants.


Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize.

Tao Y, Jiang L, Liu Q, Zhang Y, Zhang R, Ingvardsen CR, Frei UK, Wang B, Lai J, Lübberstedt T, Xu M - BMC Plant Biol. (2013)

Gene structure and LD pattern of the Scmv1 region across 94 maize inbred lines. All polymorphic sites with MAF ≥ 0.05 were used. In the gene diagram, filled black boxes represent exons, and open boxes indicate the UTRs. Dash-dot boxes mark the regions sequenced in this study. Polymorphic sties 1 to 5 are from the sequenced PCR product R1-2, 6 to 13 from A6, 14 to 20 from O1, 21 to 22 from 7–5, 23 to 25 from 2652F, and 26 to 30 from IDP11. The polymorphic sites and their locations on the gene diagram are connected by Dash-dot lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016037&req=5

Figure 4: Gene structure and LD pattern of the Scmv1 region across 94 maize inbred lines. All polymorphic sites with MAF ≥ 0.05 were used. In the gene diagram, filled black boxes represent exons, and open boxes indicate the UTRs. Dash-dot boxes mark the regions sequenced in this study. Polymorphic sties 1 to 5 are from the sequenced PCR product R1-2, 6 to 13 from A6, 14 to 20 from O1, 21 to 22 from 7–5, 23 to 25 from 2652F, and 26 to 30 from IDP11. The polymorphic sites and their locations on the gene diagram are connected by Dash-dot lines.
Mentions: To verify the candidate region and possibly refine the analysis by identifying quantitative trait nucleotide polymorphisms, we conducted an association mapping study using a panel of 94 inbred lines (Additional file 2), which were divided into six subgroups based on 70 SSR markers (Additional file 3). Multiple sequence alignment analysis identified 30 polymorphisms in six informative amplicons. Linkage disequilibrium (LD) analysis revealed lower r2 between these polymorphisms (Figure 4), with 91.03% of the r2 < 0.20. Two (single nucleotide polymorphism) SNP sites, S454 and S126, separately located on the 3′-end and intron of Zmtrx-h were significantly associated with SCMV resistance (P < 0.05; Table 4 and Additional file 4). Nonetheless, a low r2 value of 0.01 indicated two independent functional variants.

Bottom Line: The combined results assigned the Scmv1 locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence.A presence/absence variation (PAV) in the Scmv1 region and two polymorphic sites around the Zmtrx-h gene were significantly associated with SCMV resistance.These results pave the way towards cloning of Scmv1 and facilitate marker-assisted selection for potyvirus resistance in maize.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, People's Republic of China. mxu@cau.edu.cn.

ABSTRACT

Background: Sugarcane mosaic virus (SCMV) disease causes substantial losses of grain yield and forage biomass in susceptible maize cultivars. Maize resistance to SCMV is associated with two dominant genes, Scmv1 and Scmv2, which are located on the short arm of chromosome 6 and near the centromere region of chromosome 3, respectively. We combined both linkage and association mapping to identify positional candidate genes for Scmv1.

Results: Scmv1 was fine-mapped in a segregating population derived from near-isogenic lines and further validated and fine-mapped using two recombinant inbred line populations. The combined results assigned the Scmv1 locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence. None of three predicted genes that are possibly involved in the disease resistance response are similar to receptor-like resistance genes. Candidate gene-based association mapping was conducted using a panel of 94 inbred lines with variable resistance to SCMV. A presence/absence variation (PAV) in the Scmv1 region and two polymorphic sites around the Zmtrx-h gene were significantly associated with SCMV resistance.

Conclusion: Combined linkage and association mapping pinpoints Zmtrx-h as the most likely positional candidate gene for Scmv1. These results pave the way towards cloning of Scmv1 and facilitate marker-assisted selection for potyvirus resistance in maize.

Show MeSH
Related in: MedlinePlus