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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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Diagram of the sequential fine-mapping process. (A) The physical map of 17 polymorphic SSR markers available from MaizeGDB (http://www.maizegdb.org/) in the Scmv1 genome region, 2 of the 17 markers with ambiguous location were deleted. By assaying 177 unselected F2 plants, Scmv1 was narrowed to an 18.8 Mb interval flanked by SSRs umc1018 and umc1573. (B) The physical map of the Scmv1 region after fine-mapping with 28 recombinants and 13 new developed markers. (C), (D) The final physical maps of Scmv1, estimated by genotyping 15 recombinants between STS-15 and STS-5 using eight newly developed markers. The number on the left side of the chromosome segments correspond to the physical distance of AGPv2, the units of A, B, C and D were 1 Mb, 1 Mb, 10 kb, 1 kb, respectively. The numerals on the right side of the chromosome segments represent the number of recombinants between two flanking markers.
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Figure 1: Diagram of the sequential fine-mapping process. (A) The physical map of 17 polymorphic SSR markers available from MaizeGDB (http://www.maizegdb.org/) in the Scmv1 genome region, 2 of the 17 markers with ambiguous location were deleted. By assaying 177 unselected F2 plants, Scmv1 was narrowed to an 18.8 Mb interval flanked by SSRs umc1018 and umc1573. (B) The physical map of the Scmv1 region after fine-mapping with 28 recombinants and 13 new developed markers. (C), (D) The final physical maps of Scmv1, estimated by genotyping 15 recombinants between STS-15 and STS-5 using eight newly developed markers. The number on the left side of the chromosome segments correspond to the physical distance of AGPv2, the units of A, B, C and D were 1 Mb, 1 Mb, 10 kb, 1 kb, respectively. The numerals on the right side of the chromosome segments represent the number of recombinants between two flanking markers.

Mentions: Of 177 unselected F2 plants, 50 exhibited typical symptoms of SCMV infection within 2–3 weeks after the first inoculation. The numbers of resistant and susceptible plants segregated in a 3:1 ratio (χ2 = 0.83 < χ20.01, 1), in agreement with inheritance of a single dominant gene. Using the 17 polymorphic simple sequence repeat (SSR) markers available from the Maize Genetics and Genomics Database (http://www.maizegdb.org/) (Additional file 1), the Scmv1 locus was mapped between umc1018 and umc1753, with a physical distance of 18.80 Mb according to the B73 physical map (Figure 1A). Owing to the lack of high-density markers, 28 recombinants between these two markers could not be resolved. Accordingly, we developed 11 new markers (Table 1) based on the public maize Bacterial Artificial Chromosome (BAC) sequences accessible in GenBank at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov). We used these 11 new markers to resolve the 28 recombinants. Subsequent marker-phenotype analysis enabled us to progressively refine the Scmv1 region into a 710.97-kb interval between STS-5 and STS-15 (Figure 1B), with still two recombinants in between those two markers. Thereafter, the markers STS-5 and STS-15 were used to genotype 510 F2 susceptible plants, resulting in 13 new recombinants. Within the STS-5/STS-15 interval, single/low copy sequences were exploited to develop seven additional markers (Table 1). These markers were used to genotype 15 recombinants, which allowed us to delimit the Scmv1 locus into a 112.39-kb interval flanked by the two closest markers, R1-2 and STS-11 (Figures 1C and 1D). There were still six recombinants to the left and eight recombinants to the right side of the Scmv1 locus (Figure 1D). Comparison with the B73 physical map indicated that the two closest markers, R1-2 and the STS-11, reside on the adjacent BACs in GenBank: b0129G15 and b0598N23, respectively.


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)

Diagram of the sequential fine-mapping process. (A) The physical map of 17 polymorphic SSR markers available from MaizeGDB (http://www.maizegdb.org/) in the Scmv1 genome region, 2 of the 17 markers with ambiguous location were deleted. By assaying 177 unselected F2 plants, Scmv1 was narrowed to an 18.8 Mb interval flanked by SSRs umc1018 and umc1573. (B) The physical map of the Scmv1 region after fine-mapping with 28 recombinants and 13 new developed markers. (C), (D) The final physical maps of Scmv1, estimated by genotyping 15 recombinants between STS-15 and STS-5 using eight newly developed markers. The number on the left side of the chromosome segments correspond to the physical distance of AGPv2, the units of A, B, C and D were 1 Mb, 1 Mb, 10 kb, 1 kb, respectively. The numerals on the right side of the chromosome segments represent the number of recombinants between two flanking markers.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Diagram of the sequential fine-mapping process. (A) The physical map of 17 polymorphic SSR markers available from MaizeGDB (http://www.maizegdb.org/) in the Scmv1 genome region, 2 of the 17 markers with ambiguous location were deleted. By assaying 177 unselected F2 plants, Scmv1 was narrowed to an 18.8 Mb interval flanked by SSRs umc1018 and umc1573. (B) The physical map of the Scmv1 region after fine-mapping with 28 recombinants and 13 new developed markers. (C), (D) The final physical maps of Scmv1, estimated by genotyping 15 recombinants between STS-15 and STS-5 using eight newly developed markers. The number on the left side of the chromosome segments correspond to the physical distance of AGPv2, the units of A, B, C and D were 1 Mb, 1 Mb, 10 kb, 1 kb, respectively. The numerals on the right side of the chromosome segments represent the number of recombinants between two flanking markers.
Mentions: Of 177 unselected F2 plants, 50 exhibited typical symptoms of SCMV infection within 2–3 weeks after the first inoculation. The numbers of resistant and susceptible plants segregated in a 3:1 ratio (χ2 = 0.83 < χ20.01, 1), in agreement with inheritance of a single dominant gene. Using the 17 polymorphic simple sequence repeat (SSR) markers available from the Maize Genetics and Genomics Database (http://www.maizegdb.org/) (Additional file 1), the Scmv1 locus was mapped between umc1018 and umc1753, with a physical distance of 18.80 Mb according to the B73 physical map (Figure 1A). Owing to the lack of high-density markers, 28 recombinants between these two markers could not be resolved. Accordingly, we developed 11 new markers (Table 1) based on the public maize Bacterial Artificial Chromosome (BAC) sequences accessible in GenBank at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov). We used these 11 new markers to resolve the 28 recombinants. Subsequent marker-phenotype analysis enabled us to progressively refine the Scmv1 region into a 710.97-kb interval between STS-5 and STS-15 (Figure 1B), with still two recombinants in between those two markers. Thereafter, the markers STS-5 and STS-15 were used to genotype 510 F2 susceptible plants, resulting in 13 new recombinants. Within the STS-5/STS-15 interval, single/low copy sequences were exploited to develop seven additional markers (Table 1). These markers were used to genotype 15 recombinants, which allowed us to delimit the Scmv1 locus into a 112.39-kb interval flanked by the two closest markers, R1-2 and STS-11 (Figures 1C and 1D). There were still six recombinants to the left and eight recombinants to the right side of the Scmv1 locus (Figure 1D). Comparison with the B73 physical map indicated that the two closest markers, R1-2 and the STS-11, reside on the adjacent BACs in GenBank: b0129G15 and b0598N23, respectively.

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