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Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids).

De Keyser E, Shu QY, Van Bockstaele E, De Riek J - BMC Mol. Biol. (2010)

Bottom Line: As a result, plants with attractive flowering are kept too long in the breeding cycle.This is the first map of azalea up to our knowledge.AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Caritasstraat 21, 9090 Melle, Belgium. ellen.dekeyser@ilvo.vlaanderen.be

ABSTRACT

Background: Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed.

Results: An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed.

Conclusions: This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the recently published integrated maps and well-suited for mapping in a non-model crop.

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Collinearity of individual population maps (part 1). Alignment of the 16 linkage groups of the 4 integrated framework based population maps. Markers that are bold/in italic were used as bridging markers for the construction of the integrated framework map. Markers in red were bridging markers present in at least two population maps. Final maps were drawn in MapChart 2.2 [47]
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Figure 2: Collinearity of individual population maps (part 1). Alignment of the 16 linkage groups of the 4 integrated framework based population maps. Markers that are bold/in italic were used as bridging markers for the construction of the integrated framework map. Markers in red were bridging markers present in at least two population maps. Final maps were drawn in MapChart 2.2 [47]

Mentions: To overcome the observed grouping inconsistency for the individual mapping populations, the grouping results of the 4 populations were combined to a consensus grouping. Conflicting markers were finally assigned to the linkage group with the highest hit for getting mapped on the 4 populations. Quite often it was necessary to raise the LOD threshold for grouping in the individual mapping populations to uncouple groups of conflicting markers. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. Adjusting the JoinMap groupings in the individual mapping populations, most of the time allowed reducing the number of linkage groups to the chromosome number of 13. Nevertheless, this always yielded considerable groups of conflicting markers across populations; therefore 16 final consensus linkage groups were retained. On the individual population level however, AxB was reduced to 15 linkage groups and GxH to 13 (Figure 2, 3, 4, 5, 6 and 7).


Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids).

De Keyser E, Shu QY, Van Bockstaele E, De Riek J - BMC Mol. Biol. (2010)

Collinearity of individual population maps (part 1). Alignment of the 16 linkage groups of the 4 integrated framework based population maps. Markers that are bold/in italic were used as bridging markers for the construction of the integrated framework map. Markers in red were bridging markers present in at least two population maps. Final maps were drawn in MapChart 2.2 [47]
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837023&req=5

Figure 2: Collinearity of individual population maps (part 1). Alignment of the 16 linkage groups of the 4 integrated framework based population maps. Markers that are bold/in italic were used as bridging markers for the construction of the integrated framework map. Markers in red were bridging markers present in at least two population maps. Final maps were drawn in MapChart 2.2 [47]
Mentions: To overcome the observed grouping inconsistency for the individual mapping populations, the grouping results of the 4 populations were combined to a consensus grouping. Conflicting markers were finally assigned to the linkage group with the highest hit for getting mapped on the 4 populations. Quite often it was necessary to raise the LOD threshold for grouping in the individual mapping populations to uncouple groups of conflicting markers. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. Adjusting the JoinMap groupings in the individual mapping populations, most of the time allowed reducing the number of linkage groups to the chromosome number of 13. Nevertheless, this always yielded considerable groups of conflicting markers across populations; therefore 16 final consensus linkage groups were retained. On the individual population level however, AxB was reduced to 15 linkage groups and GxH to 13 (Figure 2, 3, 4, 5, 6 and 7).

Bottom Line: As a result, plants with attractive flowering are kept too long in the breeding cycle.This is the first map of azalea up to our knowledge.AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Caritasstraat 21, 9090 Melle, Belgium. ellen.dekeyser@ilvo.vlaanderen.be

ABSTRACT

Background: Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed.

Results: An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed.

Conclusions: This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the recently published integrated maps and well-suited for mapping in a non-model crop.

Show MeSH
Related in: MedlinePlus