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

Abstract

BackgroundAzalea (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.ResultsAn 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.ConclusionsThis 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.

AFLP-based genetic mapping of the “bud-flowering” trait in heather (Calluna vulgaris)

“…The number of polymorphic markers per primer pair was relatively low. In Rhododendron simsii hybrids, a genus also belonging to the Ericaceae, the number of polymorphic markers per primer combination was fivefold higher [14]. Hence, the reduced amount of polymorphism in C .…”

“…AFLP markers are sensitive to segregation distortion, but even highly distorted markers have been used to construct genetic maps in other species [14,19,20], as marker order and map length were not severely affected [21]. Segregation distortion might be a consequence of natural phenomena like e.g.…”

“…The major advantage of ML mapping compared to the RG algorithm is its reduced sensitivity to missing data, because neighbouring markers are used for approximation [30]. This is also beneficial when using not fully informative markers for genetic map construction [14] since the data set in this study was complete for all genotypes. In cross-pollinating species, the data set contains markers with different segregation types.…”

How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population

“…For this purpose, not only the expression profiles of the individual genes but also the discriminant functions will be used as a first step towards a priori eQTL mapping [86] on the genetic map of the population under study [87]. As such, the gene expression information will be used in a genetical genomics approach [78] to evaluate the impact of the entire pathway on the flower colour.…”

“…RNA was isolated from flower buds in the candle stage (25–30 mm) [23] of 70 siblings of the ‘GxH’ crossing population [87] and both parents (‘98-13-4’ and ‘Sima’). From each plant, two individual buds were sampled (a and b) as biological replicates.…”