Genetic mechanisms underlying alternate cropping in apple (Malus x domestica)
Final Report Abstract
The AlternApp project aimed at increasing the understanding of the physiological and molecular mechanisms involved in the control of flowering in apple. Genomics and conventional methods were applied in three different work packages (WP). The genetic determinism was addressed in WP1 using two segregating F1-populations (S x GS in France, and GD x R in Germany). The German population was phenotyped in 2013, 2015, 2016, 2017 and 2018. In 2014, only the number of inflorescences could be phenotyped, because spring frost resulted in the loss of all flowers. Since 2015, the population became increasingly infected by apple proliferation and was therefore re-grafted in 2016 with original trees being eradicated in 2018. As soon as the new trees will enter into the adult stage, phenotyping willcontinue. Existing phenotypic data were statistically analysed by the French partner. The GD x R population was genotyped using the Illumina Infinium 20K apple SNP array. A final genetic linkage map with a size of 1,190.6 cM was constructed, which consists of 5,879 markers. QTLs for the number of seeds per fruit were detected on linkage groups 3, 8, and 15 of the consensus map. As the work is delayed due to above mentioned reasons, phenotyping and QTL mapping will continue. The effect of physiological processes affecting alternate bearing was investigated in WP2. 130 trees of ‘Fuji’ (irregular) and ‘Royal Gala’ (regular) were half set to “OFF” and “ON” bearing status, respectively. Time series of spur buds for histology, gene expression profiling, RNA sequencing, as well as proteomic and metabolic profiling were collected. Microscopic results suggested that floral bud initiation was related to crop load. The transition from vegetative to floral meristems in apple buds differed markedly depending on variety and treatment. Using large-scale proteomic profiling 3,034 proteins were identified in buds from both treatments (“ON”/“OFF”). In buds from “ON”-trees, 130 proteins were significantly upregulated, whereas 95 proteins were upregulated in “OFF”-trees. Metabolic profiling resulted in more than 2,000 features with 159 being annotated as potential compounds (pre-identification). Fortyeight were filtered as fragments, but among the remaining 111 compounds, 23 were found to be significantly different between “ON” and “OFF” treatments. CG expression was studied in WP3. A classical RT-qPCR approach was performed on spur bud samples of 'Gala' and 'Fuji' plants to identify genes that could be used as markers for FI. Expression patterns of flowering time genes suggested a later FI for 'Gala' compared to 'Fuji'. Additionally, “OFF” plants seem to have an earlier FI compared to “ON” plants of the same cultivar. Among the genes tested, there was no gene, which could be used as a molecular marker for FI. Forty-three CGs retrieved from literature were validated using the Biomark HD system and a set of ’Golden Delicious’ samples harvested from spur buds of “ON” and “OFF” trees. Results revealed a range of genes with different expression patterns between “ON” and “OFF” trees (SEN1a, SEN1b, MIF1a, ASN1a, TEM1, MdMADS81_17, MIF1b, ERF1a, ASN1b, GA2oxb). Most interesting was the expression pattern of MdTFL1a. The expression of this gene increased from DOY 195 in “ON” trees, whereas in “OFF” trees its expression was mostly below the detection threshold. RNA sequencing resulted in more 50,000 genes expressed in apple buds. A preliminary analysis revealed 10,905 genes that are differentially expressed between “ON” and ”OFF” treatments. The complete RNAseq data set is currently being aligned to the new apple genome. The allelic variation in expressional CGs is currently under study using a DNA capture sequencing approach. This work will be continued in a collaboration between INRA Montpellier and JKI Dresden.
Publications
- AlternApp - Innovative Forschung zur Aufklärung der Alternanz bei Apfel. 50. Jahrestagung der Deutschen Gartenbauwissenschaftlichen Gesellschaft e.V. (DGG), 25 February 2015, Weihenstephan, Germany
Hanke M.-V., Flachowsky H., Wünsche J. N.
- AlternApp - Genetic mechanisms underlying alternate cropping in apple (M. x domestica). SPP1530 - 5th Annual Status Meeting and Workshop on Perennials, 06 September 2016, Siebeldingen, Germany
Flachowsky H.
- 2017. Apple bud histology: A tool to study floral bud development in relation to biennial bearing. DGG-Proceedings, Vol. 7, No. 7; p. 1-5
Milyaev A., Kofler J., Flachowsky H., Hanke M.-V., Wünsche J.-N.
(See online at https://doi.org/10.5288/dgg-pr-am-2017) - 2017. Biennial bearing in apple: Proteomic profiling of developing buds. DGG-Proceedings, Vol. 7, No. 8, p. 1-5
Kofler J., Milyaev A., Pfannstiel J., Flachowsky H., Hanke M.-V., Wünsche J.-N.
(See online at https://doi.org/10.5288/dgg-pr-jk-2017) - A European study on the time of flower induction in apple. 1st International Symposium on Flowering, Fruit Set and Alternate Bearing, 19- 23 June 2017, Palermo, Italy
Flachowsky H., Weigl, K., Djurić, G., Mićić, N., Garkava-Gustavsson, L., Zborowska, A., Si-Ammour, A., Asquini E., Sotiropoulos, T., Wünsche J.-N., Hanke M.-V.
- Apple bud histology: A tool to study floral bud development in relation to biennial bearing. 1st International Symposium on Flowering, Fruit Set and Alternate Bearing, 19-23 June 2017, Palermo, Italy
Milyaev A., Kofler J., Stefanelli, D., Flachowsky H., Hanke M.-V., Wünsche J.-N.
- Apple bud histology: A tool to study floral bud development in relation to biennial bearing. 51. German National Horticultural Science Convention, 1-4 March 2017, Osnabrück, Germany
Milyaev A., Kofler J., Flachowsky H., Hanke M.-V., Wünsche J.-N.
- Biennial bearing in apple: Proteomic profiling of developing buds. 1st International Symposium on Flowering, Fruit Set and Alternate Bearing, 19-23 June 2017, Palermo, Italy
Kofler J., Milyaev A., Pfannstiel J., Stefanelli, D., Flachowsky H., Hanke M.-V., Wünsche J.-N.
- Biennial bearing in apple: Proteomic profiling of developing buds. 51. German National Horticultural Science Convention, 1-4 March 2017, Osnabrück, Germany
Kofler J., Milyaev A., Pfannstiel J., Flachowsky H., Hanke M.-V., Wünsche J.-N.
- Physiological, metabolic and molecular basis of biennial bearing in apple. 1st International Symposium on Flowering, Fruit Set and Alternate Bearing, 19-23 June 2017, Palermo, Italy
Wünsche J.-N., Milyaev A., Kofler J., Stefanelli, D., Flachowsky H., Hanke M.-V.
- 2018. Histological and proteomic approaches to study floral bud induction in relation to biennial bearing in apple. Acta Horticulturae 1229, 277-283
Milyaev A., Kofler J., Pfannstiel J., Stefanelli, D., Flachowsky H., Hanke M.-V., Wünsche J.-N.
(See online at https://doi.org/10.17660/ActaHortic.2018.1229.42)
