Periodic Reporting for period 1 - PrunMut (Candidate mutation discovery in early-flowering mutants 'Rojo Pasión Precoz' and 'Bulida Precoz')
Periodo di rendicontazione: 2019-09-01 al 2021-08-31
Climate warming puts at risk fruit tree production in the coming decades in various temperate and subtropical regions throughout the world, especially in the Mediterranean basin. This risk is associated with the insufficient fulfillment of the essential chilling requirement for flowering and fruit set. Breeding for low-chill (early flowering) cultivars remains the most effective strategy to reduce this risk as chemical substitutes for chilling can only replace a small part of the requirements and have shown notable environmental issues. Still, breeding for low-chill in temperate fruit trees present drawbacks due to: 1) lack of early-flowering ecotypes in natural populations due to lower fitness regarding spring frost, 2) high-cost time-consuming breeding programs due to long juvenile period, planting layout and pollination system, 3) lack of extra-low chill cultivars in several species, 4) long-living cycle, so the favorable climate conditions are needed over a longer period than in annuals. Current breeding programs need more than 15 years, if favorable alleles are available, for creating and testing a new cultivar. Rapid development of temperate-fruit cultivars adapted to upcoming climatic conditions is advised, especially for species with scarce extra-low-chill commercial cultivars, such as apricot (Prunus armeniaca L.).
An advantageous alternative to traditional hybridization in breeding programs is the use of spontaneous (i.e. natural) mutants. The discovery of a favorable spontaneous mutation in a commercial cultivar is invaluable as it is already included in the cultivar genome and does not need to be introgressed. In relation to this, two spontaneous early-flowering apricot mutants ‘Rojo Pasión Precoz’ and ‘Búlida Precoz’ have been discovered in Southern Spain, derived from commercial cultivars. This unique plant material represents an excellent opportunity for deciphering the basis of early-flowering in apricot and to speed up the long-term breeding process for precocity as there is need to introgress other traits. PrunMut uses cutting-edge genomics tools to identify the candidate mutations responsible for early flowering in these spontaneous mutants. This action is expected to have a high impact in society and provide a proof-of-concept example that support the rapid adaptation of fruit industry to global warming.
PrunMut is aimed at (1) generating genomic resources for the identification candidate casual mutation in the two apricot mutants ‘Rojo Pasión Precoz’ and ‘Búlida Precoz’, also useful apricot breeding programs; (2) identifying candidate causal mutations of early flowering in the two mutants and shed light on mutation rate in this species; (3) evaluating the impact of the candidate casual mutation and give cues on the control of flowering date in the two mutants and (4) transfer of result for breeding and functional genomics. To develop markers for Prunus breeding programs aimed at early/late flowering date and to build collaborations for future functional genomics validation.
An advantageous alternative to traditional hybridization in breeding programs is the use of spontaneous (i.e. natural) mutants. The discovery of a favorable spontaneous mutation in a commercial cultivar is invaluable as it is already included in the cultivar genome and does not need to be introgressed. In relation to this, two spontaneous early-flowering apricot mutants ‘Rojo Pasión Precoz’ and ‘Búlida Precoz’ have been discovered in Southern Spain, derived from commercial cultivars. This unique plant material represents an excellent opportunity for deciphering the basis of early-flowering in apricot and to speed up the long-term breeding process for precocity as there is need to introgress other traits. PrunMut uses cutting-edge genomics tools to identify the candidate mutations responsible for early flowering in these spontaneous mutants. This action is expected to have a high impact in society and provide a proof-of-concept example that support the rapid adaptation of fruit industry to global warming.
PrunMut is aimed at (1) generating genomic resources for the identification candidate casual mutation in the two apricot mutants ‘Rojo Pasión Precoz’ and ‘Búlida Precoz’, also useful apricot breeding programs; (2) identifying candidate causal mutations of early flowering in the two mutants and shed light on mutation rate in this species; (3) evaluating the impact of the candidate casual mutation and give cues on the control of flowering date in the two mutants and (4) transfer of result for breeding and functional genomics. To develop markers for Prunus breeding programs aimed at early/late flowering date and to build collaborations for future functional genomics validation.
PrunMut is structured in four Work Packages (WPs). The work performed is as follows. The assemblies of heterozygous apricot tree Rojo Pasión (Campoy and Sun et al., 2020, Genome Biology; doi: 10.1186/s13059-020-02235-5) and the reference-guided assembly of Búlida have been generated (WP1). We have obtained a list of candidate mutations and validated the most promising ones by digital PCR (dPCR) (WP2), and created a time-course RNA-seq analysis which gives support to the validation of the candidate mutations (WP3). Collaborations have been stablished for the application in breeding and the functional validation of the most promising candidate mutations (WP4).
Results of this MSCA are reported in the already published article ‘Gamete-binning’ (Campoy and Sun, et al., 2020), and one national and three international conferences. The upcoming results of PrunMut will be reported in forthcoming research articles and presentation in international conferences.
Results of this MSCA are reported in the already published article ‘Gamete-binning’ (Campoy and Sun, et al., 2020), and one national and three international conferences. The upcoming results of PrunMut will be reported in forthcoming research articles and presentation in international conferences.
This MSCA has pushed forward the frontiers of fruit-tree breeding and genomics in a numerous ways. First, we have generated a method for assembling highly heterozygous species (Gamete-binning). Secondly, we have developed a method that allow the high-throughput evaluation of recombination by using single-cell sequencing. This, avoids tedious generation of offspring progeny and allows to sample the required material in its ecological context, which makes it possible to analyze meiotic recombination as it occurs in natural environments. Thirdly, we have generated the first haplotype-aware assembly of apricot, which is a tool that can foster the research in Prunus species by the scientific community and the development of new cultivars for the fruit industry. Lastly, we expect to present in forthcoming articles the results of the mutation identification and validation that will be available as Open Access.