Microbiome and genomic analysis in apple germplasm towards broadening genetic resources to breed for resilient varieties – AppleBIOME

Low agrobiodiversity and the reduced ability to respond to the increasing climate change-related stresses, are detrimental effects from the
current high-input agriculture. Commercial apple orchards are a prime example of intensive pesticide and irrigation practices that
counteract the EU’s ambitions to reduce external inputs and reverse agrobiodiversity degradation by 2030. In this context, new breeding
and management practices show high potential to break out of this vicious circle and allow the development of divers and resilient
agroecosystems that require less pesticides and irrigation. Breeding has been traditionally based on the phenotypic selection of segregating
populations. In the last decades, molecular markers and genomic selection have been implemented in breeding schemes. Such tools have
been mainly focused on genotype-trait associations. The plant-associated microbiome is long known for its vital contributions to crop
performance. However, agricultural practices and breeding have paid little attention to directly regulate and employ host-beneficial
microbial functions. AppleBIOME will investigate the combined action of host and microbiome genetics (holobiont approach) under high and
low-input management practices to boost the breeding for resilient varieties.
AppleBIOME relies in an exceptional germplasm resource representative of the broad genetic diversity of apple in Europe: «the Apple
REFPOP». The Apple REFPOP was designed and established as an output of the EU project FruitBreedomics and consists of 534 genotypes
(accessions and progenies) planted in 2016 following the same experimental design in six diverse biogeographical regions in Europe
(Belgium, France, Italy, Poland, Spain, and Switzerland) with a subset also being managed under low-input practices. The densely SNPgenotyped
Apple REFPOP has been successfully used to evaluate genomic predictive abilities of quantitative agronomic traits considering
genotype x environment interactions (GxE). AppleBIOME brings together the hosting institutions of the Apple REFPOP to add the
management component into the evaluation of the genetic mechanisms for the response to (a)biotic stresses. First, at each location, we will
acquire agronomic and disease related parameters (along with climatic data) for either of two management comparisons: high vs low
pesticide and high vs low water input. Genome-wide association analysis (GWAS) and genomic prediction models will (i) identify genomic
regions contributing to the stress response and (ii) estimate genomic predictive ability of the traits under environmental stress. Second, we
will analyze the phyllosphere microbiome in the Apple REFPOP at each site and management practice and in commercial orchards. Microbe
amplicon sequences will be analyzed to determine microbiome attributes such as diversity parameters, networks and key taxa that are
host-regulated and involved in stress resilience. GWAS and deep learning (DL) predictive models will then be performed to identify new loci
and candidate genes that regulate microbiome-mediate stress response. Resulting molecular markers and models will be evaluated
together with breeders for their suitability for direct use in current breeding schemes. As a whole, we will build on knowledge of the
holobiont functional diversity in apple orchards to exploit microbiome-mediated resistance. Finally, the knowledge gained will be
disseminated to stakeholders, and discussion forums will be created to weight the advantages, disadvantages, and challenges and ensure
the commercial uptake of the project outcomes. Via these close collaborations with the apple production industry and related dissemination
and exploitation activities, AppleBIOME will promote the development of novel varieties that can better respond to climate change-relevant
stresses and pave the way towards new agrobiodiversity-based breeding and cultivation systems.