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In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6–21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase.

Genomic selection (GS) has become an increasingly popular tool in plant breeding programs, propelled by declining genotyping costs, an increase in computational power, and rediscovery of the best linear unbiased prediction methodology over the past two decades. This development has led to an accumulation of extensive historical datasets with genotypic and phenotypic information, triggering the question of how to best utilize these datasets. Here, we investigate whether all available data or a subset should be used to calibrate GS models for across-year predictions in a 7-year dataset of a commercial hybrid sunflower breeding program. We employed a multi-objective optimization approach to determine the ideal years to include in the training set (TRS). Next, for a given combination of TRS years, we further optimized the TRS size and its genetic composition. We developed the Min_GRM size optimization method which consistently found the optimal TRS size, reducing dimensionality by 20% with an approximately 1% loss in predictive ability. Additionally, the Tails_GEGVs algorithm displayed potential, outperforming the use of all data by using just 60% of it for grain yield, a high-complexity, low-heritability trait. Moreover, maximizing the genetic diversity of the TRS resulted in a consistent predictive ability across the entire range of genotypic values in the test set. Interestingly, the Tails_GEGVs algorithm, due to its ability to leverage heterogeneity, enhanced predictive performance for key hybrids with extreme genotypic values. Our study provides new insights into the optimal utilization of historical data in plant breeding programs, resulting in improved GS model predictive ability.

In New Zealand grapevine propagation nurseries, Botryosphaeriaceae species have been reported to infect the source blocks of the nursery propagators leading to infection of the propagation materials. This research investigated the efficacy of different control methods which could prevent infection or eradicate the pathogen from harvested canes prior to plant propagation. In the source blocks, attempts to reduce infection of shoots by protecting trimming wounds were partially successful (P= 0.036), with 19.5% incidence in fungicide-treated shoots and 24.3% infection in the control shoots. Further sampling showed that overall 19.9% of these infections were in the bark and 9.6% in the wood. Hot water treatment (HWT) of dormant rootstock 5C canes, previously infected with Neofusicoccum luteum and N. parvum, at 50°C for 30 min resulted in internal infection incidences of 55 and 100%, respectively. HWT at 53°C reduced infection incidence to 0 and 8.5%, respectively, but killed the buds. In naturally infected canes, HWT of 50°C for 30 min reduced infection incidence from 35% in controls, to 0-15% over all Botryosphaeriaceae species. Shorter periods of HWT, at 55° for 10 min, designed to kill bark infections, were effective in Sauvignon blanc but killed the buds of Pinot noir. Sauvignon blanc canes superficially infected with N. luteum were soaked for 30 min in the fungicides carbendazim, tebuconazole, thiophanate methyl and flusilazole, with and without a polyether-modified trisiloxane adjuvant. Results showed that carbendazim with no adjuvant and tebuconazole with 0.5 mL L⁻¹ adjuvant eliminated 100% of bark infections. A further experiment that soaked 2,000 canes (Sauvignon blanc and Pinot noir) in a carbendazim solution prior to rooting found that all canes were free of Botryosphaeriaceae species infection, compared to 17% natural incidence. These results have indicated the potential efficacy of several methods for preventing or reducing infection Botryosphaeriaceae species in grapevine propagating materials.

Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γ ) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γ and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.

European agriculture faces major challenges in adapting and transforming current farming and food systems to become more sustainable. Agroecology is one transition pathway. However, what is lacking is assessing this transition with adequate tools and methodology. Here, we present the Original Agroecological Survey and Indicator System (OASIS) tool and apply it to farms in Belgium, France, and Italy as an illustration of its functionalities. In total, 53 conventional and organic farmers of three farming systems [crop production (CP); livestock production (LP), and mixed crop–livestock production (CLP)] were interviewed and data were collected for a large range of indicators (scoring from 1 to 5) across five dimensions: agroecological farming practices, economic viability, socio-political aspects, environment and biodiversity, and resilience. Overall, organic farms had slightly higher scores compared to conventional farms for the five dimensions. However, for the adoption of different agroecological practices, a clear difference was found, often with clearly higher scores for organic farms. There were also similar differences regarding most biodiversity and environment indicators and indicators for revenue and income sources. Farms that had higher overall farm scores also obtained a generally significantly higher mark for economic viability. Farmers described many parameters among the socio-political aspects dimension criteria, including several constraints that resulted in lower scores. Contrasting results for different criteria were found for the dimension of resilience, with some farms scoring higher for autonomy and independence from inputs and market, while others scored lower. As an operational result, overall, the OASIS tool proved applicable and useful in assessing agroecology at the farm level and some links beyond. However, further development could improve the tool.