developed models allowed us to predict genotypic performance under different environmental stresses. This will be a key factor in the development of common bean varieties adapted to future challenging conditions.

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker–trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

Photosynthetic phenotyping requires quick characterization of dynamic traits when measuring large plant numbers in a fluctuating environment. Here, we evaluated the light-induced fluorescence transient (LIFT) method for its capacity to yield rapidly fluorometric parameters from 0.6 m distance. The close approximation of LIFT to conventional chlorophyll fluorescence (ChlF) parameters is shown under controlled conditions in spinach leaves and isolated thylakoids when electron transport was impaired by anoxic conditions or chemical inhibitors. The ChlF rise from minimum fluorescence ( F o ) to maximum fluorescence induced by fast repetition rate ( F m−FRR ) flashes was dominated by reduction of the primary electron acceptor in photosystem II (Q A ). The subsequent reoxidation of Q A − was quantified using the relaxation of ChlF in 0.65 ms ( F r1 ) and 120 ms ( F r2 ) phases. Reoxidation efficiency of Q A − ( F r1 / F v , where F v = F m−FRR − F o ) decreased when electron transport was impaired, while quantum efficiency of photosystem II ( F v / F m ) showed often no significant effect. ChlF relaxations of the LIFT were similar to an independent other method. Under increasing light intensities, F r2 ′/ F q ′ (where F r2 ′ and F q ′ represent F r2 and F v in the light-adapted state, respectively) was hardly affected, whereas the operating efficiency of photosystem II ( F q ′/ F m ′) decreased due to non-photochemical quenching. F m−FRR was significantly lower than the ChlF maximum induced by multiple turnover ( F m−MT ) flashes. However, the resulting F v / F m and F q ′/ F m ′ from both flashes were highly correlated. The LIFT method complements F v / F m with information about efficiency of electron transport. Measurements in situ and from a distance facilitate application in high-throughput and automated phenotyping. Electronic supplementary material The online version of this article (10.1007/s11120-018-0594-9) contains supplementary m...