The Multisite PeachRefPop Collection: A True Cultural Heritage and International Scientific Tool for Fruit Trees

euAP2a, a key gene that regulates flowering time in peach (Prunus persica) by modulating thermo-responsive transcription programming

Frequent spring frost damage threatens temperate fruit production, and breeding of late-flowering cultivars is an effective strategy for preventing such damage. However, this effort is often hampered by the lack of specific genes and markers and a lack of understanding of the mechanisms. We examined a Late-Flowering Peach (LFP) germplasm and found that its floral buds require a longer chilling period to release from their dormancy and a longer warming period to bloom than the control cultivar, two key characteristics associated with flowering time. We discovered that a 983-bp deletion in euAP2a, an APETALA2 (AP2)-related gene with known roles in regulating floral organ identity and flowering time, was primarily responsible for late flowering in LFP. This deletion disrupts an miR172 binding site, resulting in a gain-of-function mutation in euAP2a. Transcriptomic analyses revealed that at different stages of floral development, two chilling-responsive modules and four warm-responsive modules, comprising approximately 600 genes, were sequentially activated, forming a unique transcription programming. Furthermore, we found that euAP2a was transiently downregulated during the activation of these thermal-responsive modules at various stages. However, the loss of such transient, stage-specific downregulation of euAP2a caused by the deletion of miR172 binding sites resulted in the deactivation or delay of these modules in the LFP flower buds, suggesting that euAP2a acts as a transcription repressor to control floral developmental pace in peaches by modulating the thermo-responsive transcription programming. The findings shed light on the mechanisms behind late flowering in deciduous fruit trees, which is instrumental for breeding frost-tolerant cultivars.

Less is more: natural variation disrupting a miR172 gene at the di locus underlies the recessive double-flower trait in peach (P. persica L. Batsch)

BACKGROUND

With the domestication of ornamental plants, artificial selective pressure favored the propagation of mutations affecting flower shape, and double-flower varieties are now readily available for many species. In peach two distinct loci control the double-flower phenotype: the dominant Di2 locus, regulated by the deletion of the binding site for miR172 in the euAP2 PETALOSA gene Prupe.6G242400, and the recessive di locus, of which the underlying factor is still unknown.

RESULTS

Based on its genomic location a candidate gene approach was used to identify genetic variants in a diverse panel of ornamental peach accessions and uncovered three independent mutations in Prupe.2G237700, the gene encoding the transcript for microRNA miR172d: a ~5.0 Kb LTR transposable element and a ~1.2 Kb insertion both positioned upstream of the sequence encoding the pre-miR172d within the transcribed region of Prupe.2G237700, and a ~9.5 Kb deletion encompassing the whole gene sequence. qRT-PCR analysis confirmed that expression of pre-miR172d was abolished in di/di genotypes homozygous for the three variants.

CONCLUSIONS

Collectively, PETALOSA and the mutations in micro-RNA miR172d identified in this work provide a comprehensive collection of the genetic determinants at the base of the double-flower trait in the peach germplasms.

Genetic architecture and genomic predictive ability of apple quantitative traits across environments

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.

Genetic and phenotypic analyses reveal major quantitative loci associated to fruit size and shape traits in a non-flat peach collection (P. persica L. Batsch)

Fruit size and shape are critical agronomical and pomological attributes and prime targets in peach breeding programs. Apart from the flat peach type, a Mendelian trait well-characterized at the genetic level, ample diversity of fruit size and shapes is present across peach germplasms. Nevertheless, knowledge of the underlying genomic loci remains limited. In this work, fruit size and shape were assessed in a collection of non-flat peach accessions and selections, under controlled fruit load conditions. The architecture of these traits was then dissected by combining association and linkage mapping, revealing a major locus on the proximal end of chromosome 6 (qSHL/Fs6.1) explaining a large proportion of phenotypic variability for longitudinal shape and also affecting fruit size. A second major locus for fruit longitudinal shape (qSHL5.1), probably also affecting fruit size, was found co-localizing at locus G, suggesting pleiotropic effects of peach/nectarine traits. An additional QTL for fruit longitudinal shape (qSHL6.2) was identified in the distal end of chromosome 6 in a cross with an ornamental double-flower peach and co-localized with the Di2 locus, controlling flower morphology. Besides assisting breeding activities, knowledge of loci controlling fruit size and shape paves the way for more in-depth studies aimed at the identification of underlying genetic variant(s).

Identifying sources of metabolomic diversity and reconfiguration in peach fruit: taking notes for quality fruit improvement

The metabolomic content determines many of the important features of a fruit, such as its taste, flavor, color, nutritional value, and abiotic or biotic resistance. Peach (Prunus persica (L.) Batsch) is one of the best genetically characterized species used as a model for Rosaceae, the drupes of which are a source of minerals, vitamins, fiber, and antioxidant compounds for healthy diets around the world. During the last few years, a great advance in the analysis of the metabolic diversity and reconfiguration in different peach varieties in response to developmental and environmental factors has occurred. These studies have shown that the great phenotypic diversity among different peach varieties is correlated with differential metabolomic content. Besides, the fruit metabolome of each peach variety is not static; on the contrary, it is drastically configured in response to both developmental and environmental signals, and moreover, it was found that these metabolic reconfigurations are also variety dependent. In the present review, the main sources of metabolic diversity and conditions that induce modifications in the peach fruit metabolome are summarized. It is postulated that comparison of the metabolic reconfigurations that take place among the fruits from different varieties may help us better understand peach fruit metabolism and their key drivers, which in turn may aid in the future design of high‐quality peach fruits.

Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple

Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a gene controlling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorly understood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is therefore necessary. In this study, we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture. Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance (0.64). Predictions for biparental families using the entire training set varied from low to high accuracy, depending on the family considered. While adding siblings or half-siblings into the training set did not clearly improve predictions, we performed an optimization of the training set size and composition for each validation set. This allowed us to increase prediction accuracies by 0.17 on average, with a maximal accuracy of 0.81 when predicting firmness in the 'Gala' × 'Pink Lady' family. Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple. In particular, we advise to rely on a large training population, with high phenotypic variability from which a 'tailored training population' can be extracted using a priori information on genetic relatedness, in order to predict a specific target population.