The domesticated apple (Malus x domestica Borkh.), belonging to the Malus genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The domesticated apple (Malus x domestica Borkh.), belonging to the Malus genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The availability of genetic linkage maps, constructed by positioning molecular markers throughout the apple genome, enables the detection and analysis of major genes and quantitative trait loci (QTLs) contributing to the quality traits of a given genotype. herefore, the primary aim of this study was to construct a genetic linkage map of the Golden Delicious x Dietrich population for the identification of QTLs associated with fruit quality traits and then to examine the apple fruit pulp proteome with a specific focus on fruit firmness. In this regard, genomic DNA was extracted from leaves of the Golden Delicious x Dietrich population and used in megaplex PCR reactions. The PCR products were analysed prior to scoring of alleles. Polymorphic markers were then used to construct genetic linkage maps. The genetic linkage maps constructed in this study comprise of 167 simple sequence repeats (SSR) markers, 33 of these were newly developed markers...

This book covers information on the economics; botany, taxonomy, and origin; germplasm resources; cytogenetics and nuclear DNA; genetic improvement efforts of scion cultivars; genetic and genomic improvement efforts of rootstocks; genetic and physical mapping; genomic resources; genome and epigenome; regulatory sequences; utility of whole-genome sequencing and gene editing in trait dissection; flowering and juvenility; cold hardiness and dormancy; fruit color development; fruit acidity and sugar content; metabolomics; biology and genomics of the microbiome; apple domestication; as well as other ‘omics’ opportunities and challenges for genetic improvement of the apple. The cultivated apple (Malus x domestica Borkh.) is one of the most important tree fruit crops of temperate regions of the world. It is widely cultivated and grown in North America, Europe, and Asia. The apple fruit is a highly desirable fruit due to its flavor, sugar and acid content, metabolites, aroma, as well as its overall texture and palatability. Furthermore, it is a rich source of important nutrients, including antioxidants, vitamins, and dietary fiber.

The domesticated apple (Malus x domestica Borkh.) of the Rosaceae family is one of the most important commercial fruit worldwide. The quality of this pomaceous fruit is crucial to breeders and farmers as it ultimately determines its acceptance for consumption and determines shelf life. The introduction of marker-assisted selection has allowed hastening of traditional breeding. This book reports the first identification of QTLs associated with nine fruit quality traits using a linkage map derived from 'Golden Delicious' x 'Dietrich' population. These loci are of great importance for identification of candidate markers and characterization of genes associated with these quality traits that can be further exploited for new cultivar conception. The book also relates the use of proteomics for comprehensive characterisation of the fruit pulp proteome using 2D-PAGE. Through comparative proteomics analysis of high and low firmness fruits, mechanisms linked with fruit firmness were elucidated. The study sheds light on the mechanisms involved with fruit quality by combining proteomic, genomic and phenotypic data and further link crop biotechnology and fruit breeding.

This thesis is an investigation of the genetics of fruit quality in cultivated apple (Malus x domestica). M. x domestica is grown around the world as one of the most popular temperate fruit crop species. Fruit quality is an important trait in apples, and understanding the genetic architecture can accelerate breeding efforts. In recent years, several important quantitative trait loci have been discovered, including genetic regions controlling components of fruit texture, taste and flavour. The objective of this thesis was to identify genetic sources of variation in fruit quality traits with the potential for application in marker assisted apple breeding. This research was necessary to evaluate how previous findings corresponded with variation in genetically distinct apple germplasm, and to determine whether both previously and newly discovered fruit quality loci could be applied to improve the human perception of apple quality. The genetic relationships among 100 diverse apple cultivars were investigated using genotyping by sequencing, and revealed a high level of diversity. Signatures of selection were detected at genomic regions previously found to be associated with fruit quality and adaptation. A genome wide association study of 85 heritage and commercial cultivars detected significant associations with known quantitative trait loci for apple flavour and texture. A novel association for apple texture was detected on chromosome 13. The novel locus could not be validated in two large and diverse apple populations, but remains a strong candidate for use in apple breeding due to its association with the human perception of apple juiciness. The results of this thesis demonstrate the potential for applying marker assisted selection in apple breeding, and for including trained sensory evaluation panels in association studies.

Apple (Malus ©7 domestica Borkh.) is one of the most highly cultivated fruit crops grown around the world and apple consumption has been increasing over the years. One of the most important determinants of fruit quality is skin color. Red coloration in apple fruit is attributed to anthocyanin accumulation. Anthocyanins are encoded by structural genes, in the anthocyanin biosynthetic pathway, which are highly regulated by transcription factors. In this thesis, studies were conducted to identify and characterize structural genes and associated transcription factors involved in the anthocyanin biosynthetic pathway. Three genes encoding apple anthocyanin reductase gene (MdANR) were isolated, designated as MdANR1, MdANR2a, and MdANR2b. It is found that MdANR2a, and MdANR2b are in fact allelic. MdANR1 and MdANR2 were mapped to the apple linkage map on linkage groups (LG) 10 and 5, respectively. The functionality of MdANR gene was investigated following its overexpression in tobacco and found to influence flower color pigmentation and pattern. Overexpression of MdANR influenced other genes in the flavonoid biosynthesis pathway by down-regulating chalcone isomerase (CHI), dihydroflavonol reductase (DFR), and leucoanthocyanidin reductase (LAR) genes. Moreover, the observed loss of flower color in transgenic tobacco lines was attributed to reduction of anthocyanin pigments. This was likely due to down-regulation of tobacco CHI and DFR genes that are important in anthocyanin production. In addition, a new floral pigmented pattern was generated by incomplete inhibition of anthocyanin production. As expected, the epicatechin accumulated at higher levels in transgenic tobacco than in wild-type tobacco. However, higher amounts of catechin but lower levels of LAR, responsible for synthesis of catechin, were found in transgenic lines when compared to wild-type tobacco. Thus, it has been proposed that ANR plays a redundant role to that of LAR. A novel MYB transcription factor (TF) gene, designated as MdMYB11, was isolated and genetically mapped onto LG15 of the apple genetic map. Alignment of deduced amino acid sequences of MdMYB11 to those of other R2R3 MYB TFs revealed that this new apple transcription factor contains the R2R3 conserved domain. Moreover, this TF is highly similar to Arabidopsis MYB subgroup 4, such as AtMYB3, 4, and 6, by which they negatively regulate genes involved in monolignol biosynthesis. Functional analysis of MdMYB11 was conducted via ectopic expression in tobacco. Expression of MdMYB11 increased anthocyanin production in tobacco flowers by inducing several anthocyanin biosynthesis pathway genes, particularly those of CHI, chalcone synthase (CHS), and UDP-glucose: flavonoid 3-o-glucosyltransferase (UFGT). In addition, this TF functioned as a repressor of both cinnamate-4-hydroxylase (C4H) and 4-coumaroyl:CoA-ligase (4CL) genes, both important in lignin biosynthesis, and possibly contributing to modulation of floral morphogenesis. Moreover, transgenic flowers had longer styles than those of wild-type flowers, suggesting that the MdMYB11 gene might be involved in pistil development. New candidate TF genes regulating apple fruit coloration were identified following global gene expression analysis of the apple transcriptome using an apple microarray. Comparison of gene expression in fruit peel of apple cv. Red Delicious subjected to continuous 0́8dark treatment0́9 versus dark-grown fruit subjected to 0́814 h-light-exposure0́9 identified 815 genes that were modulated. Following annotation (to the Arabidopsis Gene Ontology), these genes were classified into 19 categories, and were mostly involved in primary metabolism (17%) and transcription (12%). Of these, 18 genes encoded for putative TFs. Further identification of color-related TFs was conducted by comparison of expression profiles of fruit of red skinned apple cv. Red Delicious and non-red skinned apple cv. Golden Delicious, and using quantitative real-time (RT)-PCR (qRT-PCR). Two putative TF genes were found to be expressed at higher levels in fruit of 0́8Red Delicious0́9 than that in 0́8Golden Delicious0́9, thus suggesting that these TFs might be involved in fruit coloration. Altogether, these findings have provided novel information and knowledge of the role(s) of genes and transcription factors involved in the anthocyanin biosynthesis pathway. Moreover, the regulator mechanism of fruit coloration has been further elucidated following transcriptome analysis of the apple genome and functional analysis of selected genes and transcription factors.

Fleshy Fruits are a late acquisition of plant evolution. In addition of protecting the seeds, these specialized organs unique to plants were developed to promote seed dispersal via the contribution of frugivorous animals. Fruit development and ripening is a complex process and understanding the underlying genetic and molecular program is a very active field of research. Part of the ripening process is directed to build up quality traits such as color, texture and aroma that make the fruit attractive and palatable. As fruit consumers, humans have developed a time long interaction with fruits which contributed to make the fruit ripening attributes conform our needs and preferences. This issue of Frontiers in Plant Science is intended to cover the most recent advances in our understanding of different aspects of fleshy fruit biology, including the genetic, molecular and metabolic mechanisms associated to each of the fruit quality traits. It is also of prime importance to consider the effects of environmental cues, cultural practices and postharvest methods, and to decipher the mechanism by which they impact fruit quality traits. Most of our knowledge of fleshy fruit development, ripening and quality traits comes from work done in a reduced number of species that are not only of economic importance but can also benefit from a number of genetic and genomic tools available to their specific research communities. For instance, working with tomato and grape offers several advantages since the genome sequences of these two fleshy fruit species have been deciphered and a wide range of biological and genetic resources have been developed. Ripening mutants are available for tomato which constitutes the main model system for fruit functional genomics. In addition, tomato is used as a reference species for climacteric fruit which ripening is controlled by the phytohormone ethylene. Likewise, grape is a reference species for non-climacteric fruit even though no single master switches controlling ripening initiation have been uncovered yet. In the last period, the genome sequence of an increased number of fruit crop species became available which creates a suitable situation for research communities around crops to get organized and information to be shared through public repositories. On the other hand, the availability of genome-wide expression profiling technologies has enabled an easier study of global transcriptional changes in fruit species where the sequenced genome is not yet available. In this issue authors will present recent progress including original data as well as authoritative reviews on our understanding of fleshy fruit biology focusing on tomato and grape as model species.

Apple (Malus x domestica Borkh.) is a long-lived woody perennial important to international markets. Development of new apple cultivars historically has been protracted and expensive, largely due to its biology. We believe that locating markers linked to traits of interest and marker-assisted selection (MAS) at the seedling stage could accelerate this process. Quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) for traits important to the sustainability and longevity of the Canadian apple industry, such as storage disorders, disease resistance, and fruit quality were conducted in three populations. Two QTL associated with the storage disorder soft scald were detected in the parental background of one F1 cross, but were not replicated across years, or when GWAS were conducted in a different population. Apple scab (Venturia ineaqualis [Cke.] Wint.) is a fungal pathogen that plagues growers in wet, humid climates, such as Nova Scotia. Significant genotype-phenotype GWAS associations were detected across seven different chromosomes for apple scab resistance in a germplasm collection of commercial cultivars. In the same population, GWAS also revealed SNPs associated with fruit quality traits, such as apple fruit skin colour and change in firmness during storage. Finally, a large, diverse germplasm collection and GWAS were used to explore flowering time and fruit quality. Significant marker-trait associations were found for flowering time in two years, but no clear candidate genes were identified. Fruit quality studies revealed several significant genotype-phenotype associations, including harvest date, fruit firmness, and acidity. This research will form the foundation of future studies for the development of markers that will assist with the development of new apple cultivars well-suited for Canadian and international markets.