In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Background: Gibberellins (GAs) can have profound effects on growth and development in higher plants. In contrast to their flowering-promotive role in many well-studied plants, GAs can repress flowering in woody perennial plants such as apple (MalusxdomesticaBorkh.). Although this effect of GA on flowering is intriguing and has commercial importance, the genetic mechanisms linking GA perception with flowering have not been well described.Results: Application of a mixture of bioactive GAs repressed flower formation without significant effect on node number or shoot elongation. Using Illumina-based transcriptional sequence data and a newly available, high-quality apple genome sequence, we generated transcript models for genes expressed in the shoot apex, and estimated their transcriptional response to GA. GA treatment resulted in downregulation of a diversity of genes participating in GA biosynthesis, and strong upregulation of the GA catabolicGA2 OXIDASEgenes, consistent with GA feedback and feedforward regulation, respectively. We also observed strong downregulation of numerous genes encoding potential GA transporters and receptors. Additional GA-responsive genes included potential components of cytokinin (CK), abscisic acid (ABA), brassinosteroid, and auxin signaling pathways. Finally, we observed rapid and strong upregulation of both of two copies of a gene previously observed to inhibit flowering in apple,MdTFL1(TERMINAL FLOWER 1).Conclusion: The rapid and robust upregulation of genes associated with GA catabolism in response to exogenous GA, combined with the decreased expression of GA biosynthetic genes, highlights GA feedforward and feedback regulation in the apple shoot apex. The finding that genes with potential roles in GA metabolism, transport and signaling are responsive to GA suggests GA homeostasis may be mediated at multiple levels in these tissues. The observation thatTFL1-like genes are induced quickly in response to GA suggests they may be directly targeted by GA-responsive transcription factors, and offers a potential explanation for the flowering-inhibitory effects of GA in apple. These results provide a context for investigating factors that may transduce the GA signal in apple, and contribute to a preliminary genetic framework for the repression of flowering by GAs in a woody perennial plant.

Hard cider, made by fermenting apple ( Malus × domestica ) juice, was at one time the most widely consumed alcoholic beverage in America. Largely abandoned after Prohibition, within the past 2 decades the rise in popularity of craft beverages has led to the reemergence of hard cider as an alternative to beer, wine, and spirits. Today, hard cider represents one of the fastest growing sectors within the craft beverage industry. The recent interest in cider presents additional marketing opportunities for apple growers and businesses currently involved in, or considering entering, the apple cider or craft beverages industries. However, the lack of a strong history or experience in selecting, producing, and using cider apples poses a significant challenge to this emerging market. This article reviews the current state of research in cider apple production, including economic feasibility, mechanized management, and cultivar evaluation and improvement.

SUMMARY: The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.

Pears (Pyrus) represent an important part of consumer diets, and have the fourth highest production of non-citrus fruits, measured by fresh weight, in the U.S. They are maintained clonally and grown as composite plants, consisting of a scion (fruit bearing) cultivar grafted onto a rootstock cultivar. Up to 98% of existing production relies on only a few scion and rootstock cultivars, leaving the standing crop vulnerable to threats. Pears are faced with a wide range of biotic and abiotic threats and production vulnerabilities, some of which can be limited by integrating resistance and horticultural traits from wild and cultivated materials from around the world. The National Clonal Germplasm Repository (NCGR Corvallis), part of the USDA-ARS National Plant Germplasm System, maintains a large Pyrus collection from across the globe, consisting of 2793 Pyrus accessions from 37 species. The collection represents an important resource for preservation, research, and breeding efforts for pears. The crop vulnerability status of pears in the U.S. is currently moderate to high, with increasing threats and challenges. Breeding and preservation efforts, along with genetic, crop protection and production research are, however, actively targeting these needs.

Societal Impact Statement: The production of hard cider is a burgeoning industry in North America. However, traditional European cider‐specific apples are largely unsuitable for production in modern systems and have not been widely adopted. Evaluation of the biochemical variability in apples can provide a better characterization of varieties for use in hard cider production. Many varieties exhibited extensive variability in biochemical traits. Varieties with high phenolics and acidity displayed greater plasticity of these traits between seasons, which supports the concept of “vintage quality” and opens new marketing opportunities. This study provides valuable insight for apple producers to integrate cider‐specific and nonspecific varieties into their production systems.Summary: The North American fermented beverage market has undergone extensive growth in the fermented apple juice (hard cider) sector over the last decade. Traditional hard cider producing regions such as England, France, and Spain have historically utilized cider‐specific apples that have desirable balances between sugar, organic acid, and phenolics. However, in North America, culinary apples (lower acidity and phenolics) are predominantly used, and information distinguishing the varieties with novel use for hard cider production is lacking. In this study, we evaluated variation of four major apple biochemical traits (total soluble solids, pH, titratable acidity, and total phenolics) as they relate to use for hard cider production by using a meta‐analysis approach. We analyzed the variation in cider quality traits across 47 published works and more than 800 unique apple varieties, including an additional analysis of 142 varieties from cider apple germplasms in the United States. The biochemical traits of many varieties exhibited plasticity, and the characterization of a subset of varieties using two cider classification system revealed that most belonged to the “sweet” or “sharp” (acidic) categories rather than “bitter” (high phenolic content). We also compared the classification of a subset of varieties from two US germplasm resources across two seasons and found varieties that have high percent phenolics and/or malic acid experienced greater biochemical plasticity and potential classification change across vintages. Ultimately, this work provides information regarding the variability in apple biochemical traits and also suggests a unique opportunity for producers to market “vintage” quality.