Mark Mazzola and Shashika S. Hewavitharana, USDA-ARS, USA

http://dx.doi.org/10.19103/AS.2018.0040.01Published by Burleigh Dodds Science Publishing Limited, 2019.

Chapter 1Understanding tree fruit–rhizosphere microbiome relationshipsAdvances in understanding tree fruit–rhizosphere microbiome relationships for enhanced plant healthMark Mazzola and Shashika S. Hewavitharana, USDA-ARS, USA

1 Introduction 2 Contribution of the microbiome in directing plant responses to their

environment 3 Case studies: manipulation of the rhizosphere microbiome to optimize

crop production on orchard replant sites 4 Conclusion 5 Future trends 6 Where to look for further information 7 References

1 IntroductionThe plant microbiome influences a spectrum of outcomes in terms of plant growth, development, resilience to abiotic stress and overall health and productivity. Contribution of the microbiome in directing plant responses to its environment and the instrumental role of host species or genotype in determining functional composition of the microbiome have been established (Berendsen et al., 2012; Mendes et al., 2013). The rhizosphere microbiome, in particular, may regulate important physiological and developmental processes that will directly determine plant productivity, some of which may be described as unanticipated. For instance, Panke-Buisse et al. (2015) demonstrated that the rhizosphere microbiome can modulate flowering time of a plant host and that flowering phenotype can be altered through manipulation of the rhizosphere microbiome. The rhizosphere microbiome clearly influences other qualities such as plant nutrient status through various processes such as nitrogen fixation, phosphorous acquisition via mycorrhizal fungi (Gianinazzi et al., 2010) and uptake of trace elements (Lemanceau et al., 2009).

Understanding tree fruit–rhizosphere microbiome relationships

© Burleigh Dodds Science Publishing Limited, 2019. All rights reserved.

Contents

Series list xAcknowledgements xvIntroduction xvi

Part 1 Stone and pome fruits

1 Advances and challenges in peach breeding 3Dario J. Chavez and Rachel A. Itle, University of Georgia, USA; Daniel Mancero-Castillo, Universidad Agraria del Ecuador, Ecuador; Jose X. Chaparro, University of Florida, USA; and Thomas G. Beckman, USDA-ARS, USA

1 Introduction 32 History of the cooperative regional moderate chill peach variety

development project 53 Case study: breeding for resistance to PFG 114 Future trends and conclusion 205 Where to look for further information 216 References 21

2 Advances and challenges in sustainable peach production 25Luca Corelli Grappadelli, Brunella Morandi and Luigi Manfrini, University of Bologna, Italy; and Pasquale Losciale, University of Bari, Italy

1 Introduction 252 Peach fruit growth and vascular flows 273 Photosynthesis: the engine of productivity 334 Precision fruit growing applications 425 Case study 456 Conclusion and future trends 467 Where to look for further information 478 References 47


vi Contents

3 Advances and challenges in cherry breeding 55José Quero-García, INRA, University of Bordeaux, France; Amy Iezzoni, Michigan State University, USA; Gregorio López-Ortega, IMIDA, Spain; Cameron Peace, Washington State University, USA; Mathieu Fouché and Elisabeth Dirlewanger, INRA, University of Bordeaux, France; and Mirko Schuster, Julius Kühn-Institut, Germany

1 Introduction 552 Main achievements in conventional breeding 583 Methodologies 634 Advances and key cultivars 675 New approaches 686 Phenotyping protocols 757 Future trends and conclusion 778 References 78

4 Sustainable sweet cherry cultivation: a case study for designing optimized orchard production systems 89Gregory A. Lang, Michigan State University, USA

1 Introduction – opportunities and challenges 892 Morphology, growth, and fruiting 923 Plant materials for sustainable production 1024 Tools for optimizing orchard tree development 1055 Designing optimized orchard production systems 1086 Mitigating abiotic and biotic risks to sustainable production 1167 Conclusions and future trends 1228 Where to look for further information 1239 References 123

5 Challenges and opportunities in pear breeding 129Danielle Guzman and Amit Dhingra, Washington State University, USA

1 Introduction 1292 Pear cultivars 1303 Pear rootstocks 1314 Germplasm resources 1335 Pear breeding techniques 1366 Improving particular traits 1397 Future trends 1468 Where to look for further information 1479 References 147


viiContents

6 Challenges and opportunities in pear cultivation 157Todd Einhorn, Michigan State University, USA

1 Introduction 1572 Mechanisms of flowering and pollination 1583 Chemical manipulation of flowering 1634 Chemical manipulation of fruit set 1655 Chemical manipulation of vegetative growth 1736 Physical manipulation of flowering and fruit set 1767 Rootstocks for high-density orchards 1848 Canopy training in high-density orchard systems 1889 Environmental factors that affect flowering, fruit set, and yields 191

10 Summary and future trends 19811 Where to look for further information 20012 References 201

7 Advances and challenges in apple breeding 217Amanda Karlström, NIAB EMR and University of Reading, UK; Magdalena Cobo Medina, NIAB EMR and University of Nottingham, UK; and Richard Harrison, NIAB EMR, UK

1 Introduction 2172 Shortening the breeding cycle and improving selection 2243 Increasing efficiency of production 2324 Mitigating production losses and waste 2365 Summary 2406 Future challenges 2417 Where to look for further information 2428 References 242

8 Advances and challenges in sustainable apple cultivation 261Pierre-Éric Lauri and Sylvaine Simon, INRA, France

1 Introduction 2612 Apple tree growth and fruiting 2623 Bases for sustainable apple training and pruning management 2684 Challenging the apple production agroecosystem 2705 Conclusion and future trends 2776 Where to look for further information 2797 References 279

9 Sustainable plum and apricot cultivation 289Mihai Botu, University of Craiova, Romania

1 Introduction 2892 Plum and apricot production 290


viii Contents

3 Genetic resources 2934 Environmental factors affecting plum and apricot cultivation 3005 Plum cultivation 3026 Prune and apricot cultivation 3067 Conclusion and future trends 3118 Where to look for further information 3129 References 312

Part 2 Berry fruits

10 Advances and challenges in strawberry genetic improvement 319Chris Barbey and Kevin Folta, University of Florida, USA

1 Introduction 3192 Threats and solutions to sustainable production 3213 Post-harvest quality 3314 Next steps in genetics 3325 High-throughput phenotyping 3356 Future trends in research 3367 Where to look for further information 3388 References 338

11 Strawberries: a case study of how evolving market expectations impact sustainability 347M. P. Pritts, Cornell University, USA; and T. M. Sjulin, formerly Driscoll Strawberry Associates, USA

1 Introduction 3472 Development of an annual strawberry production system 3483 Shifting markets 3514 Increasing inputs with expansion of annual production in

favourable locations 3525 Sustainability of the current model of strawberry production 3536 Future trends and conclusion 3567 Where to look for further information 3608 References 361

12 Advances and challenges in raspberry and blackberry breeding 363Ramón Molina-Bravo, Universidad Nacional de Costa Rica, Costa Rica; Margaret Leigh Worthington, University of Arkansas, USA; and Gina E. Fernandez, North Carolina State University, USA

1 Introduction 3632 Rubus traits for sustainability 3643 Molecular tools and resources for Rubus 370


ixContents

4 Future trends and conclusion 3815 Where to look for further information 3836 References 383

13 Advances and challenges in sustainable raspberry/ blackberry cultivation 397Julie Graham, Alison Karley, Alison Dolan, Dominic Williams and Nikki Jennings, James Hutton Institute, UK

1 Introduction 3972 Major pest and disease stresses that affect

Rubus production 3983 Environmental impacts on crop development 4044 Effects of climate change on bramble crop management and phenology 4085 Environmental stresses 4106 Conclusion and future trends 4127 References 413

14 Advances and challenges in blueberry breeding 423Susan McCallum, James Hutton Institute, UK

1 Introduction 4232 Breeding challenges today 4243 Genetic material and their uses in breeding programmes 4264 Advances in technology to aid phenotyping 4295 Marker-assisted breeding 4306 Review of how research can improve blueberry flavour 4317 Summary 4338 Future trends in research 4349 Where to look for further information 434

10 References 435

Index 441


IntroductionTemperate fruits include stone/drupe fruits (such as peach), pome fruits (such as apple) and berries (such as strawberries). Like other crops, cultivation of these fruits faces a number of challenges. These include the need to optimize yields, sensory and nutritional quality; the dynamic threats from biotic and abiotic stresses in a changing climate; the increasing cost and decreasing availability of labour; and the need for more efficient use of resources to minimise environmental impact. This second volume of Achieving sustainable cultivation of temperate zone tree fruits and berries includes case studies of individual fruits that illuminate the specific challenges they face and ways these are being addressed.

Part 1 Stone and pome fruitsThe first part of the volume summarises research in improving the production of stone and pome fruits. Chapter 1 addresses advances and challenges in peach breeding. Characteristics such as a relatively short juvenile period, self-pollination and small genome size have made peach a model fruit for breeding and genetics research. The chapter reviews the moderate chill peach variety development program involving the USDA-ARS, the University of Georgia and the University of Florida. It shows how the program addressed the challenge of developing new early season varieties using low chilling genotypes with the appropriate sensory quality and firmness required for long-distance shipping. As the chapter explains, the improved firmness realized by the shift to non-melting germplasm has made it possible to leave ripening fruit on the tree longer, resulting in improved fruit size and appearance as well as eating quality. The chapter also reviews ways of improving disease resistance, focusing on peach fungal gummosis (PFG). It describes the steps involved in developing interspecific hybrids with improved resistance, as well as progress in understanding the genetics of PFG resistance and linkage mapping for marker-assisted selection.

Chapter 2 shifts the focus from breeding to improving sustainability in peach production. By adopting precision management techniques, growers can reduce the environmental impact of fruit growing without sacrificing quality and yields, while maintaining income. The chapter discusses how improvements in sustainable peach production can be achieved by adopting an interdisciplinary approach. Research on plant physiology provides the foundations for mechanistic models to predict crop performance in real time, allowing growers to fine-tune their orchard management. The chapter


Introduction xvii

illustrates this by describing the importance of vascular flows to peach fruit growth, including factors such as vapour pressure deficit (VPD), and how this can be used to develop deficit irrigation programs, as well as mulches to reduce soil evaporation, to optimize both fruit development and water use. The chapter also reviews the latest research on the role of photosynthesis in peach production, including the effects of temperature, light and water availability. It shows how this understanding can be used to develop methods to modulate the light environment of the orchard (e.g. via shading hail nets) in order to reduce evapotranspiration, photoinhibition and heat stress which reduce yields. The chapter also discusses how recent advances in sensor technologies can be used, for example, to improve water stress management in peach crops.

Moving from peaches to cherries, the subject of Chapter 3 is advances and challenges in cherry breeding. Cherry breeding is currently carried out in many countries, by public and private programs, and sweet cherry cultivars are continuously being released. However, classification into clear-cut groups of existing cultivars is difficult, because there is a vast continuum of morphological diversity and many traits are influenced by differences in environmental factors among growing locations, including climate and soil characteristics as well as cultural practices. Despite the high number of available commercial cultivars, both sweet and sour cherry cultivation are still based on a small number of cultivars. After offering a historical overview of cherry breeding, the chapter describes the main achievements in conventional breeding, before considering methodologies and the latest advances and key cultivars. The chapter considers new approaches and phenotyping protocols.

Continuing to examine cherries, the subject of Chapter 4 is advances and challenges in sustainable cherry cultivation. Sweet cherries are an inherently challenging crop to produce sustainably, given the significant risks of crop loss from weather events, birds, insects and diseases, and requiring extensive manual labour due to large tree canopies and small delicate fruits. Nevertheless, cherry production has increased dramatically worldwide for the past two decades, driven by strong consumer demand and innovations in plant materials, efficient orchard training systems, orchard microclimate modification technologies, and improved physiological knowledge. The chapter examines the optimization of orchard tree development and fruit yields/quality by developing a foundational understanding of cherry morphology, growth, fruiting, cultivars and rootstocks, and how to utilize these components to re-design canopy architecture and orchard production systems for more labour-efficient, sustainable production.

Moving from cherries to pears, Chapter 5 considers advances and challenges in pear breeding. Although pear (Pyrus spp.) is an economically important fruit worldwide, pear cultivars and production practices have been among the slowest of the temperate fruits to change to meet modern


Introductionxviii

consumer demands and labour-efficient orchard production. In the USA, the majority of the pear orchards are low-density plantings with large trees of long-standing cultivars that can reach up to 15 feet in height. Large vigorous trees require labour-intensive management and are relatively inefficient in terms of application of inputs such as water, pesticides, and bio-regulators. The chapter reviews the range of pear cultivars and pear rootstocks, and includes a discussion on germplasm resources. Breeding techniques and improvement of particular traits are considered, including dwarfing, precocity, cold hardiness, fire blight resistance, tree architecture and self-incompatibility.

Staying with the theme of pears, Chapter 6 examines advances and challenges in sustainable pear cultivation. Excessive vigour of European pear varieties and a dearth of dwarfing rootstocks pose significant challenges to the establishment and management of modern high-density orchards. The pronounced negative relationship between pear tree vigour and precocity requires intensive horticultural intervention to expedite a return on investment and to achieve maximum yield potential. Plantings of low to moderate tree densities are no longer economically sustainable given their characteristically inconsistent fruit quality and suboptimal yields. Nascent technologies and novel horticultural strategies have the potential to balance reproductive and vegetative development of pear trees and facilitate the cultural management of high-density orchards. The chapter provides a review of pear floral biology, and fruit setting habits and their complex interaction with environmental factors, along with practical horticultural strategies to promote balanced canopies.

Passing from pears to apples, Chapter 7 examines advances and challenges in apple breeding. Breeding new apple varieties is costly and time-consuming, often selecting for consumer-preference traits at the expense of other traits of agronomic importance. However, combining both sustainable cultivation with market acceptability would benefit growers, consumers and the environment. The chapter summarises the current status of apple breeding and genomics research, taking a forward look at the key factors that may improve selection efficiency within apple breeding programmes to simultaneously enhance both resource use efficiency traits and resilience to biotic and abiotic stress. The chapter discusses how coupling enhanced automated phenotyping, rapid cycling through generations, genome-assisted selection and genome editing using CRISPR-Cas9 can improve breeding programme productivity. The chapter also covers advances in genetic characterization of key rootstock traits.

Chapter 8 deals with advances and challenges in sustainable apple cultivation. Developing sustainable apple cultivation is dependent on both a better knowledge of tree architecture and physiology in relation to fruiting, and on how the tree interacts with its abiotic and biotic environments. Improving knowledge in these areas is crucial to take into account for more sustainable, low-input production. The chapter provides an overview of apple tree growth


Introduction xix

and fruiting, and explores methods for more sustainable apple training and pruning management.

The final chapter of the section, Chapter 9, addresses advances and challenges in sustainable plum and apricot cultivation. Sustainable fruit cultivation may depend on the combination of a number of factors, including optimal growing conditions, correct selection of cultivars and rootstocks, and application of modern crop cultivation techniques. Sustainability also implies promotion of biodiversity, improvement of microbiological processes in the soil, and protection of the environment (e.g. by avoiding pollution from fertilizer and pesticide run-off). It has been estimated that fruit production may need to increase two- to three-fold to meet future demand, but this needs to be achieved in a sustainable way. The chapter explores ways this might be achieved for plum and apricot production. The chapter covers the genetic resources available for cultivation of these fruits, and the environmental factors affecting plum and apricot cultivation.

Part 2 Berry fruitsThe second part of the volume summarises challenges for sustainably cultivating berry fruits. Chapter 10 is focussed on advances and challenges in strawberry breeding. The commercial strawberry (Fragaria × ananassa) is a popular temperate fruit that is both nutritious and widely appreciated for flavour. The chapter highlights some of the newest innovations in strawberry production, with particular emphasis on genetic improvement of the crop. The trend for developing more robust and sustainable strawberry cultivated varieties via genetics is discussed in detail and useful technologies are reviewed, including high-throughput genotyping and quantitative trait locus (QTL) analysis, targeted sequence capture, third generation sequencing and expression QTL studies. High-throughput phenotyping is also covered, which is an increasingly important area of interest, both to improve breeding through traditional selection and for integration with genomics data for discovery of novel traits.

Going into greater depth on strawberries, Chapter 11 is a case study of how evolving market expectations impact strawberry sustainability. The strawberry industry is facing the reality that it has been built on an unsustainable foundation. First, water is increasingly scarce in some of the key regions where strawberries are grown. Aquifers continue to be depleted and land is subsiding in some areas as water is withdrawn. The chapter offers a case study of the impact of market expectations on the US strawberry industry. After an introductory survey of the history of strawberry production in the USA, the chapter examines the development of an annual strawberry production system. This includes looking at the impact of shifting markets on the sustainability of strawberry production


Introductionxx

and the challenge of increasing inputs with expansion of annual production in favorable locations. Finally, the chapter assesses the sustainability of the current model of strawberry production.

The subject of Chapter 12 is advances and challenges in raspberry and blackberry breeding. Raspberries and blackberries (Rubus spp.) are important fruit crops with increasing levels of production. The chapter focuses on key challenges in achieving more sustainable production, the tools available to breeders, and the future of breeding for sustainability of raspberry and blackberry crops. The chapter examines desirable traits for sustainability, molecular tools and resources.

Continuing to focus on brambles, Chapter 13 considers advances and challenges in sustainable raspberry/blackberry cultivation. Rubus crops are important for human health and for rural economies. As demand for these berry crops increases at a time of changing climate and increasing consumer concerns about sustainability, new breeding strategies and cultivation practices are needed. The chapter addresses some of the challenges and solutions to continued sustainable growth, including managing pest and disease stresses and the effects of climate change, as well as reducing environmental impacts.

The volume’s concluding chapter, Chapter 14, deals with advances and challenges in blueberry breeding, There is a growing body of research on the biological processes underlying key physiological traits in blueberry (Vaccinium corymbosum). Studies have shown high levels of genetic diversity are present within this species, much of which remains to be harnessed. The chapter introduces both the recent advances and current challenges in the breeding of blueberries, with particular focus on demand and production in the UK. Key cultivars currently used in the industry are listed and their advantages and disadvantages are discussed. The genetic material available and its use in breeding programmes is covered, including crossing with other species within the genus Vaccinium to obtain desirable traits. The chapter includes sections on phenotyping and marker-assisted breeding, and an extensive discussion on the improvement of flavour in blueberry is also provided.

http://dx.doi.org/10.19103/AS.2018.0040.15© Burleigh Dodds Science Publishing Limited, 2019. All rights reserved.

Chapter 1Advances and challenges in peach breedingDario J. Chavez and Rachel A. Itle, University of Georgia, USA; Daniel Mancero-Castillo, Universidad Agraria del Ecuador, Ecuador; Jose X. Chaparro, University of Florida, USA; and Thomas G. Beckman, USDA-ARS, USA

1 Introduction 2 History of the cooperative regional moderate chill peach variety

development project 3 Case study: breeding for resistance to PFG 4 Future trends and conclusion 5 Where to look for further information 6 References

1 IntroductionThe genus Prunus belongs to the family Rosaceae and contains approximately 230 species divided into five subgenera: Prunophora (Prunus), Amygdalus, Cerasus, Padus and Laurocerasus (Rehder, 1940), which includes peaches and nectarines (Prunus persica), plums (P. salacina and P. domestica), cherries (P. avium and P. cerasus), almonds (P. dulcis) and apricots (P. armeniaca). In 2015, the production of Prunus edible fruits and seeds surpassed 43 million metric tons with production found across Asia, Europe, North America, South America, Australia and South Africa (FAOSTAT, 2016).

Peach is a member of subgenus Amygdalus, which includes almond, Gansu peach (P. kansuensis), Tibetan peach (P. mira), mountain peach (P. davidiana) and P. ferganensis. These species are sexually compatible with each other and produce viable and fertile hybrids (Martínez-Gómez et al., 2003). Prunus breeding programmes have used hybridization among these species for improvement of genetic resistance to insect, nematodes and pathogens (Gradziel et al., 2001).

The centre of origin and domestication for peach and almond is southeastern and eastern Asia (Hedrick, 1911). Peach domestication dates back to more than 4000 years with peach genetics evolving by inbreeding, random

Advances and challenges in peach breeding Advances and challenges in peach breeding

Advances and challenges in peach breeding4


drift from a reduced number of founders in the breeding programmes and heterosis (Faust and Timon, 2010; Li et al., 2013). During peach domestication in China, three main groups were recognized (Scorza and Okie, 1991; Wang, 1985). The southern group of peaches are found along the Yangtze River in the provinces of Jiangsu, Zhejiang, Jiangxi, Hubei, Hunan and Sichuan, and are characterized by their adaptation to mild winters and hot wet summers, similar to the climate of the southeastern United States. The northern group is found along the Yellow River in Shandong, Hebei, Henan, Shanxi, Shaanxi and Gansu provinces, and are characterized by their adaptation to cold winters and hot dry summers. The third group is adapted to arid northwest China.

From China, peaches were spread through Persia to Europe by the Romans (Scorza and Okie, 1991; Wang, 1985). Peaches made their way to North America via Spanish explorers, first through St. Augustine, Florida, United States, and Mexico (Scorza and Okie, 1991), and then were spread by Native Americans. These peaches were early ripening yellow non-melting flesh types. Later, an additional introduction occurred in the 1800s by the French and English, who brought white melting flesh peaches to the United States. However, all these materials lacked commercial quality (Scorza and Okie, 1991; Sharpe et al., 1954; Sherman et al., 1996; Wang, 1985). The first superior peach varieties in the United States came in the late 1800s and early 1900s from peach producers who identified and selected chance seedlings recovered from open pollinated (OP) seed of plants grown on their farms (Floyd, 1920; Layne and Bassi, 2008). Once these first selections were made and their superior benefits during production were observed, breeding and selection started in state and federal breeding programmes using hybridization between desired parents. However, cultivation and commercialization in the United States did not change until 1850, with the introduction of a superior cultivar, ‘Chinese Cling’, from China. After that, other superior cultivars followed ‘Chinese Cling’, such as its OP seedlings ‘Georgia Belle’ and ‘Elberta’ (Scorza and Okie, 1991). ‘Elberta’ had been widely used as a breeding parent in peach breeding programmes across the United States and can be found in the pedigree of most commercial peaches (Layne and Bassi, 2008; Scorza and Okie, 1991; Wang, 1985).

The diverse climates and growing regions in which peaches are grown successfully, plus its relatively short juvenile period (2–3 years), self-pollinated behaviour, small genome size and the identification of important Mendelian traits, have made peach a model fruit for breeding and genetics research (Abbott et al., 2002; Bielenberg et al., 2009). The assembled peach scaffolds cover nearly 99% of the peach genome and over 92% of its orientation has been confirmed. Furthermore, 74 757 Prunus ESTs have been queried against the genome at 90% identity and 85% coverage. The peach reference genome contains 27 852 predicted protein-coding genes with a mean percentage of between about 60% A + T bases and 40% G + C [(A+T)/(G+C): 1.5] (Verde et al.,


Advances and challenges in peach breeding 5

2013). This GC content is slightly higher than that observed in other species such as Arabidopsis thaliana (about 36%), indicating relatively high stability and high percentage of protein-coding genes (Verde et al., 2013).

There are a number of public and private peach breeding programmes in the United States, and their geographic locations and chilling requirements generally are classified as northern (high-chill), western (mid- to high-chill), southern-central (mid-chill) and southern (low-chill) (Layne and Bassi, 2008). In this context, few breeding programmes have focused on mid- and low-chill variety development in the United States until recently.

2 History of the cooperative regional moderate chill peach variety development project

A moderate chill peach breeding project commenced in 1986 as a cooperative regional effort involving the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS, Byron, Georgia), the University of Georgia (Tifton and, later, Griffin, Georgia) and the University of Florida (Gainesville, Florida). Originally, the project’s evaluation site was located near Quitman, Georgia, but was moved in 1991 to its current location at the University of Georgia Research and Education Center outside of Attapulgus in southwest Georgia. The main goal of this collaboration is to develop new peach and nectarine varieties adapted to the lower coastal plain shipping industry of the southeastern United States. Potentially this geographical area is broad, running from coastal South Carolina southward and then westward across South Georgia and north Florida following the Gulf coast west into Texas and then south to the Mexican border. At present, the primary production centre is in South Georgia along its border with Florida, with the largest production volume typically coming from the Quitman area in Brooks county. At the time the project started, this production area was usually the first long-distance shipping industry to send peaches to market in the spring, typically commencing in late April or early May. This industry, though small, representing at most ~5% of Georgia’s peach acreage in the 1990s (Hubbard et al., 1998), has, nevertheless, significant economic impact due to the premium paid for early season fruit. Nonetheless, there was little breeding support in terms of new variety development, and the industry relied primarily on two varieties, ‘Flordaking’ and ‘June Gold’, for much of its production volume. Both of these varieties were produced as spin-offs by breeding programmes (the University of Florida and Armstrong Nurseries in California, respectively) focused on distinctively different production areas and markets.

2.1 Breeding priorities and approach

The cooperative regional breeding project is focused on the development of early season fresh market varieties. Hence, they must meet minimum size

Advances and challenges in peach breeding6


and appearance requirements, and also possess sufficient firmness for long-distance shipping. Quality is important, but the varieties this industry relied upon initially, like most early season varieties in other production areas, presented a decidedly ‘low bar’ with respect to quality. Initially, fruit smaller than 2 inches were occasionally accepted in the market (though at a much-reduced price); however, over time, fruit smaller than 2.25 inches were no longer marketed due to consumer preferences for larger fruit. Breeding to improve size, appearance and quality is straightforward in its approach, relying primarily on careful selection of breeding parents that offer improvements in one or more desired characteristics, but whose weak points can be offset by the other parent used in the cross.

The market window that this industry targets is both narrow, typically just six weeks in duration, and early, starting in late April and running through the end of May when the main production areas in central Georgia and South Carolina typically begin to ship in volume. Addressing these two issues requires careful manipulation of chilling requirement (which in turn largely determines bloom date) and fruit development period (days from bloom to harvest). Appropriate chilling requirement genetics are important in order to minimize spring frost risk and to adequately break endodormancy for a strong bloom and vegetative bud break. Low chilling requirement genotypes can ensure routine fulfilment of chilling requirement in this climatic region (nominally USDA zone 8b-9), but also are at risk of blooming too early and suffering frequent crop losses to spring frosts. Conversely, while higher chilling requirement genotypes might delay bloom and thereby ensure little or no spring frost damage in most years, they risk the possibility of inadequate breaking of endodormancy in low-chill years, resulting in delayed and extended bloom during warmer weather and possibly incompletely formed flowers that result in low fruit set and poor fruit shape. Additionally, a substantial bloom delay typically translates into a delayed harvest date, thereby potentially creating a gap in the production stream, possibly missing the variety’s market window altogether.

The general rule for selecting varieties appropriate to a production area is to choose those with a chilling requirement no higher than 75% of the long-term (i.e. 50 years) chilling average (to ensure regular breaking of endodormancy) and no lower than 50% of the long-term chilling average (to avoid spring frost injury). In practice this is not always as easy as it sounds; recent winters have varied significantly from the long-term average (~675 chill hours) at the project’s evaluation site in Attapulgus (T.G. Beckman, unpublished data). The long-term chilling average suggests that a chilling requirement between 350 and 500 chill hours is desirable; however, over the last 10 years, the average chill accumulation has declined to 590 chill hours, suggesting a range of 300–450 h might be more prudent.


Advances and challenges in peach breeding 7

As a rule, early ripening fruit (with a typically short fruit development period) softens more quickly than does mid- or late-season fruit (Beckman and Krewer, 1999). This issue was initially a major problem for the moderate chill peach breeding project. The first crosses were made with conventional melting flesh-type germplasm like that used in most fresh market peach breeding programmes. However, when the fruit development period was shortened to hit the needed harvest window, it resulted in progeny that often were too soft for shipping and were, therefore, discarded. The resultant heavy culling of the hybrid seedling populations profoundly slowed progress and nearly caused the project to collapse (Rahn, 1997). The search for an alternative strategy focused on other flesh types, such as stonyhard (a novel ‘non-ripening’ type) and non-melting (a ‘slow to soften’ type typically used in the development of processing peaches). Both were tried initially, but non-melting germplasm proved more useful and adaptable to the development of fresh market types, which thereby moved the project forward. It is now being augmented by slow ripening ‘crispy’ types (as exemplified by ‘Big Top’ nectarine) which provide excellent firmness as fruit approach ripeness. Crispy types are superior to the typical melting type, but then ultimately soften in the hands of consumers to a product similar to that provided by main season melting-type varieties.

Disease resistance is also a breeding priority. Bacterial spot (Xanthomonas campestris pv. pruni) is of primary importance in most Eastern U.S. breeding programmes, given its potential to significantly degrade the marketability of a crop. Unfortunately, test years for bacterial spot resistance are quite variable for screening germplasm. Nonetheless, the programme utilizes several highly susceptible selections as sentinels for high disease pressure. Peach fungal gummosis (PFG), incited by Botryosphaeria dothidea is another disease endemic to the southeastern U.S. peach industry with the potential to cause yield losses of 25–40% with susceptible cultivars (Beckman et al., 2003; Ezra et al., 2017). This disease pressure is particularly strong in the hot and humid lower coastal plain. Periodic evaluation of cultivar releases and advanced breeding lines for susceptibility to PFG has been the standard methodology in breeding programmes (Beckman and Reilly, 2005; Beckman et al., 2011). However, the recent identification of potential markers for resistance to this debilitating disease (Mancero-Castillo et al., 2018) should allow more rapid elimination of selections and potential breeding lines having unacceptable susceptibility.

Tree architecture is a recent, increasingly interesting genetic selection priority in this programme, which was prompted by the discovery of a distinctive spur-type growth habit in a hybrid population that presented a much more open canopy form that required substantially less pruning than normal types (T.G. Beckman, personal observation). Although the inheritance of this trait is still not fully characterized, it appears to be a suite of traits under the control of


Index

3D camera system 3353-D canopy models 1923D imaging 3356-benzyladenine (BA) 169, 175–176

ABA. see Abscisic acid (ABA)‘Abbe Fetel’ 193Abscisic acid (ABA) 170, 171–172, 189‘Achat’ 61Affymetrix IStraw35 Axiom® SNP array 333AFLPs. see Amplified fragment length

polymorphisms (AFLPs)Agricultural Research Service (ARS) 5, 14,

17, 136, 275‘Agriculture and Agri-Food’ breeding

programme 67Agroclimate Strawberry Advisory

System 329Agroforestry systems 271AI. see Artificial intelligence (AI)Air temperature 98ALSV. see Apple latent spherical virus (ALSV)Amelanchier hybrids 186–187AMF. see Arbuscular mycorrhizal fungi (AMF)Aminoethoxyvinylglycine (AVG) 163,

167–168Amplified fragment length polymorphisms

(AFLPs) 371, 372, 373Anaerobic soil disinfestation (ASD) 355Anthocyanins 62–63, 368APAL. see Apple and Pear Australia Limited

(APAL)Apex broadening 162Apis mellifera 97Appalachian Fruit Research Station 136Apple. see Malus domesticaApple and Pear Australia Limited

(APAL) 220Apple latent spherical virus (ALSV) 225

Apple powdery mildew 237–238Apple scab 236–237Apple-Tree-based AgroForestry Systems

(AT-AFS) 271–272, 273, 274, 275, 276–277

Apricot Decline Syndrome 297Arbuscular mycorrhizal fungi (AMF) 411ARS. see Agricultural Research Service (ARS)Artificial inoculation tests 75Artificial intelligence (AI) 46Artificial spur extinction (ASE) 269ASD. see Anaerobic soil disinfestation (ASD)ASE. see Artificial spur extinction (ASE)AT-AFS. see Apple-Tree-based AgroForestry

Systems (AT-AFS)Auto-allooctoploid strawberry 334AVG. see Aminoethoxyvinylglycine (AVG)Axiom Apple 480K array 222

BA. see 6-benzyladenine (BA)BA29-C. see Provence QuinceBacterial spot resistance 7‘Banner’ 348Bark inoculation 75“Bartlett.” see “Williams’ Bon Chretien”Bavarian Centre of Pomology and Fruit

Breeding (BCPFB) 186Beauveria bassiana 366, 403‘Beurré Hardy’ 186, 187Bi-axis trees 189Bibaum® 188‘Big data’ analytics 46‘Bing’ 57Biofumigants 327Biofumigation 355Black raspberry necrosis virus (BRNV) 399Blossom blight 62, 75Blueberry breeding. see Vaccinium

corymbosum breeding

Index442


Blue mould 239Blumeriella jaapii 62Bombus spp. 64, 65, 97Boron 166Botryosphaeria conidia 11Botryosphaeria dothidea. see Peach fungal

gummosis (PFG)Botrytis cinerea 240, 323, 324, 329, 330,

370, 400–401Bourse-over-bourse formation 265, 269BpMADS4-early flowering transgenic

lines 224Bringhurst, Royce 350BRNV. see Black raspberry necrosis virus

(BRNV)Brooks, Lyle 132‘Brooks’ 59Brown rot 62Budagovski breeding programmes 275Bumblebee. see Bombus spp.‘Burlat’ 57, 60

CA. see Canopy area (CA)California Strawberry Commission 322Cane and leaf diseases 400–401Caneberries. see Rubus spp.Cane botrytis. see Botrytis cinereaCane splitting 404Canopy area (CA) 299CAPs. see Cleaved amplified polymorphic

sequences (CAPs)Captafol 12Captan 12Chandler, Craig 351Chemical manipulation

floweringinhibition 164promotion 163–164

fruit setaminoethoxyvinylglycine (AVG)

167–168fruitlet abscission 168–173gibberellins 165nutrients 166–167

vegetative growthethephon 175gibberellic acid (GA) and

6-benzyladenine (BA) 175–176

gibberellic acid (GA) inhibition 173–175

Cherry breeding 78

advances and key cultivars 67–68conventional 58–63marker-assisted breeding 68–75methodologies 63–66overview 55–58phenotyping protocols 75–77

Cherry leaf spot resistance (CLSR_G4) 72Chlorotic Leaf Roll Phytoplasma 296Cisgenesis 225‘Clapp’s Favorite’ 191‘Clara Frijs’ 193Cleaved amplified polymorphic sequences

(CAPs) 371Click pruning 179Climate change 409Climate models 367CLSR_G4. see Cherry leaf spot resistance

(CLSR_G4)Cold hardiness 142–143Colletotrichum acutatum 323, 330Colletotrichum gloeosporioides (Cg1)

240, 326‘Comice’ 186, 187“Common Prune” 295Compensation point 35Controlled crosses 63–64Cornell University 275‘Cox’s Orange Pippin’ 219CPPU. see N-(2-chloro-4-pyridyl)-N′-

phenylurea (CPPU)CRISPR-Cas9 approach 139, 223‘Cristobalina’ 58, 59Crop water stress index (CWSI) 44Cross-(in)compatibility 71Cross-pollination 96, 160Crown volume (CV) 299Cumulative yield efficiency (CYE) 233CV. see Crown volume (CV)CWSI. see Crop water stress index (CWSI)CYE. see Cumulative yield efficiency (CYE)

‘D’Anjou’ 131, 179, 182, 183, 187, 188, 189, 191, 192, 193

Decision support system 46‘Dehesa’ 274Dhingra, Amit 136Didymella applanata 400Diurnal irrigation scheduling 45DMC. see Dry matter content (DMC)Dormant pruning 107Double-stranded DNA (dsDNA) 324–325‘Draper’ 431


Index 443

Driscoll’s 322, 348, 350Drones. see Unmanned aerial vehicles

(UAVs)Drosophila suzukii 370, 401–402Dry matter content (DMC) 76, 231dsDNA. see Double-stranded DNA (dsDNA)Dwarfing 58, 139–141Dwarf vigor rootstocks 299

‘Early Korvik’ 59East Malling Research Station 133ECa. see Electrical conductivity (ECa)Ecological intensification 270Effective pollination period (EPP) 161–162,

196Electrical conductivity (ECa) 43‘Eline’ 185–186Elsinoë veneta 401‘Emperor Francis’ 68ENZAFRUIT International Ltd 220EPP. see Effective pollination period (EPP)eQTL. see Expression QTL (eQTL)‘Erdi bötermö’ 63‘Erdi Jubileum’ 63Eriosoma lanigerum 236Erwinia amylovora 175, 236, 238ESTs. see Expressed sequence tags (ESTs)EUBerry project 364European apple canker 238–239European Commission 43Evans, Kate 136Evapotranspiration 41Exogenous dormancy mechanism 65Expressed sequence tags (ESTs) 371–372,

373Expression QTL (eQTL) 335Extinction 265, 269

‘Fanal’ 63“Farmingdale” 144‘Favorit’ 63F-box gene 71F-box proteins 145‘Fermina’ 59‘Fertard’ 60Field selection 66Fire blight 143–144, 238FLC. see Flowering locus C (FLC)FlexQTL software 333, 338‘Flordacrest’ 10‘Flordaguard’ rootstock 13, 17‘Flordaking’ 10

Flowering locus C (FLC) 406Forced air cooling 331Fragaria × ananassa

genetic improvementchemical controls 323–325competition 321–322controlled environments 330–331disease-resistant cultivars 325–327emerging pathogens 328–329emerging pests 327–328expression QTL 335high-throughput genotyping and QTL

analysis 333–334high-throughput phenotyping

335–336labour and mechanical

harvesting 322–323overview 319–321post-harvest quality 331–332targeted capture sequencing 334third-generation sequencing 334–335weather-based crop protection

329–330market expectations 357–360

annual production system 348, 350–351

increasing inputs 352–353overview 347–348shifting 351–352sustainability of production

model 353–356Fruit growth and vascular flows 27–28

during day 28–30factors influencing 30

orchard microclimate 31source/sink relationships 33water availability 32

during season 28Fruit phenotyping 231Fruit-to-fruit competition 33Fusarium graminearum 324

GA. see Gibberellic acid (GA)Gametophytic self-incompatibility (GSI) 61,

71, 145, 159Gas chromatography-mass spectrometry

(GC-MS) 336GBS. see Genotyping-by-sequencing (GBS)GC-MS. see Gas chromatography-mass

spectrometry (GC-MS)GDR. see Genome Database for Rosaceae

(GDR)

Index444


GEBV. see Genomic estimated breeding values (GEBV)

Gene mutations 138General combining ability 64Genetically modified organisms

(GMOs) 223, 225, 294Genome Database for Rosaceae

(GDR) 338, 371Genome-wide association studies

(GWAS) 222, 223, 333Genomic estimated breeding values

(GEBV) 227Genomic mutations 138Genomic selection (GS) 227–229Genotyping-by-sequencing (GBS) 74, 223,

373, 407Geostatistical approach 43Gibberellic acid (GA) 164, 189

and 6-benzyladenine (BA) 175–176inhibition 173–175

Gibberellin 97Gisela dwarfing rootstock 101, 104GlobalGAP 26GMOs. see Genetically modified organisms

(GMOs)‘Golden Delicious’ 219, 222Gossypium hirsutum 366Green, Kym 111Greenhouse gas 320, 330Grey mould 240, 324, 329, 370‘Griotte du Nord’ 57‘Griotte Noir Tardive’ 57GS. see Genomic selection (GS)GSI. see Gametophytic self-incompatibility

(GSI)‘Gulfatlas’ 10–11‘Gulfcrest’ 10, 11‘Gulfcrimson’ 10, 11‘Gulfking’ 10, 11‘Gulfprince’ 8, 10, 11‘Gulfsnow’ 10Gum exudation 12GWAS. see Genome-wide association

studies (GWAS)

Hartmann, Walter 294Heritable phenotypic marker (MTL)

372–373, 373Hi-C. see High-throughput chromatin

conformation capture (Hi-C)High-throughput chromatin conformation

capture (Hi-C) 380

High-throughput phenotyping platforms (HTPPs) 232, 235

High vigor rootstocks 299Hofmeister’s rule 93Honeybee. see Apis mellifera‘HoneySweet’ 294‘Horizon 2020’ Framework Program 43HTPPs. see High-throughput phenotyping

platforms (HTPPs)Hunts Point Terminal Market 355Hybridization 63–65Hydraulic conductance 27Hydrocooling. see Forced air coolingHyperspectral imaging 412, 430

IAA. see Indole-3-acetic acid (IAA)IBPGR. see International Board for Plant

Genetic Resources (IBPGR)Indole-3-acetic acid (IAA) 160, 165, 189Integrated pest management (IPM) 324,

327–328, 360, 398, 402, 409Intercropping 272, 273International Board for Plant Genetic

Resources (IBPGR) 265International Prune Association (IPA) 306IPM. see Integrated pest management (IPM)

‘James Grieve’ 219Jazz® 220‘Jewel’ 431John Innes Institute 59‘Jonathan’ 219‘Joualle’ 274‘June Gold’ 10‘Juneprince’ 8, 10

KAC-V. see Kearney Agricultural Centre Perpendicular V (KAC-V)

KASP. see Kompetitive Allele Specific PCR (KASP)

Kearney Agricultural Centre Perpendicular V (KAC-V) 36

KGB. see Kym Green Bush (KGB)Knip-boom nursery trees 105Kompetitive Allele Specific PCR (KASP)

74–75‘Kronio’ 58Kym Green Bush (KGB) 106, 111, 113, 115

LA:F ratios. see Leaf area-to-fruit (LA:F) ratiosLAI. see Leaf area index (LAI)Land equivalent ratio (LER) 271–272


Index 445

Lang, Greg 111‘Lapins’ 59Large raspberry aphids 399–400Later summer pruning 108Late spring pruning 107LC-MS (liquid chromatography-mass

spectrometry) 336Leaf area index (LAI) 267Leaf area-to-fruit (LA:F) ratios 101–102Leaf node method 75Leaf spot 62, 75LER. see Land equivalent ratio (LER)LG. see Linkage group (LG)LHC. see Light harvesting complexes (LHC)Life cycle assessments 320Light harvesting complexes (LHC) 34Linkage group (LG) 68–70, 139LOD. see Logarithm of odds (LOD)Logarithm of odds (LOD) 19‘Łutovka’ 57

MAB. see Marker-assisted breeding (MAB)Malus domestica

breeding 241–242accelerating cycles 224–225genomic selection 227–229genomic tools 221–224marker-assisted selection 226–227phenotyping 231–232post-harvest 239–240pre-harvest 236–239production 217–220resources to optimise genetic

gain 229–231resource-use efficiency 235scions and rootstocks 220–221yield efficiency 233–235

cultivationagroecological practices to foster

ecosystem services 271–273growth, flowering and fruiting 267–268living meristems and extinction

phenomenon 264–266overview 261–262plant arrangement 275–276plant assemblage 275productive and sustainable

agroecosystems 270–271spatial and temporal agroecological

engineering 276–277training and pruning

management 268–270

tree architecture and shape typology 262–264

tree-based agroforestry system 273–274

Malus sylvestris 261Marchand Drapeau canopy 110Marker-assisted breeding (MAB) 371

blueberry 430–431deployment strategies 73–74DNA tests 71–72future trends 74–75genetic studies 68–70

Marker-assisted selection (MAS) 68, 224, 226–227, 366

Mazzard seedling rootstocks 104‘McIntosh’ 219Mechanical harvesting 63, 323Medium vigor rootstocks 299‘Melitopolska chorna’ 59Metamitron 170–171Metarhizium anisopliae 403Methyl bromide 353, 355Michigan State University 431Microsatellites 133, 134Millennium Ecosystem Assessment 270‘Mirobolan galben’ 304Moderate chill peach breeding project

priorities and approach 5–8progress 8, 10–11

Monilinia laxa 62Monilinia spp. 75‘Montmorency’ 57Montreal Protocol 353MTL. see Heritable phenotypic marker (MTL)‘Multifunctional woody polycultures’ 271Multiple cropping systems 273Multispectral airborne imagery 43Mutagenesis 138

NAA. see Naphthaleneacetic acid (NAA)NABGRF. see North American Bramble

Growers Foundation, Inc. (NABGRF)NAFTA. see North American Free Trade

Agreement (NAFTA)Naphthaleneacetic acid (NAA) 163, 169‘Napoleon’ 60NARBA. see North American Raspberry and

Blackberry Association (NARBA)National Plant Germplasm System 134National Strawberry Sustainability Initiative

(NSSI) 356NCBI Short Read Archive 338

Index446


N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) 169–170

NDVI. see Normalized difference vegetation index (NDVI)

Near-infrared spectroscopy (NIRS) 76, 231Neonectria ditissima 236, 238Next-generation sequencing (NGS) 370,

371NHB. see Northern highbush breeding

programmes (NHB)‘Nich Ohmer’ 348‘Nimba’ 60NIRS. see Near-infrared spectroscopy (NIRS)Non-fruiting spurs 95, 100–101Non-fumigant-based methods 327Non-sterile warm stratification method 65Normalized difference vegetation index

(NDVI) 43, 44, 45, 412North American Bramble Growers

Foundation, Inc. (NABGRF) 364North American Free Trade Agreement

(NAFTA) 321, 322North American Raspberry and Blackberry

Association (NARBA) 365North Carolina Rubus Breeding

Program 367Northern highbush breeding programmes

(NHB) 427, 429NSSI. see National Strawberry Sustainability

Initiative (NSSI)

“Old Home” 144Open pollinations 63–64Optimized soil-adjusted vegetation index

(OSAVI) 44Orchard management 27, 40, 99OSAVI. see Optimized soil-adjusted

vegetation index (OSAVI)Otiorhynchus sulcatus 402

‘Pacific Red’ 60‘Pandy’ 57PAR. see Photosynthetically active radiation

(PAR)P-Ca. see Prohexadione–calcium (P–Ca)PCR. see Polymerase chain reaction (PCR)PDS. see Phytoene desaturase (PDS)PDV. see Prune dwarf virus (PDV)Peach

breeding 20cooperative regional moderate chill

project 5–11

overview 3–5for resistance to PFG 11–13

sustainable production 47applications 42–45case study 45–46climate change 26fruit growth and vascular flows 27–28photosynthesis 33–42precision fruit growing 26–27and resilience 26

Peach fungal gummosis (PFG) resistance 7, 11, 12

evaluation methodology 13–14genetics 14–16validation and linkage mapping 17–19

Pear. see Pyrus spp.Penicillium expansum 239‘Penny’ 60PFG. see Peach fungal gummosis (PFG)

resistance; Precision fruit growing (PFG)

PGA. see Proximity-guided assembly (PGA)PGR. see Plant growth regulator (PGR)PhenoArch platform 232Phloem flow 27–28, 29, 33Photochemical reflectance index normalized

by considering the chlorophyll content (PRInorm) 44

Photochemical reflectance index (PRI) 412Photoinhibition 40Photorespiration 34–35, 37, 40Photosynthesis

light 35–37process 34–35temperature 37–39water 40–42

Photosynthetically active radiation (PAR) 36Photosystems I and II (PSI and PSII) 34, 170Phragmidium rubi-idaei 401Physical manipulation of flowering and

fruit setcanopy pruning 178–181girdling, notching, and scoring 176–178root pruning 181–184

Phytoene desaturase (PDS) 223Phytophthora cactorum (Pc1) 326Phytophthora fragariae 326Phytophthora root rot 404, 407Pink Lady® 220Plant and Food Research 230Plant growth regulator (PGR) 158Plasticulture 320


Index 447

Plum and apricot cultivation 302, 304, 306, 312

environmental factors 300rainfall 301–302soil 302temperature 301

genetic resources 293cultivars and breeding 294–298rootstocks 298–300

overview 289–290production 290, 292prune 306–307, 311

Plum pox virus (PPV) 294, 296, 311PNRSV. see Prunus necrotic ringspot virus

(PNRSV)Podosphaera leucotricha 236, 237Poly-cross system 65Polymerase chain reaction (PCR) 370Polyphenols 63Postharvest summer pruning 107–108PPV. see Plum pox virus (PPV)Precision fruit growing (PFG) 25, 26–27, 46,

91–92Precocity 141–142Preharvest summer pruning 107‘Pré-verger’ 274PRI. see Photochemical reflectance index (PRI)PRI Cooperation Program 237Primordial subtending meristem 94–95Primordial terminal meristem 95PRInorm. see Photochemical reflectance

index normalized by considering the chlorophyll content (PRInorm)

Prohexadione–calcium (P–Ca) 173–175“Provence Quince” 133, 186Proximity-guided assembly (PGA) 380Prune dwarf virus (PDV) 121Prunus avium

abiotic and biotic stresses 58–60cultivation

climate change 91cultivars 102–103diseases and insects 120–122endodormancy and

ecodormancy 98–99innovations in canopy

architectures 110–113market opportunities 90–91microclimate modification 117–120nursery tree establishment 105–106photosynthesis and leaf area-to-fruit

relationship 99–102

precision fruit growing 91–92production sustainability 89–90pruning and growth

manipulation 107–108reproductive morphology and fruit

growth 94–98rootstocks 103–105soil water and fertility 116–117training systems 108–110, 113–115vegetative morphology and canopy

structure 92–94extension of harvest period 60fruit-related traits 60structure and flower characteristics 58

Prunus domestica 290Prunus necrotic ringspot virus (PNRSV) 121Prunus salicina 290PSI and PSII. see Photosystems I and II (PSI

and PSII)Pterostilbene 423Purpureocillium lilacinum 366Pyrus communis 132, 133, 134Pyrus spp.

breeding 147cultivars 130–131germplasm resources 133–136improving particular traits 139–146overview 129–130rootstocks 131–133techniques 136–139

cultivationcanopy training 188–191chemical manipulation 163–176dwarfing rootstock 184–188effective pollination period

(EPP) 161–162floral initiation 162–163flower inflorescence and fertility

status 158–161light 191–193overview 157–158physical manipulation 176–184temperature 193–194, 196–197water 197–198

Pyrus ussuriensis 196

QD. see Quantum dots (QD)Quantitative trait loci (QTL) 19, 68–70, 134,

135, 222, 223, 233–234, 235, 326, 333–334, 372–373, 372–373, 406, 430

Quantum dots (QD) 382

Index448


Quince A 186, 196Quince C 185, 186Quince H 185, 186Quince rootstock 132–133, 196

RAD. see Restriction site-associated DNA (RAD)

‘Rainier’ 59Random Amplified Polymorphic DNA

(RAPD) 133, 139, 371Raspberry and blackberry. see Rubus spp.Raspberry leaf mottle virus (RLMV) 399Rauh model 263‘Red Delicious’ 219‘Regina’ 59Reiteration phenomenon 263Relay cropping. see sequential croppingRenseq. see R-gene sequencing (Renseq)Restriction site-associated DNA (RAD) 370RFLP (restriction fragment length

polymorphism) 68R-gene sequencing (Renseq) 334Rhizopus rot 324Ribonuclease S-RNAse glycoprotein 45Ribulose bis-phosphate carboxylase-

oxygenase (RuBisCO) 34, 39RLG6. see Rubus linkage group (RLG) 6RLMV. see Raspberry leaf mottle virus (RLMV)RNA interference (RNAi) 324–325Robotic harvesting 323RootNav tool 232Root phenotyping 232Root rot 398–399Rootstock-induced dwarfing 233RosBREED 333, 383R/QTL statistical software 19RuBisCO. see Ribulose bis-phosphate

carboxylase-oxygenase (RuBisCO)Rubus linkage group (RLG) 6 399–400Rubus spp.

breeding 381–382climate resilience 367–368health benefits and fruit quality

368–369linkage maps, MTLs and QTLs 372–373molecular markers 371–372nutrient efficiency 365–366overview 363–364plant architecture and

morphology 369R. occidentalis and R. idaeus

genomes 380

resistance to insects and diseases 369–370

rhizosphere competence 366–367cultivation

combined stress studies 411effects of climate change and

phenology 408–409environmental impacts 404–408heat stress 410overview 397–398pest and disease stresses 398–404phenotyping and plantation stress

management 411–412Rubus yellow net virus (RYNV) 399

Saturation point 35, 40SB. see Spanish Bush (SB)SC. see Self-compatibility (SC)Scarrone model 263SCARs. see Sequence characterized

amplified regions (SCARs)‘Schattenmorelle’ 57, 61, 63‘Scifresh’ 220Scion dwarf types 58Seed germination 65–66Self-compatibility (SC) 71, 103Self-incompatibility (SI) 145–146Self-incompatible cultivars 61Self-pollination 160Semi-dwarfing rootstock 58Semidwarf vigor rootstocks 299Sequence characterized amplified regions

(SCARs) 371Sequential cropping 273SFB gene. see F-box geneSFPs. see Single feature polymorphisms

(SFPs)SHB. see Southern highbush breeding

programmes (SHB)Short sequence repeat (SSR) 371–372, 373Short vegetative phase proteins (SVP) 406SI. see Self-incompatibility (SI)SIGS. see Spray-induced gene silencing

(SIGS)Simple sequence repeat (SSR) 68, 71–72,

73, 133, 135–136, 139, 222Single feature polymorphisms (SFPs) 370Single nucleotide polymorphism (SNP) 68,

72, 135–136, 222, 370, 372Singlet state 34SL. see Steep Leader (SL)S-locus F-box genes (SLF) 159


Index 449

SmartRoot tool 232Smart spray application 45SNP. see Single nucleotide polymorphism

(SNP)Soil fumigants 320, 327Soil management procedures 271Solarization 355Solaxe training system 108, 109Soluble solid content (SSC) 8, 231Soluble sugar content (SSC) 76Sorbitol 28Sour cherry 60

biotic and abiotic stress 62extension of harvest period 63fertility 61fruit-related traits 62–63structure 61

Southeastern Fruit and Tree Nut Research Laboratory 14

Southern highbush breeding programmes (SHB) 427

Spanish Bush (SB) 106Specific combining ability 64Spectral reflectance 412, 429Spectral signatures 412, 430SPL. see Squamosa promoter binding like

(SPL)Spotted wing drosophila (SWD) 401–402Spray-induced gene silencing (SIGS)

324–325Spur blight. see Didymella applanataSpurs 95Spur-type cultivars 267Squamosa promoter binding like (SPL) 406S-RNase gene 71SSA. see Super Slender Axe (SSA)SSC. see Soluble solid content (SSC); Soluble

sugar content (SSC)SSR. see Short sequence repeats (SSR);

Simple sequence repeat (SSR)‘Staccato’ 60Steep Leader (SL) 106‘Stella’ 58, 102‘Stevnsbaer’ 63Strawberry. see Fragaria × ananassa‘Streuobst’ 274Sucrose 28Super Slender Axe (SSA) 113, 114SVP. see Short vegetative phase proteins

(SVP)SWD. see Spotted wing drosophila (SWD)Sweet cherry. see Prunus avium

TA. see Titratable acidity (TA)Tall Spindle Axe (TSA) 109, 113TCARI. see Transformed chlorophyll

absorption in reflectance index (TCARI)

TCSA. see Trunk cross-sectional area (TCSA)Terminal-bearing cultivars 267Tetranychus uticae 404Theobroma cacao 366Thermal imaging cameras 231–232Thinning 168–173Titratable acidity (TA) 8, 76Trans/cis early flowering gene 224Transformed chlorophyll absorption in

reflectance index (TCARI) 44Transpiration 27, 29, 41Traumatic reiteration 263Tree architecture 144, 262–264Tree phenotyping 231Tree-to-atmosphere water exchanges 32Trichoderma hamatum 366Trunk cross-sectional area (TCSA) 233, 299TSA. see Tall Spindle Axe (TSA)

UAVs. see Unmanned aerial vehicles (UAVs)UC. see University of California (UC)UF. see University of Florida (UF)UFO. see Upright Fruiting Offshoots (UFO)Umbrella-type canopy 264University of Bologna 67University of California (UC) 348University of Florida (UF) 5, 351, 431University of Georgia Research and

Education Center 5University of Hohenheim 294Unmanned aerial vehicles (UAVs) 44, 232Upright and spurtype canopy 264Upright Fruiting Offshoots (UFO) 106, 112,

113, 115U.S. Department of Agriculture (USDA) 5,

14, 17, 136, 275, 322U.S. National Academy of Sciences 328U.S. National Clonal Germplasm

Repository 134, 381USDA. see U.S. Department of Agriculture

(USDA)

Vaccinium angustifolium 427Vaccinium corymbosum breeding 433–435

challenges 424–426genetic material and uses 426–429marker-assisted breeding 430–431

Index450


overview 423–424phenotyping 429–430research improving flavor 431–432

Vaccinium myrtillus 429‘Valerij Chkalov’ 59Valsa mali 236Vapour pressure deficit (VPD) 27, 29, 31,

33, 39, 45Variable rate application 46VCL. see Vogel Central Leader (VCL)Vegetative budbreak 98–99Vegetative shoot meristems 93Venturia inaequalis 236–237‘Verger haute tige’ 274Vertical Shoot Position (VSP) 111–112Very high vigor rootstocks 299Vine weevil 402–403Viral diseases 403–404Virus-induced gene silencing 225VOCs. see Volatile organic compounds

(VOCs)Vogel Central Leader (VCL) 113

Volatile organic compounds (VOCs) 331–332, 424, 432

Voth, Victor 350VPD. see Vapour pressure deficit (VPD)VSP. see Vertical Shoot Position (VSP)

Washington State University (WSU) 73, 74, 136, 230

Water potential gradients 27, 28Water use efficiency (WUE) 26, 39, 43–45,

235Whiting, Matthew 112“Williams’ Bon Chretien” 131, 132, 133,

191, 192, 196, 197–198WSU. see Washington State University (WSU)WUE. see Water use efficiency (WUE)

Xanthomonas fragariae (RXf1) 326Xylem flow 27–28, 29, 33

Yellow rust. see Phragmidium rubi-idaei

Zaiger Genetics 67

Documents

Mark Mazzola and Shashika S. Hewavitharana, USDA-ARS, USA