Heirloom apple cultivars represent an important specialty crop for producers and a genetic resource for the dessert apple industry. These cultivars are plagued with misidentifications, which hinders utilization and long-term preservation. Phenotypic identification, used for centuries, is unable to distinguish among the thousands of existing U.S. heirlooms. DNA profiling provides an objective basis for cultivar identification. Washington State University’s “MyFruitTree” (myfruittree.org), built upon the RosBREED project and with international collaborations, has accumulated a DNA profile dataset of thousands of apple individuals focused on the U.S. genepool. Users submit leaf samples for trees of interest, and MyFruitTree’s cost-recovery research opportunity determines the cultivar identity (or reveals their uniqueness and pedigree position). However, a common and valid question is, “How do you know that is the correct identity?” The core panel of robustly identified cultivars was based on public breeding germplasm, modern cultivars, and their ancestors, which were DNA profiled in the RosBREED project last decade. Since then, examined trees from collections in the U.S. and abroad have greatly expanded the number of DNA profiles with cultivar labels. But those labels are not always correct, especially when a tree is derived from only a single source. Therefore, a system was derived for assigning confidence to the cultivar labels associated with DNA profiles. Cultivar name evidence is assembled in the categories of provenance, phenotype, and genotype for both the DNA-profiled tree and the historically named cultivar, and congruence is examined. This system is applied at two levels: streamlined and comprehensive. The streamlined approach for the current DNA profile dataset efficiently determined whether each individual belongs confidently in the “Reference Panel” or is relegated to “Accessory Profiles” pending further evidence. A Reference Panel was assembled of hundreds of U.S. heirlooms (and more than a thousand close relatives from other regions). The comprehensive approach involves attention from a transdisciplinary tribunal of experts who carefully weigh evidence that an apple individual – often a proposed new discovery of an otherwise lost heirloom – is indeed a historically named cultivar. As MyFruitTree accumulates more DNA profiles submitted by cultivar collection managers and apple enthusiasts nationwide, the cultivar name assignment system is being applied to unidentified trees with strong provenance evidence of cultivar status. Establishing accurate cultivar identities of valued trees via DNA profiling is providing the critical foundation for a coordinated national effort to sustain preservation and utilization of apple crop diversity.
U.S. heirloom apple cultivars are an underutilized and threatened resource, that DNA fingerprinting can help save and remobilize. These heirlooms are old cultivars that were named, clonally propagated, and distributed more than a century ago. Many heirloom cultivars have great historical value, some are still grown commercially, and others could be reintroduced to enhance rural prosperity and diversify options for consumers. While some heirloom cultivars are ancestors of modern cultivars, many others could be valuable for future breeding. However, most heirlooms have been long neglected, and thousands once documented are already extinct. Before more heirlooms disappear forever, mystery trees need to be distinguished from known cultivars, identified, and adequately preserved. Leaf samples for more than 2000 apple trees in collections, national heritage sites, old orchards, and backyards across the U.S. were crowdsourced from about 150 “MyFruitTree” submitters and DNA fingerprinted using KASP genotyping with 48 SNPs. The cultivar identity or uniqueness of each tree was determined by comparing obtained DNA profiles to a previously developed dataset of several thousand apple cultivars and individuals. Trees with replicates were prioritized into five categories according to several criteria for likelihood of representing heirloom cultivars. After removing duplicate samples, poor genotypic data, and non-apple samples, about 60% (1202) of samples were identified as cultivars and most were heirlooms. Of the unidentified samples, 85% (665) were unique, and 15% (118) of the samples represented replicated trees. We found five “Priority 1” trees (filled cultivar pedigree gaps or from three U.S. regions) and four “Priority 2” trees (detected in two regions). Hundreds more trees likely representing unknown heirlooms were also identified in single regions. Collaborators across the country, including historians and citizen scientists, can now closely examine the highest priority trees to uncover their historic cultivar names, while ensuring they are propagated so that they are preserved and valued once again. As more old apple trees are DNA fingerprinted, it is expected that current “unique” DNA profiles will be replicated in the same or other regions. Replicated trees must represent propagated, valued, and likely named cultivars, increasing the opportunities to rediscover lost heirlooms.
Peach trees require quantitative exposure to winter chilling (chilling requirement, CR) for spring bloom. The chill accumulation time points are determined using weather data of air temperatures between 32 and 45 ºF, using various calculation methods such as the simple chill hour (CH) method or more sophisticated methods like Utah and Chill portions (CP) that account for negations of chilling due to warm weather during the dormancy. All these methods rely on air temperature and do not consider the soil temperature during the dormancy and its effect on the tree’s perception and account for chill accumulation. Peach flowers and developing fruit are highly sensitive to freezing temperatures and are killed following even a limited exposure. In the past decade, mild winters and early spring frosts have significantly reduced or eliminated the annual peach production in the southeast U.S. Low-chill winters have become increasingly common in the southeastern peach-producing regions, and when followed by warm springs, result in early bud break and early flowering, increasing the risk of crop loss to frost. Due to a replant issue caused by Armillaria root rot, almost all acreage under the new peach orchards in the southeast, including South Carolina, are planted on berms adopting root collar excavation as a method to extend the life of orchards on infested soil. We observed significant differences between the air temperature and temperature of undisrupted soil and soil within berms at various depths (3, 6, 12 and 18 in) during dormancy. The effect of observed temperature differences on ‘Cresthaven’ tree chill accumulation calculation and transition between endo- and eco-dormancy stages was investigated by collecting vegetative bud and root tissue from all four depths at six chill hour time points (400, 500, 600, 700, 800 and 900). Preliminary data show significant gene expression differences between bud and root tissue and different gene expression profiles related to the chill accumulation in each tissue. Detailed analyses of the gene expression profiles between the tissues at the different chill accumulation stages and their effect on chilling and heat accumulation, bloom time, and the transition between the dormancy stages in peaches will be discussed.
Since no Huanglongbing (HLB)-resistant citrus cultivar is available in the world, selection of elite natural mutants of commercial citrus for HLB-resistance/tolerance becomes a much more appealing breeding approach, especially in HLB-epidemic regions. In this study, we have selected and evaluated more than 30 citrus mutants from commercial citrus varieties in the past eight years in Florida. After greenhouse and field trials with high HLB disease pressure, we have identified several citrus lines with improved HLB-resistance/tolerance, which can be released or used for large scale of field trials. Our analyses of these lines have revealed that citrus resistobiome plays a role in the HLB resistance/tolerance, which involves a plant virus that can enhance plant resistance and illustrated the pursuit of breeding for biocontrol and a healthy microbiome. Meanwhile, we revealed that transposons have driven the selection and diversification of sweet orange (SWO). We identified six transposon families with up to 8900-fold activity increases in modern sweet orange cultivars tracing back to a common ancestor ~500 years ago. Notably, these six families of transposons contribute significantly to the formation of major cultivar groups, with frequent independent activations or accelerations observed in the breeding history of SWO. We will discuss the molecular mechanisms underlying the improved HLB-resistance, especially how the resistobiome plays a role in the improved HLB resistance/tolerance, and how to implement this new approach by utilizing and expanding the breeding of citrus resistobiome for the control of citrus HLB.
Avocado (Persea americana) is renowned for its high nutritional value and its global consumption is steadily increasing. Currently, only a few cultivars with limited genetic variability are cultivated, and there is a need for developing new avocado cultivars with enhanced horticultural, fruit quality and nutritional traits as well as resistance to diseases and pests. Application of marker assisted selection can significantly accelerate breeding new avocado varieties, which can take 15 - 20 years using traditional breeding methods. Towards the application of molecular markers in avocado breeding, in this report, genome-wide association studies (GWAS) of nine fruit quality traits of a diversity panel of 110 avocado accessions were explored using 4,706 high-quality single nucleotide polymorphisms (SNPs) using multiple models. In addition, genetic diversity and population structure were also investigated, which unveiled three main populations corresponding to the three major avocado botanical races representing Mexican, West Indian, and Guatemalan ecotypes. Phylogenetic study and quantitative genetic analyses suggested a closer relationship between the Guatemalan and West Indian races compared to the Mexican race. Genome-wide association study revealed twelve markers distributed over eleven genomic regions strongly associated with fruit quality traits including fruit color, shape, taste, and skin texture. Annotation analyses of these genomic regions revealed candidate genes affecting these traits. These findings contribute to a comprehensive understanding of the genetic composition of avocado germplasm, which will be useful for identifying genes governing fruit quality traits as well as for accelerating breeding and parent selection efforts in the avocado breeding pipeline.
Avocado (Persea americana) is the major fruit cultivated in southern Florida counties with a value exceeding 20 million dollars annually. While production in other regions is dominated by the Hass cultivar, south Florida is unique in production of the increasingly popular, green-skinned varieties. Recently, the avocado industry in South Florida has been devastated by laurel wilt (LW), an insect-disease complex spread by Raffaelea lauricola (Rf), a fungal symbiont of redbay ambrosia beetle (Xyleborus glabratus Eichhoff). Current management practices including prophylactic fungicide injections, tree rejuvenation and ambrosia beetle population reduction are costly and onerous . Unfortunately, no mature avocado trees tolerant to LW are available to growers and genetic mechanism of LW tolerance observed in some avocado seedlings is unknown. In this study, a chromosomal genome of avocado cv. ‘Simmonds’, a ‘West Indian’ (Lowland) ecotype was assembled from Pacific Biosciences HiFi reads. The genome assembly contained 451 scaffolds spanning 98.89% of the avocado genome, a N50 of 82.34MB and a BUSCO score of 95%. This assembly served as a reference genome to generate 9198 genome wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS) reads of a germplasm collection comprising 80 accessions of three avocado ecotypes (Mexican, Guatemalan and West Indian) and 18 novel hybrids exhibiting seedling tolerance to LW. Phylogentic analyses revealed three major clusters with majority of LW tolerant seedlings clustering amongst Hass derived hybrids as well as cultivars belonging to Mexican and Guatemalan ecotypes such as 'Winter Mexican', and 'Ettinger'. This work provides genomic resources for characterization of genetic tolerance of LW in avocado germplasm collections and is a significant step in developing LW tolerant hybrids to support local avocado industry.
The scientific and commercial interest in pomegranate (Punica granatum L.) cultivation has increased noticeably during the last two decades. Because of the high concentration of bioactive compounds and its nutraceutical properties, pomegranate has been defined as a super food. The consumption of pomegranate juice or arils has been related to several possible benefits on human health. Recent studies have highlighted an antioxidant and anti-inflammatory activity of this fruit which seem to prevent cardiovascular, neoplastic, neurological, metabolic, and intestinal disease. The areas of cultivation of this crop are exposed to current and future challenges like long term-drought conditions and invasive pests and diseases. Increasing the biodiversity of pomegranate has been proposed has the main strategy to reduce the risk of food system vulnerability related to monoculture and the valorization of marginal land. In order to develop advanced genetic tools to improve pomegranate breeding program efficiency we present the de novo sequencing of the ‘Wonderful’ pomegranate genome. DNA isolated from diploid leaf tissues was sequenced using long read sequencing technology (PacBio), while DNA extracted from haploid pollen grains was sequenced using short reads (Illumina). Genomic data from single haploid gamete cells were analyzed using the R package called ‘Hapi’. This allowed to infer chromosomal haplotypes obtaining a higher resolution for DNA variants detection and investigating recombination events in single gametes. Although ‘Wonderful’ represents the industry standard in the United States, several cultivars with desirable traits, such as low acidity and soft seednesses, have been identified in the national germplasm. The results of this study will provide the genomic data required to investigate differences among cultivars and create trait-gene associations. This will allow breeders to facilitate the integration of desired quality traits into new germplasm resources.
