Search

Abstract Background Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose ‘terroir’, the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions. Results To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. Conclusions These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.

Few plants have captured the imagination and palettes of the world like those which bear edible fruits, providing novel insights into the relationships between plants and people. This special collection of reviews and research highlights the unique challenges and opportunities we face when studying, breeding, and working to conserve these species. The 18 articles included here examine fruiting plants across diverse scales and topics, from the genome to global sustainability, and from fruit morphology to species' geographic distributions, yet they showcase only a fraction of the immense evolutionary, phenotypic, and genomic diversity present in fruit‐bearing plants. Across the special collection, our hope is to not only offer highlights of fruit diversity and importance but also provide a taste of future research in this area. We hope you enjoy the fruits of our labor.

Societal Impact Statement Apples are affordable and accessible fruit with tremendous biodiversity. Among over 10,000 identified apple cultivars, only a few are commercially available. Habitual fruit consumption is correlated with the prevention of Type 2 diabetes and related complications. Particularly, (poly)phenols found in apples are major contributors to their antidiabetic properties. Here, we have screened (poly)phenol‐rich extracts of 476 apple accessions in Canada's Apple Biodiversity Collection for antidiabetic properties. The results of this work provide insights into the prevention and management of Type 2 diabetes by identifying high (poly)phenol‐containing specialty apples for use in fresh fruit form or value‐added functional food ingredients. Summary The recent trend in sedentary lifestyles and nutritionally‐imbalanced diets has elevated the prevalence of Type 2 diabetes in many parts of the world. Some pharmacological glycemic management can cause undesirable gastrointestinal side effects or hypoglycemia. Thus, there is a growing interest in safe glycemic management using dietary (poly)phenols. In this study, (poly)phenol‐rich extracts of 476 apple accessions from Canada's Apple Biodiversity Collection (ABC) and six major apple (poly)phenols were assessed for in vitro antidiabetic properties against the activities of α‐glucosidase, α‐amylase, and dipeptidyl peptidase‐4 (DPP‐4) and the formation of advanced glycation end products (AGE). Apple (poly)phenol extracts varied in their antidiabetic activities in a dose‐dependent manner. High (poly)phenol‐containing apples demonstrated that their total phenolic contents (TPC) were inversely correlated with the IC50 values of α‐glucosidase, α‐amylase, and AGE formation, but not DPP‐4. Concentrations of major (poly)phenol compounds such as procyanidin B2, phloridzin, and epicatechin in apples were significantly inversely correlated with IC50 values of α‐glucosidase in the high (poly)phenol‐containing apples. High TPC apples are not suitable for marketing for fresh fruit consumption due to bitterness and astringency; however, these apples show potential to use in the development of value‐added functional food ingredients or nutraceuticals for blood glucose management. The high TPC apple, “S23‐03‐749,” an advanced breeding line of dessert apple, presents a novel option as a specialty apple cultivar for the dietary management of glycemia.

Apple quality traits such as fruit texture, sugar content, and firmness retention during storage are key targets for breeders. Understanding the genetic control of fruit quality traits can enable the development of genetic markers, useful for marker-assisted breeding of new apple cultivars. We made use of over 260,000 single nucleotide polymorphisms (SNPs) genotyped across 1,054 apple accessions from Canada's Apple Biodiversity Collection to perform genome-wide association for 21 fruit quality and phenology traits. We identified two loci on chromosome 15 and 16 associated with phenolic content and a locus on chromosome 10 associated with softening. In addition, we determined that allelic variation at the NAC18.1 transcription factor was associated with numerous traits including harvest date, firmness at harvest, and firmness after storage. Our analyses suggest that NAC18.1 independently acts as a high level regulator of multiple ripening related traits and we propose a model for the allelic effects at NAC18.1 on apple ripening and softening.

An apple's aroma is a major determinant of its desirability by consumers. To better understand the aroma of apples, 2-dimensional gas-chromatography mass-spectrometry (2D-GCMS) was used to quantify 106 volatile organic compounds (VOCs) from 515 apple varieties. We identified esters and aldehydes as the most abundant classes of VOCs, with butyl acetate and hexyl acetate being present in nearly every variety. Principal component analysis (PCA) revealed that the primary axis of variation in the apple volatilome is correlated with harvest date, with early-harvested apples expressing a greater number and higher concentration of VOCs compared to late-harvested apples. Genome-wide association studies (GWAS) using 250,579 single nucleotide polymorphisms (SNPs) identified a significant association between SNPs near the alcohol acyltransferase (AAT1) locus and the abundance of several esters. Additionally, strong associations were observed between SNPs at the NAC18.1 transcription factor locus and the abundances of 1-hexanol and 1-butanol, which serve as precursors for hexyl acetate and butyl acetate, respectively. These findings provide a foundation for understanding the genetic basis of apple aroma production and pave the way for the genomics-assisted enhancement of the aroma profiles of apple varieties to meet consumer preferences.

Societal impact statement Plant biodiversity is fundamental to the future of food security and agriculture. Berries are the most economically important fruit crops in Canada. Within this article, we explore the nutritional, cultural, and botanical importance of berries, including crop wild relatives (plant species that are closely related to domesticated crops) and plants that are significant to Indigenous Peoples. Using berries as a case study, we explore opportunities for the conservation, use, and public engagement of crop wild relatives. Our objective is to lay the groundwork for future collaborative efforts across these diverse plants. Summary Conservation of plant biodiversity, in particular crop wild relatives including those tended and cultivated by Indigenous Peoples, is critical to food security and agriculture. Building on the 2019 road map for crop wild relatives, we examine berries as a case study for crop wild relative conservation, use, and public engagement. We focus on berries due not only to their economic, cultural, and nutritional importance but also because they are consumed fresh, providing a unique opportunity for individuals and communities to connect with plants. We outline health benefits, geographic distribution, and species at risk for Canadian berries. We describe practices, strategies, and approaches used by Indigenous Peoples to steward berries and emphasize the importance of traditional knowledge. We highlight opportunities for in situ and ex situ berry conservation and use of berries in plant breeding and Indigenous foodways. Our aim is to lay the groundwork for future collaborative efforts in these areas and to showcase berries as a useful case study for conservation of food plant biodiversity and public engagement.

Societal Impact Statement Apples are among the most widely consumed fruits in the world, with a third of all apples being pressed into apple juice or fermented into cider. Cider has grown in popularity in Canada and the United States, and North American cider makers are increasingly interested in using traditional European ‘cider apples’ rather than using commonly grown ‘dessert apples’ that are grown primarily for fresh consumption. While we find that commonly grown dessert apples do differ from European cider apples for a small number of cider making characteristics, our results show that dessert apples are most often indistinguishable from cider apples across 10 traits. Our work provides a first step towards quantifying the differences between these two apple types.

The microbiome, an influential factor affecting plant health and growth, is attracting increasing interest with respect to wine grape production. The purpose of this study was to characterize the microbiome (fungi and bacteria) of the soil, cover crop roots, and grape (Vitis spp.) roots across rootstock and depth in a cool-climate, organic vineyard. The cover crop consisted of a fescue (Festuca sp.) grass, while grape roots were sampled from New York Muscat, a cool-climate hybrid, across three root types (ungrafted, 3309C and Riparia Gloire) at three root depths (0 to 15, 15 to 30, and 30 to 50 cm). The grape root microbiome was more specialized, with fewer observed amplicon sequence variants for both bacteria (16S) and fungi (internal transcribe spacer) than found in the cover crop and the surrounding soil. Grape roots were dominated by bacterial genera Pseudomonas, Niastella, and Rhizobium; most prominent fungal genera were Plectosphaerella, Trichosporon, and Ilyonectria. Although no correlations were found between α-diversity metrics and soil parameters, Pseudaleuria relative abundance was correlated with Mn, Fe, and Na levels. Soil depth explained a small portion of bacterial but not fungal variance and taxonomic composition. Rootstock type explained a portion of both bacterial and fungal variance and taxonomic composition, substantiating the role of host plant genetics in the development of the grape root microbiome. This is the first characterization of the grape root microbiome in a cool-climate Canadian vineyard.

Societal Impact Statement A future with a secure and safe food supply requires humanity to preserve and exploit the vast variation available across agricultural plant species. Apples are one of the most widely consumed fruits and provide significant nutritional value worldwide. Here, we characterize key agricultural traits in a diverse collection of apples to provide a foundation for future apple improvement. We show that commercially successful apple varieties capture only a small fraction of apple diversity, and demonstrate that significant improvement is possible by tapping into existing genetic diversity. Summary ●Here we present a comprehensive evaluation of apple diversity through phenotyping of Canada's Apple Biodiversity Collection (ABC) which contains over 1000 apple accessions. ●We assessed, over a 4‐year period, more than 20,000 individual apples and quantified variation across 39 phenotypes, including phenology and fruit quality both at harvest and after 3 months of cold storage. ●We observe that apples in the ABC display a wide range of phenotypic variation that may prove useful for future apple improvement. For example, apples can differ by nearly 61‐fold in weight, 18‐fold in acidity, and 100‐fold in phenolic content. We quantified the dramatic changes to apple physiology that occur during 3 months of cold storage: on average, apples lost 39% of their firmness, 31% of their acidity, and 9% of their weight, but gained 7% in soluble solids. Harvest date, flowering date, and time to ripen were all positively correlated with firmness, which suggests that the developmental pathways that drive phenological events throughout the growing season may play a role in determining an apple's texture. Finally, we show that apple breeding has selected for a significant decline in phenolic content over the past 200 years: apple cultivars released after 1940 had a 30% lower median phenolic content than cultivars released before 1940. ●The data and analyses presented here not only provide a comprehensive quantification of the range across, and relationships among diverse apple phenotypes, but they also enable genetic mapping studies that will provide the foundation for future apple improvement via genomics‐assisted breeding.

Abstract Plants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above‐ground plant tissues, such as leaves, reflects both above‐ and below‐ground activities of the plant, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study how genetically distinct root systems influence the elemental composition of a common shoot system. We measured elemental composition of over 7,000 leaves in the grapevine cultivar “Chambourcin” growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition, and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above‐ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.

An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada’s Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.

Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of pre-harvest ripening and associated textural changes following harvest are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ∼800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). We introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.

Abstract Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.

Horticulture: dissecting the effects of grafting Researchers in the US have uncovered how rootstocks affect scions following grafting, which will help to develop more resilient crops. A team led by Allison Miller of Saint Louis University grafted the ‘Chambourcin’ grape variety onto three different rootstocks and investigated the effect on leaf shape, ion concentration, and gene expression in the scion. They discovered that the rootstock influenced how leaf shape changed in response to different irrigation conditions. A similar irrigation-dependent effect of rootstock was found for the ion composition in the shoot. The team also identified roughly 100 genes with altered expression in each of the grafted vines, including five genes which were altered by all three graft combinations. These findings are a first step toward understanding the relationship between rootstocks and scions and modulating it to produce crops better adapted to challenging environments.

Genetics: Apple genome sequencing begins to bear fruit Almost 10 years since the first draft of the apple genome was published, the insights it has afforded are being used to improve crops, while next generation DNA sequencing is enabling the breeding value of individual plants to be more rapidly assessed. In this review, Cameron Peace at Washington State University in Pullman, US, and colleagues describe the impact whole genome sequencing of the Golden Delicious apple has had on our understanding of how cultivated apples evolved, and the genomic regions controlling fruit firmness and flavor, tree growth dynamics, responses to water and nutrient availability, and other such traits. These early discoveries have also paved the way for trait-predictive tests which should further accelerate the breeding of improved apple trees, and epigenetic studies to better understand how environmental factors trigger heritable changes in apple characteristics.

Abstract Grape growers use rootstocks to provide protection against pests and pathogens and to modulate viticulture performance such as shoot growth. Our study examined two grapevine scion varieties (‘Chardonnay’ and ‘Cabernet Sauvignon’) grafted to 15 different rootstocks and determined the effect of rootstocks on eight traits important to viticulture. We assessed the vines across five years and identified both year and variety as contributing strongly to trait variation. The effect of rootstock was relatively consistent across years and varieties, explaining between 8.99% and 9.78% of the variation in growth‐related traits including yield, pruning weight, berry weight and Ravaz index (yield to pruning weight ratio). Increases in yield due to rootstock were generally the result of increases in berry weight, likely due to increased water uptake by vines grafted to a particular rootstock. We demonstrated a greater than 50% increase in yield, pruning weight, or Ravaz index by choosing the optimal rootstock, indicating that rootstock choice is crucial for grape growers looking to improve vine performance.

Abstract Background Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Results Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. Conclusions By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from NGS technologies. It enables the user to quickly and easily examine the effects of varying thresholds and filters on the number and quality of the resulting genotype calls. In this manner, users can decide on thresholds that are most suitable for their purposes. We show that LinkImputeR can significantly augment the value and utility of NGS data sets, especially in non-model organisms with poor genomic resources.

Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple ( L.) cultivars. We linked genotype and phenotype information by combining genotyping-by-sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography–mass spectrometry (GC-MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl-transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker-assisted selection (MAS).

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.

Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches’ broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective long-term strategy to address Moniliophthora diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao.

In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a putative clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Using the GBS approach allowed us to estimate ploidy levels, which were in accordance with flow cytometry results. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allows detection of a much more detailed population structure and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purpose of identifying clones and pedigree relations in a diverse apple gene bank and discuss the advantages and constraints of the two approaches.

Apple (Malus spp.) is a widely grown and valuable fruit crop. Leaf shape is important for flowering in apple and may also be an early indicator for other agriculturally valuable traits. We examined 9,000 leaves from 869 unique apple accessions using linear measurements and comprehensive morphometric techniques. We identified allometric variation as the result of differing length-to-width aspect ratios between accessions and species of apple. The allometric variation was due to variation in the width of the leaf blade, not the length. Aspect ratio was highly correlated with the first principal component (PC1) of morphometric variation quantified using elliptical Fourier descriptors (EFDs) and persistent homology (PH). While the primary source of variation was aspect ratio, subsequent PCs corresponded to complex shape variation not captured by linear measurements. After linking the morphometric information with over 122,000 genome-wide single nucleotide polymorphisms (SNPs), we found high SNP heritability values even at later PCs, indicating that comprehensive morphometrics can capture complex, heritable phenotypes. Thus, techniques such as EFDs and PH are capturing heritable biological variation that would be missed using linear measurements alone.

Apple ( X Borkh.) is one of the world’s most valuable fruit crops. Its large size and long juvenile phase make it a particularly promising candidate for marker-assisted selection (MAS). However, advances in MAS in apple have been limited by a lack of phenotype and genotype data from sufficiently large samples. To establish genotype-phenotype relationships and advance MAS in apple, we extracted over 24,000 phenotype scores from the USDA-Germplasm Resources Information Network (GRIN) database and linked them with over 8000 single nucleotide polymorphisms (SNPs) from 689 apple accessions from the USDA apple germplasm collection clonally preserved in Geneva, NY. We find significant genetic differentiation between Old World and New World cultivars and demonstrate that the genetic structure of the domesticated apple also reflects the time required for ripening. A genome-wide association study (GWAS) of 36 phenotypes confirms the association between fruit color and the MYB1 locus, and we also report a novel association between the transcription factor, NAC18.1, and harvest date and fruit firmness. We demonstrate that harvest time and fruit size can be predicted with relatively high accuracies ( > 0.46) using genomic prediction. Rapid decay of linkage disequilibrium (LD) in apples means millions of SNPs may be required for well-powered GWAS. However, rapid LD decay also promises to enable extremely high resolution mapping of causal variants, which holds great potential for advancing MAS.

Grapevine leaves have diverse shapes and sizes which are influenced by many factors including genetics, vine phytosanitary status, environment, leaf and vine age, and node position on the shoot. To determine the relationship between grapevine leaf shape or size and leaf canopy temperature, we examined five seedling populations grown in a vineyard in California, USA. The populations had one parent with compound leaves of the Vitis piasezkii type and a different second parent with non-compound leaves. In previous work, we had measured the shape and size of the leaves collected from these populations using 21 homologous landmarks. Here, we paired these morphological data with canopy temperature measurements made using a handheld infrared thermometer. After recording time of sampling and canopy temperature, we used a linear model between time of sampling and canopy temperature to estimate temperature residuals. Based on these residuals, we determined if the canopy temperature of each vine was cooler or warmer than expected, based on the time of sampling. We established a relationship between leaf size and canopy temperature: vines with larger leaves were cooler than expected. By contrast, leaf shape was not strongly correlated with variation in canopy temperature. Ultimately, these findings indicate that vines with larger leaves may contribute to the reduction of overall canopy temperature; however, further work is needed to determine whether this is due to variation in leaf size, differences in the openness of the canopy or other related traits.