Toward plant breeding for multicrop systems.

Increasing cropping system diversity has great potential to address environmental problems associated with modern agriculture, such as erosion, soil carbon loss, nutrient runoff, water pollution, and loss of biodiversity. As with other agricultural sciences, plant breeding has primarily been conducted in the context of dominant monoculture cropping systems, with little focus on multicrop systems. Multicrop systems have increased temporal and/or spatial diversity and include a diverse set of crops and practices. In order to support a transition to multicrop systems, plant breeders must shift their breeding programs and objectives to better represent more diverse systems, including diverse rotations, alternate-season crops, ecosystem service crops, and intercropping systems. The degree to which breeding methods need to change will depend on the cropping system context in question. Plant breeding alone, however, cannot drive adoption of multicrop systems. Alongside shifts in breeding approaches, changes are needed within broader research, private sector, and policy contexts. These changes include policies and investments that support a transition to multicrop systems, increased collaboration across disciplines to support cropping system development, and leadership from both the public and private sectors to develop and promote adoption of new cultivars.

Perennial Baki™ Bean Safety for Human Consumption: Evidence from an Analysis of Heavy Metals, Folate, Canavanine, Mycotoxins, Microorganisms and Pesticides.

Global food production relies on annual grain crops. The reliability and productivity of these crops are threatened by adaptations to climate change and unsustainable rates of soil loss associated with their cultivation. Perennial grain crops, which do not require planting every year, have been proposed as a transformative solution to these challenges. Perennial grain crops typically rely on wild species as direct domesticates or as sources of perenniality in hybridization with annual grains. Onobrychis spp. (sainfoins) are a genus of perennial legumes domesticated as ancient forages. Baki™ bean is the tradename for pulses derived from sainfoins, with ongoing domestication underway to extend demonstrated benefits to sustainable agriculture. This study contributes to a growing body of evidence characterizing the nutritional quality of Baki™ bean. Through two studies, we investigated the safety of Baki™ bean for human consumption. We quantified heavy metals, folate, and canavanine for samples from commercial seed producers, and we quantified levels of mycotoxins, microorganisms, and pesticides in samples from a single year and seed producer, representing different varieties and production locations. The investigated analytes were not detectable or occurred at levels that do not pose a significant safety risk. Overall, this study supports the safety of Baki™ bean for human consumption as a novel pulse crop.

Massive phenotyping of multiple cranberry populations reveals novel QTLs for fruit anthocyanin content and other important chemical traits.

Because of its known phytochemical activity and benefits for human health, American cranberry (Vaccinium macrocarpon L.) production and commercialization around the world has gained importance in recent years. Flavonoid compounds as well as the balance of sugars and acids are key quality characteristics of fresh and processed cranberry products. In this study, we identified novel QTL that influence total anthocyanin content (TAcy), titratable acidity (TA), proanthocyanidin content (PAC), Brix, and mean fruit weight (MFW) in cranberry fruits. Using repeated measurements over the fruit ripening period, different QTLs were identified at specific time points that coincide with known chemical changes during fruit development and maturation. Some genetic regions appear to be regulating more than one trait. In addition, we demonstrate the utility of digital imaging as a reliable, inexpensive and high-throughput strategy for the quantification of anthocyanin content in cranberry fruits. Using this imaging approach, we identified a set of QTLs across three different breeding populations which collocated with anthocyanin QTL identified using wet-lab approaches. We demonstrate the use of a high-throughput, reliable and highly accessible imaging strategy for predicting anthocyanin content based on cranberry fruit color, which could have a large impact for both industry and cranberry research.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

BACKGROUND: The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. RESULTS: We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. CONCLUSIONS: GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).

Fragman: an R package for fragment analysis.

BACKGROUND: Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. RESULTS: We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® (ABI) either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry (Vaccinium macrocarpon) genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. CONCLUSION: Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.

Development and validation of 697 novel polymorphic genomic and EST-SSR markers in the American cranberry (Vaccinium macrocarpon Ait.).

The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.

Effect of sainfoin (Onobrychis viciifolia Scop.) seed-based diet on rats: A comprehensive evaluation of hemogram, biochemistry, and histopathology.

Sainfoin species (Onobrychis spp.) have been employed for centuries as an essential forage for ruminant animals, both for grazing and as hay. The seeds produced by sainfoin have also been investigated as an animal feed source and were indicated to be a particularly protein-rich supplement for monogastric animals. This study explores the effects of two sainfoin seed inclusion rates in rat diets compared to a control diet, focusing on blood biochemical parameters and a comprehensive histopathological evaluation of multiple organ systems. Thus, we provide a novel contribution to the body of evidence investigating sainfoin seeds as a protein supplement in monogastric animal diets. In this 21-day experiment, seven rats each were assigned to the control group, a 5% sainfoin seed group, and a 10% sainfoin seed group. The control group received standard feed and water; the second group received feed with 5% sainfoin seeds; and the third group received feed with 10% sainfoin seeds. At the experiment's end, necropsies and evaluations were conducted. Histopathological exams revealed normal organ structures in all 21 samples, regardless of the group. Blood analysis showed statistically significant decreases in creatine, ALT, P, Ca, and Mg levels in the sainfoin seed groups compared to the control group, with most values nearing reference levels, suggesting potential benefits. Notably, no adverse effects were observed when sainfoin seeds were included at 5% and 10% in the rat feed. These findings contribute to a growing body of research investigating the inclusion of sainfoin seeds in monogastric animal diets, which is a foundational component of assessing sainfoin's potential as a novel pulse crop for human consumption.

Amino acid and fatty acid profiles of perennial Baki™ bean.

To realize the potential of sainfoins to contribute to sustainable agriculture and expand on demonstrated uses and benefits, de novo domestication is occurring to develop perennial Baki™ bean, the trade name used by The Land Institute for pulses (i.e., grain legumes) derived from sainfoins. The objective of this study was to characterize amino acid and fatty acid profiles of depodded seeds from commercial sainfoin (Onobrychis viciifolia) seed lots, and compare these results with data published in the Global Food Composition Database for Pulses. The fatty acid profile consisted primarily of polyunsaturated fatty acids (56.8%), compared to monounsaturated (29.0%) and saturated fatty acids (14.2%), and n-3 fatty acids (39.5%), compared to n-9 (28.4%) and n-6 (17.6%) fatty acids. The essential fatty acid linolenic acid (18,3 n-3) was the most abundant fatty acid (39.2%), followed by oleic acid (18,1 cis-9) (27.8%), and the essential fatty acid linoleic acid (18,2 n-6) (17.3%). The amino acid profile consisted primarily of the nonessential amino acids glutamic acid (18.3%), arginine (11.6%), and aspartic acid (10.8%), followed by the essential amino acids leucine (6.8%), and lysine (5.8%). Essential amino acid content met adult daily requirements for each amino acid. This indicates that sainfoin seeds may be a complete plant protein source. However, further research is necessary to better understand protein quality, defined by protein digestibility in addition to the amino acid profile. By demonstrating favorable fatty acid and amino acid profiles to human health, these results contribute to a growing body of evidence supporting the potential benefits of perennial Baki™ bean, a novel, perennial pulse derived from sainfoins.

Sainfoin (Onobrychis spp.) crop ontology: supporting germplasm characterization and international research collaborations.

Sainfoin (Onobrychis spp.) is a perennial forage legume that is also attracting attention as a perennial pulse with potential for human consumption. The dual use of sainfoin underpins diverse research and breeding programs focused on improving sainfoin lines for forage and pulses, which is driving the generation of complex datasets describing high dimensional phenotypes in the post-omics era. To ensure that multiple user groups, for example, breeders selecting for forage and those selecting for edible seed, can utilize these rich datasets, it is necessary to develop common ontologies and accessible ontology platforms. One such platform, Crop Ontology, was created in 2008 by the Consortium of International Agricultural Research Centers (CGIAR) to host crop-specific trait ontologies that support standardized plant breeding databases. In the present study, we describe the sainfoin crop ontology (CO). An in-depth literature review was performed to develop a comprehensive list of traits measured and reported in sainfoin. Because the same traits can be measured in different ways, ultimately, a set of 98 variables (variable = plant trait + method of measurement + scale of measurement) used to describe variation in sainfoin were identified. Variables were formatted and standardized based on guidelines provided here for inclusion in the sainfoin CO. The 98 variables contained a total of 82 traits from four trait classes of which 24 were agronomic, 31 were morphological, 19 were seed and forage quality related, and 8 were phenological. In addition to the developed variables, we have provided a roadmap for developing and submission of new traits to the sainfoin CO.

Plant Breeding for Intercropping in Temperate Field Crop Systems: A Review.

Monoculture cropping systems currently dominate temperate agroecosystems. However, intercropping can provide valuable benefits, including greater yield stability, increased total productivity, and resilience in the face of pest and disease outbreaks. Plant breeding efforts in temperate field crops are largely focused on monoculture production, but as intercropping becomes more widespread, there is a need for cultivars adapted to these cropping systems. Cultivar development for intercropping systems requires a systems approach, from the decision to breed for intercropping systems through the final stages of variety testing and release. Design of a breeding scheme should include information about species variation for performance in intercropping, presence of genotype × management interaction, observation of key traits conferring success in intercropping systems, and the specificity of intercropping performance. Together this information can help to identify an optimal selection scheme. Agronomic and ecological knowledge are critical in the design of selection schemes in cropping systems with greater complexity, and interaction with other researchers and key stakeholders inform breeding decisions throughout the process. This review explores the above considerations through three case studies: (1) forage mixtures, (2) perennial groundcover systems (PGC), and (3) soybean-pennycress intercropping. We provide an overview of each cropping system, identify relevant considerations for plant breeding efforts, describe previous breeding focused on the cropping system, examine the extent to which proposed theoretical approaches have been implemented in breeding programs, and identify areas for future development.

Re-imagining crop domestication in the era of high throughput phenomics.

De novo domestication is an exciting option for increasing species diversity and ecosystem service functionality of agricultural landscapes. Genomic selection (GS), the application of genomic markers to predict phenotypic traits in a breeding population, offers the possibility of rapid genetic improvement, making GS especially attractive for modifying traits of long-lived species. However, for some wild species just entering the domestication pipeline, especially those with large and complex genomes, a lack of funding and/or prior genome characterization, GS is often out of reach. High throughput phenomics has the potential to augment traditional pedigree selection, reduce costs and amplify impacts of genomic selection, and even create new predictive selection approaches independent of sequencing or pedigrees.

Perennial groundcovers: an emerging technology for soil conservation and the sustainable intensification of agriculture.

Integrating perennial groundcovers (PGC) - sometimes referred to as living mulches or perennial cover crops - into annual cash-crop systems could address root causes of bare-soil practices that lead to negative impacts on soil and water quality. Perennial groundcovers bring otherwise absent functional traits - namely perenniality - into cash-crop systems to preserve soil and regenerate water, carbon, and nutrient cycles. However, if not optimized, they can also cause competitive interactions and yield loss. When designing PGC systems, the goal is to maximize complementarity - spatial and temporal separation of growth and resource acquisition - between PGC and cash crops through both breeding and management. Traits of interest include complementary root and shoot systems, reduced shade avoidance response in the cash-crop, and PGC summer dormancy. Successful deployment of PGC systems could increase both productivity and profitability by improving water- and nutrient-use-efficiency, improving weed and pest control, and creating additional value-added opportunities like stover harvest. Many scientific questions about the inherent interactions at the cell, plant, and ecosystem levels in PGC systems are waiting to be explored. Their answers could enable innovation and refinement of PGC system design for multiple geographies, crops, and food systems, creating a practical and scalable pathway towards resiliency, crop diversification, and sustainable intensification in agriculture.

Morphometric approaches to promote the use of exotic germplasm for improved food security and resilience to climate change: a kura clover example.

Adaptation of agriculture to climate change and its associated ecological pressures will require new crops, novel trait combinations, and previously unknown phenotypic attributes to deploy in climate resilient cropping systems. Genebanks, a primary source of exotic germplasm for novel crops and breeding materials, need comprehensive methods to detect novel and unknown phenotypes without a priori information about the species or trait under consideration. We demonstrate how persistent homology (PH) and elliptical Fourier descriptors (EFD), two morphometric techniques easily applied to image-based data, can serve this purpose by cataloging leaf morphology in the USDA NPGS kura clover collection and demarcating a leaf morphospace for the species. Additionally, we identify a set of representative accessions spanning the leaf morphospace and propose they serve as a kura clover core collection. The core collection will be a framework for monitoring the effects of climate change on kura clover in situ diversity and determining the role of ex situ accessions in modern agriculture.

Reprint of: Morphometric approaches to promote the use of exotic germplasm for improved food security and resilience to climate change: A kura clover example.

Adaptation of agriculture to climate change and its associated ecological pressures will require new crops, novel trait combinations, and previously unknown phenotypic attributes to deploy in climate resilient cropping systems. Genebanks, a primary source of exotic germplasm for novel crops and breeding materials, need comprehensive methods to detect novel and unknown phenotypes without a priori information about the species or trait under consideration. We demonstrate how persistent homology (PH) and elliptical fourier descriptors (EFD), two morphometric techniques easily applied to image-based data, can serve this purpose by cataloging leaf morphology in the USDA NPGS kura clover collection and demarcating a leaf morphospace for the species. Additionally, we identify a set of representative accessions spanning the leaf morphospace and propose they serve as a kura clover core collection. The core collection will be a framework for monitoring the effects of climate change on kura clover in situ diversity and determining the role of ex situ accessions in modern agriculture.

New Food Crop Domestication in the Age of Gene Editing: Genetic, Agronomic and Cultural Change Remain Co-evolutionarily Entangled.

The classic domestication scenario for grains and fruits has been portrayed as the lucky fixation of major-effect "domestication genes." Characterization of these genes plus recent improvements in generating novel alleles (e.g., by gene editing) have created great interest in de novo domestication of new crops from wild species. While new gene editing technologies may accelerate some genetic aspects of domestication, we caution that de novo domestication should be understood as an iterative process rather than a singular event. Changes in human social preferences and relationships and ongoing agronomic innovation, along with broad genetic changes, may be foundational. Allele frequency changes at many loci controlling quantitative traits not normally included in the domestication syndrome may be required to achieve sufficient yield, quality, defense, and broad adaptation. The environments, practices and tools developed and maintained by farmers and researchers over generations contribute to crop yield and success, yet those may not be appropriate for new crops without a history of agronomy. New crops must compete with crops that benefit from long-standing participation in human cultural evolution; adoption of new crops may require accelerating the evolution of new crops' culinary and cultural significance, the emergence of markets and trade, and the formation and support of agricultural and scholarly institutions. We provide a practical framework that highlights and integrates these genetic, agronomic, and cultural drivers of change to conceptualize de novo domestication for communities of new crop domesticators, growers and consumers. Major gene-focused domestication may be valuable in creating allele variants that are critical to domestication but will not alone result in widespread and ongoing cultivation of new crops. Gene editing does not bypass or diminish the need for classical breeding, ethnobotanical and horticultural knowledge, local agronomy and crop protection research and extension, farmer participation, and social and cultural research and outreach. To realize the ecological and social benefits that a new era of de novo domestication could offer, we call on funding agencies, proposal reviewers and authors, and research communities to value and support these disciplines and approaches as essential to the success of the breakthroughs that are expected from gene editing techniques.

Image-based phenotyping for identification of QTL determining fruit shape and size in American cranberry (Vaccinium macrocarpon L.).

Image-based phenotyping methodologies are powerful tools to determine quality parameters for fruit breeders and processors. The fruit size and shape of American cranberry (Vaccinium macrocarpon L.) are particularly important characteristics that determine the harvests' processing value and potential end-use products (e.g., juice vs. sweetened dried cranberries). However, cranberry fruit size and shape attributes can be difficult and time consuming for breeders and processors to measure, especially when relying on manual measurements and visual ratings. Therefore, in this study, we implemented image-based phenotyping techniques for gathering data regarding basic cranberry fruit parameters such as length, width, length-to-width ratio, and eccentricity. Additionally, we applied a persistent homology algorithm to better characterize complex shape parameters. Using this high-throughput artificial vision approach, we characterized fruit from 351 progeny from a full-sib cranberry population over three field seasons. Using a covariate analysis to maximize the identification of well-supported quantitative trait loci (QTL), we found 252 single QTL in a 3-year period for cranberry fruit size and shape descriptors from which 20% were consistently found in all years. The present study highlights the potential for the identified QTL and the image-based methods to serve as a basis for future explorations of the genetic architecture of fruit size and shape in cranberry and other fruit crops.

Multivariate GBLUP Improves Accuracy of Genomic Selection for Yield and Fruit Weight in Biparental Populations of Vaccinium macrocarpon Ait.

The development of high-throughput genotyping has made genome-wide association (GWAS) and genomic selection (GS) applications possible for both model and non-model species. The exploitation of genome-assisted approaches could greatly benefit breeding efforts in American cranberry (Vaccinium macrocarpon) and other minor crops. Using biparental populations with different degrees of relatedness, we evaluated multiple GS methods for total yield (TY) and mean fruit weight (MFW). Specifically, we compared predictive ability (PA) differences between univariate and multivariate genomic best linear unbiased predictors (GBLUP and MGBLUP, respectively). We found that MGBLUP provided higher predictive ability (PA) than GBLUP, in scenarios with medium genetic correlation (8-17% increase with corg~0.6) and high genetic correlations (25-156% with corg~0.9), but found no increase when genetic correlation was low. In addition, we found that only a few hundred single nucleotide polymorphism (SNP) markers are needed to reach a plateau in PA for both traits in the biparental populations studied (in full linkage disequilibrium). We observed that higher resemblance among individuals in the training (TP) and validation (VP) populations provided greater PA. Although multivariate GS methods are available, genetic correlations and other factors need to be carefully considered when applying these methods for genetic improvement.

Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping.

The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

GiNA, an Efficient and High-Throughput Software for Horticultural Phenotyping.

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables.

The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants.

This is the first de novo assembly and annotation of a complete mitochondrial genome in the Ericales order from the American cranberry (Vaccinium macrocarpon Ait.). Moreover, only four complete Asterid mitochondrial genomes have been made publicly available. The cranberry mitochondrial genome was assembled and reconstructed from whole genome 454 Roche GS-FLX and Illumina shotgun sequences. Compared with other Asterids, the reconstruction of the genome revealed an average size mitochondrion (459,678 nt) with relatively little repetitive sequences and DNA of plastid origin. The complete mitochondrial genome of cranberry was annotated obtaining a total of 34 genes classified based on their putative function, plus three ribosomal RNAs, and 17 transfer RNAs. Maternal organellar cranberry inheritance was inferred by analyzing gene variation in the cranberry mitochondria and plastid genomes. The annotation of cranberry mitochondrial genome revealed the presence of two copies of tRNA-Sec and a selenocysteine insertion sequence (SECIS) element which were lost in plants during evolution. This is the first report of a land plant possessing selenocysteine insertion machinery at the sequence level.