National Plant Germplasm System Research Articles

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Annual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species.

Origin of current intermediate wheatgrass germplasm being developed for Kernza grain production

AbstractIntermediate wheatgrass (IWG, Thinopyrum intermedium [Host] Barkworth & D. R. Dewey) has been developed as a perennial grain crop for human consumption along with providing environmental benefits and ecosystem services. Grain and products derived from IWG cultivars improved for food production have been marketed under the registered trademark, Kernza. Development of IWG as a perennial grain crop began in 1980s with a phenotypic recurrent selection program as the Rodale Institute (RI) and the Big Flats Plant Material Center (BFPMC) used IWG plant introductions (PI) from the National Plant Germplasm System (NPGS) to improve populations of IWG. Initial selections were provided to The Land Institute (TLI) where they were subsequently improved for grain production, yet the identity of the founder material of improved, food-grade IWG has not been publicly documented. Recently recovered original documents have been used to reconstruct the early breeding program to identify the most likely 20 PIs that form the founders of modern food-grade IWG. Molecular data using genotyping-by-sequencing in current elite breeding material, and remnant seed and plant material from the initial RI selections have provided supporting evidence for the historical records. The genetic origin for food-grade IWG is focused between the Black Sea and Caspian Sea in the Stavropol region of Russia, with smaller contributions likely from collections as distant as Kazakhstan in the east to Turkey in the west. This work connects the flow of germplasm and utility of NPGS PIs to present day IWG grain cultivars being developed in multiple breeding programs around the world.

Genetic Diversity of New Almond Accessions from Central Asian and Cold-adapted North American Germplasm

We evaluated the genetic diversity of a newly available collection of 94 almond [Prunus dulcis (Mill.) D.A. Webb] accessions from the former Improving Perennial Plants for Food and Bioenergy (IPPFBE) Foundation. Most of the collection (87 accessions) were collected as seeds from trees growing in the central Asian nations of Kyrgyzstan, Tajikistan, and Uzbekistan, and included several examples of Prunus bucharica (Korsh.) Hand.-Mazz, and related wild species. Of the remaining accessions, six were sourced from a nursery in northern Utah in the United States, and one was a seedling of ‘Nonpareil’, a major commercial cultivar. DNA fingerprints were generated from 10 simple sequence repeat markers. To evaluate the comparative diversity of these new accessions, 66 accessions from the US Department of Agriculture, National Plant Germplasm System (NPGS) almond germplasm collection near Davis, CA, USA, were also included. These NPGS accessions were chosen to represent those collected in similar regions of Central Asia and the Caucasus. The fingerprints were analyzed via hierarchical clustering, principal components analysis (PCA), and discriminant analysis of principal components (DAPC). Hierarchical clustering suggested that half of the Utah-sourced accessions are closely related to each other and to the ‘Nonpareil’ seedling. Additional close relationships were detected (including at least one duplication or mislabeling), and two P. bucharica accessions from the IPPFBE collection were separated from the rest of the collection. A plot of the first two principal components clearly separated wild almond relatives (P. bucharica and Prunus fenzliana Fritsch) from the remaining accessions. PCA after removal of the wild species separated the ‘Nonpareil’ seedling, the Utah-sourced accessions, and many of the IPPFBE accessions (mostly from Uzbekistan) from nearly all other individuals. The third principal component identified an additional population structure that separated groups of predominantly IPPFBE or NPGS accessions. DAPC showed a considerable admixture of accessions from Azerbaijan, and a little to no admixture of accessions from Georgia and Tajikistan. These results suggest that central Asian/Caucasian almond germplasm is generally distinct from ‘Nonpareil’ and its relatives, and that although there is overlap between the NPGS and IPPFBE collections from this region, the IPPFBE collection does enhance the diversity of available almond germplasm.

‘Newell’ bermudagrass: A public release from the USDA Cynodon collection

AbstractWarm‐season perennial grasses are the backbone of the pasture‐based livestock industry in the lower southeastern United States, and bermudagrass (Cynodon spp.) is the most widely planted forage species, covering ∼15 million ha. The genus Cynodon is native to southern Africa, and germplasm collections possess high genetic and phenotypic variability. The USDA National Plant Germplasm System maintains a collection of bermudagrass plant introductions (PIs) in Griffin, GA, and USDA‐ARS, Tifton, GA, maintains additional germplasm. Multi‐location trials were established in four states (Florida, Georgia, North Carolina, and Oklahoma) to screen Cynodon germplasm for herbage accumulation (HA), nutritive value (NV), and bermudagrass stem maggot (BSM) (Atherigona reversura Villeneuve). Due to the large genotype × environment interaction for HA, we focused on selecting accessions adapted to South Georgia and Florida, and further studies were performed in Florida. Several PIs showed improved HA and NV compared with ‘Tifton 85’. PI 316510, originally introduced from Ingelheim, Germany, produced high HA in Citra, FL, and Tifton, GA, with improved NV traits. In addition, PI 316510 had faster establishment and similar BSM tolerance to Tifton 85. We confirmed PI 316510 as tetraploid (2n = 4x = 36) through chromosome counts and flow cytometry, and it is genetically distinct from other commercial cultivars. PI 316510 has been publicly released under the name ‘Newell’, and it is vegetatively propagated. Planting material can be requested from the UF‐IFAS Forage Breeding program.

European Taxonomists in Profile: A Data-Driven Approach

This presentation focuses on the service aspect of taxonomy in Europe, encompassing the description, identification, and nomenclature of taxa. This aspect of taxonomy supports all biological research, and working taxonomists contribute to it in different degrees (Dayrat 2005). Taxonomy also serves as a research discipline, emphasising the evolutionary aspects of biodiversity, but this study specifically investigates only the supply of taxonomists as a service and compares this with the demand for taxonomy, which arises from policy that requires information on European biodiversity for development or implementation. To profile taxonomists, we adopt an automated approach using OpenAlex, an open bibliography of scholarly publications, to extract comprehensive data on authors, their affiliated institutions, and their respective taxa of expertise. This automated approach avoids the well-known biases of self-reported questionnaires, thus ensuring robust coverage across all taxa, and minimising potential geographic, gender and demographic biases. In addition to analysing the current availability of taxonomic expertise (supply side), this study explores the gaps in taxonomic expertise by examining significant taxa from research and policy perspectives (demand side). Leveraging datasets such as the list of invasive species on the horizon for Europe (Roy et al. 2018), the Crop Wild Relative Data section of the U.S. National Plant Germplasm System (USDA 2023) and the International Union for Conservation of Nature's Red List of Threatened Species (IUCN 2022), we assess the demand for taxonomic expertise. A flow diagram (Fig. 1) illustrates our step-by-step methodology. Beginning with data extraction from OpenAlex, we categorised and analysed more than 650 taxonomic journals published over the past ten years. We filtered these for relevant papers only from European institutions. This resulted in a subset of 31 thousand publications from which we identified 44 thousand authors, and were able to map their taxonomic expertise and their geographic spread. This comprehensive workflow provides detailed demographic data directly derived from bibliographic information, extending on the Red List of Insect Taxonomists (Hochkirch et al. 2022) and enabling repeatable analyses to monitor trends and changes over time. For example, we can track the usage of ORCID identifers by European taxonomists, which we calculate is currently at 64%. By considering the demand side rather than assuming equal policy importance across all taxa, our study offers nuanced insights into the contribution of taxonomists in addressing conservation and policy needs in Europe. Furthermore, by highlighting impacts, challenges, and potential solutions, we underscore the significance of taxonomy as a vital service. The recommendations aim to prioritise taxonomy, enhance its contributions to biodiversity conservation efforts, and provide guidance to policymakers, researchers, and stakeholders invested in sustaining Europe's rich biodiversity.

Registration of ‘DALSA 1618’ St. Augustinegrass

Abstract‘DALSA 1618’ (Reg. no. CV‐291, PI 702594) is a first‐generation intraspecific St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] hybrid developed by Texas A&M AgriLife Research in Dallas, TX, from a cross between a drought‐resistant polyploid female parent, TAES 5384 (PI 300130, GRIN National Plant Germplasm System), and a semi‐dwarf shade‐tolerant diploid pollen donor, ‘Amerishade’. DALSA 1618 was formerly tested as ‘TAES 5896‐09’ and ‘TXSA‐156’. Superior performance and quality from 2010 to 2015 in space‐plant nurseries across multiple environments led to advancing DALSA 1618 to replicated trials in 10 National Turfgrass Evaluation Program (NTEP) locations across the southcentral and southeastern United States. DALSA 1618 was one of the top performers in the 2016 NTEP (2016–2020). It established faster than ‘CitraBlue’ and similarly to other tested commercial cultivars. DALSA 1618 exhibited high turfgrass quality in standard and ancillary trials and earlier spring greenup, which was generally better than ‘Floratam’. Drought resistance of DALSA 1618 was similar to Floratam (a drought‐resistant aneuploid). Tolerance to moderately dense shade was tested in Dallas, TX, from 2017 to 2020, where DALSA 1618 exhibited improved shade tolerance relative to Floratam. This array of environmental testing indicates DALSA 1618 possesses a unique combination of drought and shade tolerance that would allow its use across the southcentral and southeastern United States.

Safeguarding plant genetic resources in the United States during global climate change

AbstractPlant genetic resources (PGR) underpin the security of global agriculture. Rapid global climate change presents formidable challenges for ex situ and in situ PGR management programs that operate over extended timeframes. The U.S. Department of Agriculture National Plant Germplasm System (NPGS) maintains more than 605,000 PGR accessions representing over 16,300 plant species in 20 genebank locations. These PGR are maintained in cold storage as seeds and vegetative tissues that must be periodically regenerated; or as actively growing plants in fields, greenhouses, screenhouses, and in vitro; or in some cases within in situ reserves. The complicated relationships between crops and their growth environments present unique challenges regarding PGR maintenance under a changing climate. Here we present potential effects of climate change on ex situ PGR maintenance and reproductive success, pollinators and beneficial insects, pathogens and pests, infrastructure considerations, and wild populations within NPGS in situ reserves. We provide a novel tool that summarizes past US temperature and precipitation data alongside future climate projections to guide ongoing planning for the effects of climate change for NPGS genebanks throughout the United States. A series of case studies exemplify instances where climate change has already impacted NPGS PGR management. Ongoing improvements to NPGS PGR management in response to climate change require continued observations of the current effects, careful and innovative planning, and creative approaches to ensure that PGR are successfully conserved for future generations.

Characterization of the seed virome of alfalfa (Medicago sativa L)

BackgroundSeed transmission of plant viruses can be important due to the role it plays in their dissemination to new areas and subsequent epidemics. Seed transmission largely depends on the ability of a virus to replicate in reproductive tissues and survive during the seed maturation process. It occurs through the infected embryo or mechanically through the contaminated seed coat. Alfalfa (Medicago sativa L.) is an important legume forage crop worldwide, and except for a few individual seedborne viruses infecting the crop, its seed virome is poorly known. The goal of this research was to perform initial seed screenings on alfalfa germplasm accessions maintained by the USDA ARS National Plant Germplasm System in order to identify pathogenic viruses and understand their potential for dissemination.MethodsFor the detection of viruses, we used high throughput sequencing combined with bioinformatic tools and reverse transcription-polymerase chain reactions.ResultsOur results suggest that, in addition to common viruses, alfalfa seeds are infected by other potentially pathogenic viral species that could be vertically transmitted to offspring.ConclusionsTo the best of our knowledge, this is the first study of the alfalfa seed virome carried out by HTS technology. This initial screening of alfalfa germplasm accessions maintained by the NPGS showed that the crop’s mature seeds contain a broad range of viruses, some of which were not previously considered to be seed-transmitted. The information gathered will be used to update germplasm distribution policies and to make decisions on the safety of distributing germplasm based on viral presence.

Assessment of Grain Protein in Tropical Sorghum Accessions from the NPGS Germplasm Collection

The development of higher nutritional sorghum varieties requires the identification of high protein content germplasm that expands the genetic diversity of breeding programs. Therefore, a near-infrared (NIR) spectroscopy method was developed to predict the protein concentration of whole-grain sorghum with R2 = 0.83, root-mean-square error of prediction = 1.44%, and bias = 0.16%. We evaluated 228 tropical accessions from West and Central Africa maintained by the National Plant Germplasm System (NPGS) of the United States for protein content for three years. The analysis found that the protein concentrations among accessions varied from 5.05 to 15.00% with an average of 10.24%. Correlation analysis between years revealed changes in protein content and ranking across years for multiple accessions. However, heritability of protein concentration was moderately high (H2 = 0.81) indicating most of the observed variation could be determined by genetic differences among accessions. Sixteen tropical accessions with the highest protein concentration (>12.84%) may be used in breeding programs for the development of new and improved nutritional varieties. This assessment documented the range of natural variation for protein content in the NPGS sorghum tropical germplasm collection that could be used to enhance breeding programs focused on biofortification.

Lessons from a soybean collection

AbstractThe United States Department of Agriculture (USDA) Soybean Germplasm Collection was established in 1949. Growth of the collection has been uneven throughout its history. Restrictions on germplasm exchanges and collections will likely prevent rapid growth of the collection in the foreseeable future. Because the USDA Soybean Germplasm Collection has limited opportunities to grow and is well evaluated and characterized for both phenotypic and genotypic traits, it is a mature collection. Mature collections will require fewer resources for acquiring, documenting, evaluating, and characterizing accessions which will permit an emphasis on research that will foster increased utilization. Pure lining accessions of self‐pollinated species is superior for maintaining genetic diversity. Genetic drift, natural selection, and sample contamination are problems for mixed seed lots. We document unintended changes for this type of accession. Mixed seed lots also limit meaningful evaluation. Research is a critical part of effective germplasm curation. We report successful research within the USDA Soybean Germplasm Collection that identified exotic accessions that contributed haplotypes that increase the yield of the highest yielding cultivars and are absent from the commercially used gene pool of the northern United States. Crosses with wild soybean produced lines that yielded more than the soybean parent. We developed procedures to produce fertile progenies from crosses between soybean and Glycine tomentella and identified derived lines that exceeded the yield of the soybean parent. Research on accessions within the National Plant Germplasm system is critical if the preserved germplasm is to be used to its fullest potential.

Genomic insights into the NPGS intermediate wheatgrass germplasm collection

AbstractThe National Plant Germplasm System (NPGS) is a vital resource for genetic diversity, yet utilization of this resource requires a thorough understanding of the germplasm and genetic diversity. Intermediate wheatgrass (IWG, Thinopyrum intermedium) is a perennial grass species that has been improved for forage production through breeding utilizing the NPGS collection and has also been targeted for domestication as a perennial grain crop. To better characterize the IWG collection, we combined previously published forage data with new agronomic and genomic data. A total of 331 NPGS accessions were genomically profiled with genotyping‐by‐sequencing (GBS) and a genome‐wide association study (GWAS) was used to evaluate trait architecture. Along with the GWAS, in silico bulk samples were profiled by recoding GBS data to conduct association mapping through allele counting with extreme‐phenotype (XP)‐GWAS. Genomic analysis revealed two subpopulations, which were defined as European and Asian groups, and are differentiated around the Black Sea region. Phenotypic observations for forage and agronomic traits differed between the two groups (p < 0.05), even though greater than 70% of the genetic variance was partitioned within individual accessions. Finally, XP‐GWAS revealed 303 marker–trait associations for five agronomic and four forage traits. These results suggest that genetic diversity within the NPGS collection should lead to genetic gains for both forage and grain breeding as well as opportunities for breeding programs to enhance genetic diversity. More broadly, the methods we applied could be applicable to low‐resourced species, leveraging existing, and new data, to strengthen genetic characterization and breeding efficiency.

Variation in Seed Germination and Amylase Activity of Diverse Carrot [Daucus carota (L.)] Germplasm under Simulated Drought Stress

Drought is one of the major environmental challenges constraining the production of agricultural crops, including carrot. Seed germination is the initial and most critical stage of crop establishment, and it is very sensitive to drought stress because water scarcity affects the enzymatic solubilization of stored metabolites in seeds that provide energy for the growth of germinating embryo. Few studies evaluating the effect of drought stress on carrot seed germination of more than a few cultivars grown under stress have been published. Therefore, the present study was designed to define the appropriate osmotic potential for evaluating drought tolerance of carrot, evaluate the response of diverse carrot germplasm to drought stress during seed germination to identify drought-tolerant accessions that may be used by plant breeders, and evaluate the relation between amylase activity and germination rate of drought-tolerant and drought-sensitive accessions. To identify an appropriate screening osmotic potential, two commercial cultivars and two United States Department of Agriculture inbreeds were evaluated at six osmotic potentials (00, −0.30, −0.51, −0.58, −0.80, and −1.05 MPa); −0.58 MPa was identified as the optimal osmotic potential for screening the drought tolerance of carrot seed. Cultivated and wild carrot plant introductions (PIs) (n = 200 and n = 50, respectively) from the National Plant Germplasm System were evaluated for drought tolerance under nonstress and simulated drought stress conditions (00 MPa and −0.58 MPa, respectively) by calculating the absolute decrease (AD) in percent germination, inhibition index (II), relative drought tolerance (RDT), and drought tolerance index (DTI). All measurements of drought tolerance identified significant differences among accessions; the AD in seed germination ranged from 0.0% to 69.3%, II ranged from 0.0% to 80.2%, RDT ranged from 0.2 to 1.0, and DTI ranged from 0.13 to 1.47. All wild carrot accessions displayed low levels of drought tolerance, but PI 652387 and PI 177381 (both from Turkey) and PI 274297 (Pakistan) were most drought-sensitive, whereas cultivated accessions PI 643114 (United States), PI 652208 (China), and PI 502347 (Uzbekistan) were most drought-tolerant. Tolerant accessions displayed much higher α-amylase activity under nonstress conditions than sensitive accessions, and α-amylase activity of tolerant accessions was also reduced less with seed germination under increasing osmotic potential (range, 0.0 to −1.05 MPa) than sensitive accessions over 24, 48, and 72 hours of seed germination. This is the first evaluation of drought stress tolerance during seed germination and the enzymatic response of diverse carrot germplasms under simulated drought stress.

Variation for turfgrass performance in a set of Lolium perenne germplasm evaluated under limited irrigation

AbstractPerennial ryegrass (Lolium perenne L.) is a major turfgrass species in temperate regions around the world. Unfortunately, it lacks drought tolerance compared with other cool‐season turfgrass species and often requires substantial inputs of freshwater as supplemental irrigation to achieve high turfgrass quality. To address the need for more drought‐tolerant perennial ryegrass, we conducted an evaluation of perennial ryegrass germplasm from the U.S. National Plant Germplasm System under deficit irrigation conditions and two mowing heights at Kaysville and Logan, UT during 2017 and 2018. We characterized turfgrass dark green color, ground cover, density, and quality using digital photography to capture images that we then converted to trait values using the TurfAnalyzer software. The higher mowing height resulted in greater ground cover, density, and quality. The collection of 49 germplasm accessions and 11 cultivars exhibited substantial variation for turfgrass dark green color, ground cover, density, and quality. Cultivars included as checks generally had greater turfgrass color and density, but the germplasm accessions generally had greater turfgrass ground cover and quality. Selection among these germplasm accessions will provide elite germplasm with utility for improving these traits in applied perennial ryegrass turfgrass breeding programs.

Unraveling phenotypic diversity in Cynodon spp. germplasm for forage accumulation and nutritive value in the transition zone

AbstractCharacterizing phenotypic variation in germplasm collections is crucial for plant breeding. Cynodon spp. accessions maintained at the USDA National Plant Germplasm System (NPGS), and the core forage collection were screened in a replicated trial under two nitrogen rates (0 and 150 kg ha−1 per harvest) in Ardmore, OK. The goals for this study were to: (a) estimate genetic parameters for forage accumulation (FA) and nutritive value (NV), (b) estimate genotype × harvest (rgh) and genotype × environment (rge) interaction for all traits, (c) quantify FA and NV for commercial cultivars and selected accessions. The experiment was setup as a row‐column design with two replicates and augmented representation of controls: Tifton 85, Wrangler, Midland, and Cheyenne. The trial was harvested five times (twice in 2016 and three times in 2017) and data were analyzed using linear mixed models. Genetic parameters revealed the presence of significant phenotypic variation for FA and NV. Low genotype × harvest and genotype × environment interactions indicated genotypic stability and potential for selecting improved accessions for FA and NV. Several plant introductions (PIs) were identified for their improved FA and NV. The application of N increased FA and CP concentration in all harvests but did not significantly impact phenotypic variation in other NV traits. Phenotypic data will be deposited in the Germplasm Resource Information Network (GRIN)‐Global database.

Evaluation of the resistance to Chinese predominant races of Puccinia triticina and analysis of effective leaf rust resistance genes in wheat accessions from the U.S. National Plant Germplasm System.

Puccinia triticina, which is the causative agent of wheat leaf rust, is widely spread in China and most other wheat-planting countries around the globe. Cultivating resistant wheat cultivars is the most economical, effective, and environmentally friendly method for controlling leaf rust-caused yield damage. Exploring the source of resistance is very important in wheat resistance breeding programs. In order to explore more effective resistance sources for wheat leaf rust, the resistance of 112 wheat accessions introduced from the U.S. National Plant Germplasm System were identified using a mixture of pathogenic isolates of THTT, THTS, PHTT, THJT and THJS which are the most predominant races in China. As a result, all of these accessions showed high resistance at seedling stage, of which, ninety-nine accessions exhibited resistance at adult plant stage. Eleven molecular markers of eight effective leaf rust resistance genes in China were used to screen the 112 accessions. Seven effective leaf rust resistance genes Lr9, Lr19, Lr24, Lr28, Lr29, Lr38 and Lr45 were detected, except Lr47. Twenty-three accessions had only one of those seven effective leaf rust resistance gene. Eleven accessions carried Lr24+Lr38, and 7 accessions carried Lr9+Lr24+Lr38, Lr24+Lr38+Lr45, Lr24+Lr29+Lr38 and Lr19+Lr38+Lr45 respectively. The remaining seventy-one accessions had none of those eight effective leaf rust resistance genes. This study will provide theoretical guidance for rational utilization of these introduted wheat accessions directly or for breeding the resistant wheat cultivars.

DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M.orientalis, and M. sylvestris genebank accessions.

The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species’ centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were compared with a dataset of more than 5000 unique M. domestica apple cultivars. Only 212 accessions (151 M. sieversii, 26 M. orientalis, and 35 M. sylvestris) were identified as “pure” species representatives because their DNA profiles did not exhibit genotypic signatures of recent hybridization with M. domestica. Twenty-one accessions (17 M. sieversii, 1 M. orientalis, and 3 M. sylvestris) previously labeled as wild species were instead fully M. domestica. Previously unrealized hybridization and admixture between wild species and M. domestica was identified in 230 accessions (215 M. sieversii, 9 M. orientalis, and 6 M. sylvestris). Among these species-mislabeled accessions, ‘Alexander’, ‘Gold Reinette’, ‘Charlamoff’, ‘Rosmarina Bianca’, and ‘King of the Pippins’ were the most frequently detected M. domestica parents or grandparents. These results have implications for collection management, including germplasm distribution, and might affect conclusions of previous research focused on these three progenitor species in the NPGS apple collection. Specifically, accessions received from the NPGS for breeding and genomics, genetics, and evolutionary biology research might not be truly representative of their previously assigned species.

Developing country demand for crop germplasm conserved by the U.S. National Plant Germplasm System

BackgroundFuture food production depends on the availability of crop varieties with more resistance to pests and diseases, temperature extremes, irregular moisture, and saltier soils. Plant breeders will need diverse germplasm to create improved varieties, especially in developing countries. The U.S. National Plant Germplasm System (NPGS) supplies germplasm to users worldwide.MethodsTo assess the demand for NPGS germplasm, we used: (1) distribution data from the Genetic Research Information Network; and (2) information collected directly from recipients of NPGS materials. Data collected included user characteristics, types of germplasm requested and received, the purpose of requests, the usefulness of materials received, and expectations for future use.ResultsFor ten major crops, the NPGS distributed approximately 100,000 samples to users in developing countries during 2011–2015. NPGS germplasm ranged from final cultivars to crop wild relatives. These respondents requested proportionately more cultivars than are present in the NPGS. In developing countries, nearly all samples were received by scientists (98%). The most frequent purpose for requesting samples was basic research, followed by adding to collections, evaluating for specific traits, and breeding/prebreeding. These respondents found 38% of samples useful in breeding or in other ways. Another 38% of samples were still being evaluated. Previous research indicates the usefulness of samples is partially dependent on the data accompanying them. Compared with results from an earlier study, more samples had useful data. Finally, 64% of respondents in developing countries expected their use of the NPGS to increase, while only 8% expected their use to decrease.ConclusionsThe NPGS supplies significant amounts of crop germplasm to developing countries. The use of NPGS samples for basic research increased in developing countries. These respondents found more samples useful than those from an earlier study. NPGS samples were more likely to have useful data than in the past, which may enhance their usefulness. Finally, respondents in developing countries were more likely than other users to expect constant or increasing use of NPGS germplasm, underscoring the importance of NPGS materials for developing countries.

Genetic analysis of the Asiatic cotton (Gossypium arboreum) petal spot phenotypes

AbstractThe cotton species Gossypium arboreum L. is self‐pollinated, and most accessions in the United States Department Agriculture, National Plant Germplasm System, produce flowers with red pigmented petal spots, which represents the primitive phenotype and more attractive to pollinators. Few accessions have the ghost spot phenotype, and genetic analysis of this trait was conducted for PI 615742. Two F2 populations were developed by crossing PI 615742 with G. arboreum accessions PI 452097, having red petal spots, and with PI 529708, showing the spotless phenotype. The PI 615742 × PI 529708 population data indicate a single completely dominant gene which confers the ghost spot phenotype. Petal spot phenotypes observed for the PI 615742 × PI 452097 population indicate red pigmented spots are also conferred by a single completely dominant gene. These results support a two‐gene model in which the presence of petal spots and pigment development are controlled by independent genes that co‐segregate with stem pigmentation. The accessions and population data can aid in characterizing the mechanisms controlling floral traits and pigment expression.

Assessment of phenotypic diversity in the USDA, National Plant Germplasm System (NPGS) guayule germplasm collection

Phenotypic characterization on historical breeding lines and wild genetic resources from the 1950′s to 1990′s of the rubber-bearing plant guayule (Parthenium argentatum A. Gray) and hybrids was conducted. Variation among germplasm on seed weight and germination was determined along with leaf traits and trichomes using image analyses. Flow cytometry was performed to estimate diversity in ploidy levels. Tetraploid guayule was the predominant type in the germplasm collection (64%), followed by triploids (34%), pentaploids (1.5%), and hexaploid (1%). No plants with octaploid or higher ploidy level were observed. Guayule 100-seed weight averaged 57.5 mg and was determined to have significant positive correlation to 7 and 14-day seed germination and seed size for this seed lot. Phenotypic similarity among germplasm was determined from quantitative analysis of leaf traits and trichomes. Measurements of other traits on young leaves were highly correlated to those on mature leaves. Most leaf traits within each development stage were found to be positively correlated. Guayule leaves averaged 6.85 cm long and 2.06 cm wide, with 1–6 serrations. Leaf serration height ranged from 2.9 to 6.4 mm. Germplasm lines AZ-2, AZ-3, and N566 had the greatest number of serrations, while R1093 and W6–429 with the least number. Trichome density was consistent between young and mature leaves with average density of 17 trichomes per 0.04 mm2. Accessions R1100, AZ-3, and CAL-4 had the highest trichome density (>21 trichomes per 0.04 mm2). The results from analyzing the relatively high number of plants for seed parameters, leaf traits and ploidy are useful for optimizing germplasm collection and to better aid agronomic management practices and utilization of guayule germplasm for crop improvement activities.

Genetic characterization of the brown lint phenotype for desi cotton (Gossypium arboreum) accession PI 408765 (cv. ‘Sanguineum‐1’)

AbstractCotton fibre can show a range in brown colouration, and these coloured lint fibres can be used for textile production reducing the environmental and human health hazards associated with synthetic dyes; however, coloured cotton cultivars have lower yield potential and reduced lint quality. A greater understanding of the genetics of lint colouration would be useful for the development of improved cultivars. Gossypium arboreum L. accession PI 408765 (cv. ‘Sanguineum‐1’) having the brown lint phenotype was identified from the United States Department Agriculture, National Plant Germplasm System cotton collection and crossed with G. arboreum accessions PI 529729 (cv. ‘Garo Hill’) having white lint and with PI 615733 (cv. ‘Zi‐Hua Guang Zi’) having brown lint. Lint colour data from the F2 populations support a single incomplete dominant gene model for the brown lint phenotype. Additionally, the brown lint phenotypes for PI 408765 and PI 615733 are controlled by two independent genes. Plants in these populations showed a range of brown lint colouration, and these data would be useful to further characterize the mechanisms controlling brown lint development.