Genomic sequence data are becoming prevalent in databases; however, associated phenotypic data are much more expensive and difficult to obtain. Standardized ontologies for trait classification provide a mechanism by which searches can be efficiently performed. Through standardization efforts, results can be compared across years, researchers, and locations. Examples of databases that have developed standardized ontologies within medical, animal, and plant research programs demonstrate that standardization is both possible and desirable. With standardization, genotypic and phenotypic data can be analyzed to materials for improved yield, quality, and stress tolerance.
Gayle M. Volk and David Stern
Garlic (Allium sativum L.) cultivars grown under diverse conditions have highly elastic environmental responses, particularly relating to skin color and yield. Ten diverse garlic cultivars were grown at 12 locations in the United States and Canada for 2 consecutive years to identify the environmentally responsive phenotypic traits of garlic. Clove arrangement, number of topsets, topset size, topset color, number of cloves, clove weight, clove skin color, and clove skin tightness were generally stable for each cultivar regardless of production location and conditions. Scape presence varied with cultivar and location, but for the most part, cultivars classified as hardneck types produced scapes and those classified as softnecks did not produce scapes. Bulbs grown at the northern Colorado, Minnesota, Pennsylvania, Vermont, and Washington locations were generally larger than the other locations. Soil potassium levels were positively correlated with bulb circumference and fresh weight. Soil sulfur and manganese levels were correlated with bulb sulfur and manganese content. Bulb wrapper color and intensity were highly dependent on location and cultivar. The Silverwhite cultivar was consistently white and ‘Ajo Rojo’, ‘German White’, ‘Inchelium’, ‘Sakura’, and ‘Spanish Roja’ were generally white with some faint violet or brown stripes or splotches across the locations. In contrast, cultivars Chesnok Red, Purple Glazer, Red Janice, and Siberian were more likely to have moderate or dark violet stripes, streaks, or splotches, particularly when grown at the northern Colorado, Minnesota, Nevada, New York, Ontario, Pennsylvania, or Washington locations. These results can help farmers identify niche regional markets that provide novel products to consumers. From these results, it was shown that garlic cultivars or classes grown under diverse conditions have highly elastic soil nutrient responses, particularly relating to skin color and yield.
Gayle M. Volk and Christopher M. Richards
The USDA-ARS National Plant Germplasm System (NPGS) provides critical genetic resources to researchers and breeders worldwide. Users of the NPGS materials need access to data for genetic and descriptive characteristics of the plant materials. New tables and codes have been added to the Germplasm Resources Information Network (GRIN) database to hold raw data relating to molecular markers and alleles. The revised tables accommodate multiple marker types; provide raw data for individuals; accept polyploid data; and provide a record of methods, standards, and control values. A long-term goal is to make the GRIN molecular tables fully interoperable with the National Center for Biotechnology Information database as well as bioinformatic databases (model organism and clade organism databases). The development of this capacity provides critical data infrastructure for future genotype–phenotype association studies and gene discovery.
Gayle M. Volk and Christopher M. Richards
Wild plant genetic resources are increasingly becoming valuable for breeding, genomics, and ornamental horticulture programs. Wild relatives of horticultural species may offer desirable traits that are not available in cultivated varieties, but “wilds” often also have traits that are highly undesirable. Advances in comparative genomics and marker-assisted breeding facilitate the inclusion of the valued traits from wild materials in plant breeding programs. As technologies advance, wild plant genetic resources will become even more valuable for future research developments. This serves as an introduction to a series of proceedings articles from the American Society of Horticultural Science meetings in 2010 workshop entitled “Horticultural Value of Wild Genetic Resources.”
Gayle M. Volk and Christopher M. Richards
Plant genetic resource collections provide novel materials to the breeding and research communities. Crop wild relatives may harbor completely novel forms of allelic variation for biotic and abiotic resistance as well as masked genes for improved quality and production. This variation has been shaped by the environment from which the plant materials were collected. With detailed original source information, genetic assessments of germplasm collections can go beyond the basic measurements of collection diversity and breeding for simple traits to assessments of natural variation in environmental contexts. Availability of detailed documentation of passport, phenotypic, and genetic data increases the value of all genebank accessions. Inclusion of georeferenced sources, habitats, and sampling data in collection databases facilitates interpretation of genetic data for genebank accessions with wild origins.
Gayle M. Volk and Adam D. Henk
Apples (Malus Mill.) have been economically and socially important throughout the centuries in North America. Apple cultivar (Malus ×domestica Borkh.) collections that include historic cultivars are valued for their unique diversity, historical significance, and also as a resource to identify unknown trees; however, not all of the historically significant apple cultivars are currently included in these collections. We used historic books, publications, and nursery catalogs to develop an inventory of apple cultivars that were propagated and grown in the United States before 1908. We collected synonym, introduction date, and original source country information for 891 historic apple cultivars. Most of the historic American cultivars originated as seedlings first planted in the United States. Some cultivars were brought to the United States from the United Kingdom, France, Russia, Germany, and other European countries. We classified historic apple cultivars based on their availability over time and popularity in nursery catalogs. Ninety percent of the most popular historic apple cultivars in the United States were available in 2015 in the U.S. and U.K. national collections and within several commercial and private collections. This work identified high priority historic cultivars that are not currently protected within genebanks that could be added to genebank collections in the future.
Nahla V. Bassil and Gayle M. Volk
Leigh E. Towill and Gayle M. Volk
Arabidopsisthaliana shoot tips provide a model to study processes important for cryopreservation. Cryopreservation was accomplished using both vitrification and two-step cooling methods. With vitrification methods, shoot formation after liquid nitrogen (LN) exposure was as high as 100% and 95% for shoot tips exposed to PVS2 at 0 °C and to PVS3 at 23 °C, respectively. A two-step cooling method also gave greater than 90% survival if shoot tips were cooled at 0.3 °C per minute to below –30 °C before immersing the samples into LN. The high levels of shoot formation after LN exposure in Arabidopsis thaliana shoot tips will allow the use of mutants to examine how alterations in biochemical, metabolic, and developmental processes affect survival and growth.
Gayle M. Volk, Adam D. Henk, and Christopher M. Richards
Garlic (Allium sativum L.) has been clonally propagated for thousands of years because it does not produce seed under standard cultivation conditions. A single garlic accession frequently displays a high degree of phenotypic plasticity that is likely to be dependent upon soil type, moisture, latitude, altitude, and cultural practices. The diversity observed by collectors has occasionally led to the renaming of varieties as they are exchanged among growers and gardeners. As a result, there are numerous garlic varieties available both commercially and within the USDA National Plant Germplasm System (NPGS) that may be identical genotypically, yet have unique cultivar names. To address this possibility, we performed amplified fragment-length polymorphism (AFLP) analysis on a comprehensive selection of 211 Allium sativum and Allium longicuspis accessions from NPGS and commercial sources. We used several statistical approaches to evaluate how these clonal lineages are genetically differentiated and how these patterns of differentiation correspond to recognized phenotypic classifications. These data suggest that while there are extensive duplications within the surveyed accessions, parsimony and distance based analyses reveal substantial diversity that is largely consistent with major phenotypic classes.
Jonathan Magby, Gayle M. Volk, Adam Henk, and Steve Miller
Thousands of apple trees were planted in Wyoming’s orchards and homesteads in the 1800s, many of which are still alive today. Unfortunately, cultivar identity of these trees has mostly been lost or obscured. The purpose of this research was to identify heritage apple cultivars in Wyoming using genetic fingerprinting (microsatellite) techniques and to use this information to make recommendations on candidate cold-hardy cultivars for specialty crop and breeding programs. Leaf samples were collected from 510 heritage apple trees from 91 sites in 19 locales across Wyoming. Known cultivars from the U.S. Department of Agriculture (USDA)–National Plant Germplasm System, Seed Savers Exchange, and Washington State University apple collections were used as standards to determine cultivar identities. Overall, 328 (64%) of the previously unidentified apples trees were identified to 47 known cultivars. Fifteen of these known cultivars comprised more than 80% of the samples that were identified, with all 15 of those cultivars developed in states and countries with average temperatures or winter conditions similar to Wyoming. Seventy-one of the heritage trees were identified as the Wealthy cultivar. Other commonly identified cultivars were Haralson, Patten’s Greening, Yellow Transparent, Northwestern Greening, and McMahon. It is likely that a combination of popularity and cultivar origin affected the choice of cultivars that were grown in Wyoming. Although most original Wyoming heritage apple trees are reaching the end of their life span, many surviving trees continue to produce fruit. This strongly suggests that despite lower resistance to certain pathogens than many modern cultivars, these heritage trees should be considered for use today. The results provide insights into possible cultivars that could be grown in Wyoming and also in other states with similar harsh growing conditions.