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Volk GM, Peace CP, Henk AD, Howard NP. DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions. Front Plant Sci 2022; 13:1015658. [PMID: 36311081 PMCID: PMC9606829 DOI: 10.3389/fpls.2022.1015658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
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.
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Affiliation(s)
- Gayle M. Volk
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
| | - Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Adam D. Henk
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Volk GM, Bonnart R, de Oliveira ACA, Henk AD. Minimizing the deleterious effects of endophytes in plant shoot tip cryopreservation. Appl Plant Sci 2022; 10:e11489. [PMID: 36258787 PMCID: PMC9575093 DOI: 10.1002/aps3.11489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/23/2022] [Accepted: 03/15/2022] [Indexed: 05/05/2023]
Abstract
Plant cryopreservation technologies are used within gene banks for the long-term preservation of vegetatively propagated collections. Surface-sterilized plant tissues grown in the field, greenhouse/screenhouse, growth chamber, or in vitro are the source of shoot tips subjected to vitrification-based cryopreservation methods. Here, we describe the methods used to minimize microbial contamination during the tissue culture initiation process. We also discuss the occurrence and possible elimination of endophytes after extended in vitro culture and during recovery after liquid nitrogen exposure. We describe two case studies in which bacterial endophytes were observed in Citrus gene bank accessions during recovery after cryopreservation. These were identified using the MinION Oxford Nanopore system and Kirby-Bauer disc diffusion assays to examine the bacterial responses to antibiotic exposure. The methods used in this case study could be applied to identify endophytes to better target antimicrobial treatments of plant tissue collections.
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Affiliation(s)
- Gayle M. Volk
- USDA‐ARS National Laboratory for Genetic Resources Preservation1111 S. Mason St.Fort CollinsColorado80521USA
| | - Remi Bonnart
- USDA‐ARS National Laboratory for Genetic Resources Preservation1111 S. Mason St.Fort CollinsColorado80521USA
| | | | - Adam D. Henk
- USDA‐ARS National Laboratory for Genetic Resources Preservation1111 S. Mason St.Fort CollinsColorado80521USA
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Gross BL, Henk AD, Bonnart R, Volk GM. Changes in transcript expression patterns as a result of cryoprotectant treatment and liquid nitrogen exposure in Arabidopsis shoot tips. Plant Cell Rep 2017; 36:459-470. [PMID: 27999976 DOI: 10.1007/s00299-016-2095-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Transcripts related to abiotic stress, oxidation, and wounding were differentially expressed in Arabidopsis shoot tips in response to cryoprotectant and liquid nitrogen treatment. Cryopreservation methods have been implemented in genebanks as a strategy to back-up plant genetic resource collections that are vegetatively propagated. Cryopreservation is frequently performed using vitrification methods, whereby shoot tips are treated with cryoprotectant solutions, such as Plant Vitrification Solution 2 (PVS2) or Plant Vitrification Solution 3 (PVS3); these solutions remove and/or replace freezable water within the meristem cells. We used the model system Arabidopsis thaliana to identify suites of transcripts that are up- or downregulated in response to PVS2 and PVS3 treatment and liquid nitrogen (LN) exposure. Our results suggest that there are many changes in transcript expression in shoot tips as a result of cryoprotection and that these changes exceed the number detected as a result of LN exposure. In total, 180 transcripts showed significant changes in expression level unique to treatment with either the cryoprotectant or cryopreservation followed by recovery. Of these 180 transcripts, 67 were related to stress, defense, wounding, lipid, carbohydrate, abscisic acid, oxidation, temperature (cold/heat), or osmoregulation. The responses of five transcripts were confirmed using qPCR methods. The transcripts responding to PVS2 + LN suggest an oxidative response to this treatment, whereas the PVS3 + LN treatment invoked a more general metabolic response. This work shows that the choice of cryoprotectant can have a major influence on the patterns of transcript expression, presumably due to the level and extent of stress experienced by the shoot tip. As a result, there may be divergent responses of study systems to PVS2 and PVS3 treatments.
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Affiliation(s)
- Briana L Gross
- University of Minnesota Duluth, 207 Swenson Science Building, 1035 Kirby Drive, Duluth, MN, 55812, USA
| | - Adam D Henk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 S. Mason St., Fort Collins, CO, 80521, USA
| | - Remi Bonnart
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 S. Mason St., Fort Collins, CO, 80521, USA
| | - Gayle M Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 S. Mason St., Fort Collins, CO, 80521, USA.
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Abstract
UNLABELLED • PREMISE OF THE STUDY The genus Malus represents a unique and complex evolutionary context in which to study domestication. Several Malus species have provided novel alleles and traits to the cultivars. The extent of admixture among wild Malus species has not been well described, due in part to limited sampling of individuals within a taxon.• METHODS Four chloroplast regions (1681 bp total) were sequenced and aligned for 412 Malus individuals from 30 species. Phylogenetic relationships were reconstructed using maximum parsimony. The distribution of chloroplast haplotypes among species was examined using statistical parsimony, phylogenetic trees, and a median-joining network.• KEY RESULTS Chloroplast haplotypes are shared among species within Malus. Three major haplotype-sharing networks were identified. One includes species native to China, Western North America, as well as Malus domestica Borkh, and its four primary progenitor species: M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., M. sylvestris (L.) Mill., and M. prunifolia (Willd.) Borkh; another includes five Chinese Malus species, and a third includes the three Malus species native to Eastern North America.• CONCLUSIONS Chloroplast haplotypes found in M. domestica belong to a single, highly admixed network. Haplotypes shared between the domesticated apple and its progenitors may reflect historical introgression or the retention of ancestral polymorphisms. Multiple individuals should be sampled within Malus species to reveal haplotype heterogeneity, if complex maternal contributions to named species are to be recognized.
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Affiliation(s)
- Gayle M Volk
- USDA-ARS National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521
| | - Adam D Henk
- USDA-ARS National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521
| | - Angela Baldo
- USDA-ARS Dale Bumpers National Rice Research Center, 2890 Hwy. 130 E., Stuttgart, Arkansas 72160
| | - Gennaro Fazio
- USDA-ARS Plant Genetic Resources Unit, 630 West North Street, Geneva, New York 14456-0462
| | - C Thomas Chao
- USDA-ARS Plant Genetic Resources Unit, 630 West North Street, Geneva, New York 14456-0462
| | - Christopher M Richards
- USDA-ARS National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521
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Gross BL, Henk AD, Richards CM, Fazio G, Volk GM. Genetic diversity in Malus ×domestica (Rosaceae) through time in response to domestication. Am J Bot 2014; 101:1770-9. [PMID: 25326619 DOI: 10.3732/ajb.1400297] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, they can also affect diversity during crop improvement. Here, we investigate the impact of the improvement process on the genetic diversity of domesticated apple in comparison with other perennial and annual fruit crops.• METHODS Apple cultivars that were developed at various times (ranging from the 13th through the 20th century) and 11 of the 15 apple cultivars that are used for 90% of the apple production in the United States were surveyed for genetic diversity based on either 9 or 19 simple sequence repeats (SSRs). Diversity was compared using standard metrics and model-based approaches based on expected heterozygosity (He) at equilibrium. Improvement bottleneck data for fruit crops were also collected from the literature.• KEY RESULTS Domesticated apples showed no significant reduction in genetic diversity through time across the last eight centuries. Diversity was generally high, with an average He > 0.7 for apples from all centuries. However, diversity of the apples currently used for the bulk of commercial production was lower.• CONCLUSIONS The improvement bottleneck in domesticated apples appears to be mild or nonexistent, in contrast to improvement bottlenecks in many annual and perennial fruit crops, as documented from the literature survey. The low diversity of the subset of cultivars used for commercial production, however, indicates that an improvement bottleneck may be in progress for this perennial crop.
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Affiliation(s)
- Briana L Gross
- Biology Department, University of Minnesota Duluth, 207 Swenson Science Building, 1035 Kirby Drive, Duluth, Minnesota 55812 USA
| | - Adam D Henk
- USDA-ARS, National Center for Genetic Resource Preservation, 1111 S. Mason Street, Fort Collins, Colorado 80521 USA
| | - Christopher M Richards
- USDA-ARS, National Center for Genetic Resource Preservation, 1111 S. Mason Street, Fort Collins, Colorado 80521 USA
| | - Gennaro Fazio
- USDA-ARS, Plant Genetic Resources Unit, Geneva, New York 14456 USA
| | - Gayle M Volk
- USDA-ARS, National Center for Genetic Resource Preservation, 1111 S. Mason Street, Fort Collins, Colorado 80521 USA
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Richards CM, Volk GM, Reilley AA, Henk AD, Lockwood DR, Reeves PA, Forsline PL. Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genetics & Genomes 2009; 5:339-347. [PMID: 0 DOI: 10.1007/s11295-008-0190-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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Ashfield T, Bocian A, Held D, Henk AD, Marek LF, Danesh D, Peñuela S, Meksem K, Lightfoot DA, Young ND, Shoemaker RC, Innes RW. Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes. Mol Plant Microbe Interact 2003; 16:817-26. [PMID: 12971605 DOI: 10.1094/mpmi.2003.16.9.817] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Alleles or tightly linked genes at the soybean (Glycine max L. Merr.) Rpg1 locus confer resistance to strains of Pseudomonas syringae pv. glycinea that express the avirulence genes avrB or avrRpm1. We have previously mapped Rpg1-b (the gene specific for avrB) to a cluster of resistance genes (R genes) with diverse specificities in molecular linkage group F. Here, we describe the high-resolution physical and genetic mapping of Rpg1-b to a 0.16-cM interval encompassed by two overlapping BAC clones spanning approximately 270 kilobases. Rpg1-b is part of a complex locus containing numerous genes related to previously characterized coiled coil-nucleotide binding site-leucine rich repeat (CC-NBS-LRR)-type R genes that are spread throughout this region. Phylogenetic and Southern blot analyses group these genes into four distinct subgroups, some of which are conserved in the common bean, Phaseolus vulgaris, indicating that this R gene cluster may predate the divergence of Phaseolus and Glycine. Members from different subgroups are physically intermixed and display a high level of polymorphism between soybean cultivars, suggesting that this region is rearranging at a high frequency. At least five CC-NBS-LRR-type genes cosegregate with Rpg1-b in our large mapping populations.
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Affiliation(s)
- Tom Ashfield
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Abstract
The RPS5 and RFL1 disease resistance genes of Arabidopsis ecotype Col-0 are oriented in tandem and are separated by 1.4 kb. The Ler-0 ecotype contains RFL1, but lacks RPS5. Sequence analysis of the RPS5 deletion region in Ler-0 revealed the presence of an Ac-like transposable element, which we have designated Tag2. Southern hybridization analysis of six Arabidopsis ecotypes revealed 4-11 Tag2-homologous sequences in each, indicating that this element is ubiquitous in Arabidopsis and has been active in recent evolutionary time. The Tag2 insertion adjacent to RFL1 was unique to the Ler-0 ecotype, however, and was not present in two other ecotypes that lack RPS5. DNA sequence from the latter ecotypes lacked a transposon footprint, suggesting that insertion of Tag2 occurred after the initial deletion of RPS5. The deletion breakpoint contained a 192-bp insertion that displayed hallmarks of a nonhomologous DNA end-joining event. We conclude that loss of RPS5 was caused by a double-strand break and subsequent repair, and cannot be attributed to unequal crossing over between resistance gene homologs.
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Affiliation(s)
- A D Henk
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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Abstract
The broad host-range cloning vectors, pJRD215 and pMMB67EH, were evaluated for stability and cloning efficiency in Pasteurella multocida. Transformation of P. multocida by electroporation was unreliable and poorly efficient regardless of whether the transforming DNA was isolated from E. coli or P. multocida. Both vectors contain a mob site that enabled transfer by conjugation from E. coli to P. multocida with high efficiency. Kanamycin, streptomycin, and ampicillin resistance encoded by the vectors were expressed in P. multocida. LacZ was cloned in pMMB67EH, an expression vector, and was transferred to P. multocida by conjugation. The transconjugants expressed a functional beta-galactosidase as determined by o-nitrophenyl-beta-D-galactopyranoside (ONPG) test. We propose the use of these cosmid and expression vectors as a shuttle vectors for cloning in P. multocida.
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Affiliation(s)
- M D Lee
- College of Veterinary Medicine, University of Georgia, Athens 30601, USA.
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Abstract
The objective of this study was to identify a transposon that will randomly and stably integrate in the genome of Pasteurella multocida. Using the suicide conjugative delivery system, pLOF, containing a kanamycin resistance marked Tn10 insertion element, we determined that Tn10 is effective in producing insertional mutations in this species. Combined conjugation/transposition events occurred once per 10,000 donor cells. Only 1.4% of the isolates resulted from vector integration and the genomic insertions were random and stable as determined by DNA/DNA hybridization after 10 serial subcultures lacking antibiotic selection. Twenty-two percent of the isolates were auxotrophic, 4% were tryptophan auxotrophs. Mutants derived by this method will be useful for studying putative virulence determinants of Pasteurella.
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Affiliation(s)
- M D Lee
- Department of Medical Microbiology, College of Veterinary Medicine, University of Georgia, Athens 30602, USA.
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