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Meehan TD, Saunders SP, DeLuca WV, Michel NL, Grand J, Deppe JL, Jimenez MF, Knight EJ, Seavy NE, Smith MA, Taylor L, Witko C, Akresh ME, Barber DR, Bayne EM, Beasley JC, Belant JL, Bierregaard RO, Bildstein KL, Boves TJ, Brzorad JN, Campbell SP, Celis‐Murillo A, Cooke HA, Domenech R, Goodrich L, Gow EA, Haines A, Hallworth MT, Hill JM, Holland AE, Jennings S, Kays R, King DT, Mackenzie SA, Marra PP, McCabe RA, McFarland KP, McGrady MJ, Melcer R, Norris DR, Norvell RE, Rhodes OE, Rimmer CC, Scarpignato AL, Shreading A, Watson JL, Wilsey CB. Integrating data types to estimate spatial patterns of avian migration across the Western Hemisphere. Ecol Appl 2022; 32:e2679. [PMID: 35588285 PMCID: PMC9787853 DOI: 10.1002/eap.2679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 06/15/2023]
Abstract
For many avian species, spatial migration patterns remain largely undescribed, especially across hemispheric extents. Recent advancements in tracking technologies and high-resolution species distribution models (i.e., eBird Status and Trends products) provide new insights into migratory bird movements and offer a promising opportunity for integrating independent data sources to describe avian migration. Here, we present a three-stage modeling framework for estimating spatial patterns of avian migration. First, we integrate tracking and band re-encounter data to quantify migratory connectivity, defined as the relative proportions of individuals migrating between breeding and nonbreeding regions. Next, we use estimated connectivity proportions along with eBird occurrence probabilities to produce probabilistic least-cost path (LCP) indices. In a final step, we use generalized additive mixed models (GAMMs) both to evaluate the ability of LCP indices to accurately predict (i.e., as a covariate) observed locations derived from tracking and band re-encounter data sets versus pseudo-absence locations during migratory periods and to create a fully integrated (i.e., eBird occurrence, LCP, and tracking/band re-encounter data) spatial prediction index for mapping species-specific seasonal migrations. To illustrate this approach, we apply this framework to describe seasonal migrations of 12 bird species across the Western Hemisphere during pre- and postbreeding migratory periods (i.e., spring and fall, respectively). We found that including LCP indices with eBird occurrence in GAMMs generally improved the ability to accurately predict observed migratory locations compared to models with eBird occurrence alone. Using three performance metrics, the eBird + LCP model demonstrated equivalent or superior fit relative to the eBird-only model for 22 of 24 species-season GAMMs. In particular, the integrated index filled in spatial gaps for species with over-water movements and those that migrated over land where there were few eBird sightings and, thus, low predictive ability of eBird occurrence probabilities (e.g., Amazonian rainforest in South America). This methodology of combining individual-based seasonal movement data with temporally dynamic species distribution models provides a comprehensive approach to integrating multiple data types to describe broad-scale spatial patterns of animal movement. Further development and customization of this approach will continue to advance knowledge about the full annual cycle and conservation of migratory birds.
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Ralston J, Lorenc L, Montes M, DeLuca WV, Kirchman JJ, Woodworth BK, Mackenzie SA, Newman A, Cooke HA, Freeman NE, Sutton AO, Tauzer L, Norris DR. Length polymorphisms at two candidate genes explain variation of migratory behaviors in blackpoll warblers ( Setophaga striata). Ecol Evol 2019; 9:8840-8855. [PMID: 31410284 PMCID: PMC6686290 DOI: 10.1002/ece3.5436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/30/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Migratory behaviors such as the timing and duration of migration are genetically inherited and can be under strong natural selection, yet we still know very little about the specific genes or molecular pathways that control these behaviors. Studies in candidate genes Clock and Adcyap1 have revealed that both of these loci can be significantly correlated with migratory behaviors in birds, though observed relationships appear to vary across species. We investigated geographic genetic structure of Clock and Adcyap1 in four populations of blackpoll warblers (Setophaga striata), a Neotropical-Nearctic migrant that exhibits geographic variation in migratory timing and duration across its boreal breeding distribution. Further, we used data on migratory timing and duration, obtained from light-level geolocator trackers to investigate candidate genotype-phenotype relationships at the individual level. While we found no geographic structure in either candidate gene, we did find evidence that candidate gene lengths are correlated with five of the six migratory traits. Maximum Clock allele length was significantly and negatively associated with spring arrival date. Minimum Adcyap1 allele length was significantly and negatively associated with spring departure date and positively associated with fall arrival date at the wintering grounds. Additionally, we found a significant interaction between Clock and Adcyap1 allele lengths on both spring and fall migratory duration. Adcyap1 heterozygotes also had significantly shorter migration duration in both spring and fall compared to homozygotes. Our results support the growing body of evidence that Clock and Adcyap1 allele lengths are correlated with migratory behaviors in birds.
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Affiliation(s)
- Joel Ralston
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Lydia Lorenc
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Melissa Montes
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - William V. DeLuca
- Department of Environmental ConservationUniversity of MassachusettsAmherstMAUSA
| | | | - Bradley K. Woodworth
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Amy Newman
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | | | - Alex O. Sutton
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Lila Tauzer
- Wildlife Conservation Society CanadaWhitehorseYTCanada
| | - D. Ryan Norris
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
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3
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DeLuca WV, Woodworth BK, Mackenzie SA, Newman AEM, Cooke HA, Phillips LM, Freeman NE, Sutton AO, Tauzer L, McIntyre C, Stenhouse IJ, Weidensaul S, Taylor PD, Norris DR. A boreal songbird's 20,000 km migration across North America and the Atlantic Ocean. Ecology 2019; 100:e02651. [DOI: 10.1002/ecy.2651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/16/2019] [Indexed: 11/05/2022]
Affiliation(s)
- William V. DeLuca
- Department of Environmental Conservation University of Massachusetts Amherst Massachusetts 01003 USA
| | - Bradley K. Woodworth
- Department of Integrative Biology University of Guelph Guelph Ontario N1G 2W1 Canada
- School of Biological Sciences The University of Queensland Brisbane St. Lucia Queensland 4072 Australia
| | | | - Amy E. M. Newman
- Department of Integrative Biology University of Guelph Guelph Ontario N1G 2W1 Canada
| | - Hilary A. Cooke
- Wildlife Conservation Society Canada 169 Titanium Way Whitehorse Yukon Y1A 0E9 Canada
| | - Laura M. Phillips
- Denali National Park and Preserve PO Box 9 Denali Park Alaska 99755 USA
| | - Nikole E. Freeman
- Department of Integrative Biology University of Guelph Guelph Ontario N1G 2W1 Canada
| | - Alex O. Sutton
- Department of Integrative Biology University of Guelph Guelph Ontario N1G 2W1 Canada
| | - Lila Tauzer
- Wildlife Conservation Society Canada 169 Titanium Way Whitehorse Yukon Y1A 0E9 Canada
| | - Carol McIntyre
- National Park Service 4175 Geist Road Fairbanks Alaska 99709 USA
| | - Iain J. Stenhouse
- Biodiversity Research Institute 276 Canco Road Portland Maine 04103 USA
| | - Scott Weidensaul
- 778 Schwartz Valley Road Schuylkill Haven Pennsylvania 17972 USA
| | - Philip D. Taylor
- Department of Biology Acadia University Wolfville Nova Scotia B4P 2R6 Canada
| | - D. Ryan Norris
- Department of Integrative Biology University of Guelph Guelph Ontario N1G 2W1 Canada
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Morbey YE, Guglielmo CG, Taylor PD, Maggini I, Deakin J, Mackenzie SA, Brown JM, Zhao L. Evaluation of sex differences in the stopover behavior and postdeparture movements of wood-warblers. Behav Ecol 2017. [DOI: 10.1093/beheco/arx123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gómez C, Bayly NJ, Norris DR, Mackenzie SA, Rosenberg KV, Taylor PD, Hobson KA, Daniel Cadena C. Fuel loads acquired at a stopover site influence the pace of intercontinental migration in a boreal songbird. Sci Rep 2017; 7:3405. [PMID: 28611372 PMCID: PMC5469819 DOI: 10.1038/s41598-017-03503-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/28/2017] [Indexed: 11/24/2022] Open
Abstract
Long-distance migratory organisms are under strong selection to migrate quickly. Stopovers demand more time than flying and are used by individuals to refuel during migration, but the effect of fuel loads (fat) acquired at stopover sites on the subsequent pace of migration has not been quantified. We studied stopover behaviour of Grey-cheeked Thrush (Catharus minimus) at a site in northern Colombia and then tracked their migration using an intercontinental radio-telemetry array. Tracking confirmed long-distance flights of more than 3000 km, highlighting the key importance of a single stopover site to the migration strategy of this species. Our results suggest that these songbirds behave as time-minimizers as predicted by optimal migration theory, and that fuel loads acquired at this South American stopover site, together with departure date, carry-over to influence the pace of migration, contributing to differences in travel time of up to 30 days in birds subsequently detected in the U. S. and Canada. Such variation in the pace of migration arising from a single stopover site, likely has important fitness consequences and suggests that identifying important fuelling sites will be essential to effectively conserve migratory species.
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Affiliation(s)
- Camila Gómez
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia. .,SELVA: Investigación para la conservación en el Neotropico, Bogotá, Colombia.
| | - Nicholas J Bayly
- SELVA: Investigación para la conservación en el Neotropico, Bogotá, Colombia
| | - D Ryan Norris
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Philip D Taylor
- Bird Studies Canada, Port Rowan, Ontario, Canada.,Acadia University, Wolfville, Nova Scotia, Canada
| | - Keith A Hobson
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada.,Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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DeLuca WV, Woodworth BK, Rimmer CC, Marra PP, Taylor PD, McFarland KP, Mackenzie SA, Norris DR. Transoceanic migration by a 12 g songbird. Biol Lett 2016; 11:20141045. [PMID: 25832815 DOI: 10.1098/rsbl.2014.1045] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many fundamental aspects of migration remain a mystery, largely due to our inability to follow small animals over vast spatial areas. For more than 50 years, it has been hypothesized that, during autumn migration, blackpoll warblers (Setophaga striata) depart northeastern North America and undertake a non-stop flight over the Atlantic Ocean to either the Greater Antilles or the northeastern coast of South America. Using miniaturized light-level geolocators, we provide the first irrefutable evidence that the blackpoll warbler, a 12 g boreal forest songbird, completes an autumn transoceanic migration ranging from 2270 to 2770 km (mean ± s.d.: 2540 ± 257) and requiring up to 3 days (62 h ± 10) of non-stop flight. This is one of the longest non-stop overwater flights recorded for a songbird and confirms what has long been believed to be one of the most extraordinary migratory feats on the planet.
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Affiliation(s)
- William V DeLuca
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
| | - Bradley K Woodworth
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | - Peter P Marra
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Philip D Taylor
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada B4P 2R6
| | | | - Stuart A Mackenzie
- Bird Studies Canada-Long Point Bird Observatory, Port Rowan, Ontario, Canada N0E1M0
| | - D Ryan Norris
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Müller F, Taylor PD, Sjöberg S, Muheim R, Tsvey A, Mackenzie SA, Schmaljohann H. Towards a conceptual framework for explaining variation in nocturnal departure time of songbird migrants. Mov Ecol 2016; 4:24. [PMID: 27833750 PMCID: PMC5066284 DOI: 10.1186/s40462-016-0089-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/22/2016] [Indexed: 05/16/2023]
Abstract
Most songbird migrants travel between their breeding areas and wintering grounds by a series of nocturnal flights. The exact nocturnal departure time for these flights varies considerably between individuals even of the same species. Although the basic circannual and circadian rhythms of songbirds, their adaptation to migration, and the factors influencing the birds' day-to-day departure decision are reasonably well studied, we do not understand how birds time their departures within the night. These decisions are crucial, because the nocturnal departure time defines the potential flight duration of the migratory night. The distances covered during the nocturnal migratory flights in the course of migration in turn directly affect the overall speed of migration. To understand the factors influencing the arrival of the birds in the breeding/wintering areas, we need to investigate the mechanisms that control nocturnal departure time. Here, we provide the first conceptual framework for explaining the variation commonly observed in this migratory trait. The basic schedule of nocturnal departure is likely regulated by both the circannual and circadian rhythms of the innate migration program. We postulate that the endogenously controlled schedule of nocturnal departures is modified by intrinsic and extrinsic factors. So far there is only correlative evidence that birds with a high fuel load or a considerable increase in fuel load and significant wind (flow) assistance towards their migratory goal depart early within the night. In contrast, birds migrating with little fuel and under unfavorable wind conditions show high variation in their nocturnal departure time. The latter may contain an unknown proportion of nocturnal movements not directly related to migratory flights. Excluding such movements is crucial to clearly identify the main drivers of the variation in nocturnal departure time. In general we assume that the observed variation in the nocturnal departure time is explained by individually different reactions norms of the innate migration program to both intrinsic and extrinsic factors.
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Affiliation(s)
- Florian Müller
- Institute of Avian Research “Vogelwarte Helgoland”, An der Vogelwarte 21, 26386 Wilhelmshaven, Germany
| | - Philip D. Taylor
- Department of Biology, Acadia University, 33 Westwood Avenue, Wolfville, NS B4P 2R6 Canada
- Bird Studies Canada, 115 Front Street, Port Rowan, ON N0E 1M0 Canada
| | - Sissel Sjöberg
- Department of Biology, Lund University, Biology Building, Sölvegatan 35, 223 62 Lund, Sweden
| | - Rachel Muheim
- Department of Biology, Lund University, Biology Building, Sölvegatan 35, 223 62 Lund, Sweden
| | - Arseny Tsvey
- Biological Station Rybachy, Zoological Institute RAS, RU-238535 Rybachy, Kaliningrad region Russia
| | | | - Heiko Schmaljohann
- Institute of Avian Research “Vogelwarte Helgoland”, An der Vogelwarte 21, 26386 Wilhelmshaven, Germany
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8
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Taylor PD, Mackenzie SA, Thurber BG, Calvert AM, Mills AM, McGuire LP, Guglielmo CG. Landscape movements of migratory birds and bats reveal an expanded scale of stopover. PLoS One 2011; 6:e27054. [PMID: 22073253 PMCID: PMC3207824 DOI: 10.1371/journal.pone.0027054] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 10/10/2011] [Indexed: 12/03/2022] Open
Abstract
Many species of birds and bats undertake seasonal migrations between breeding and over-wintering sites. En-route, migrants alternate periods of flight with time spent at stopover – the time and space where individuals rest and refuel for subsequent flights. We assessed the spatial scale of movements made by migrants during stopover by using an array of automated telemetry receivers with multiple antennae to track the daily location of individuals over a geographic area ∼20×40 km. We tracked the movements of 322 individuals of seven migratory vertebrate species (5 passerines, 1 owl and 1 bat) during spring and fall migratory stopover on and adjacent to a large lake peninsula. Our results show that many individuals leaving their capture site relocate within the same landscape at some point during stopover, moving as much as 30 km distant from their site of initial capture. We show that many apparent nocturnal departures from stopover sites are not a resumption of migration in the strictest sense, but are instead relocations that represent continued stopover at a broader spatial scale.
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9
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Abstract
1. Some bat species make long-distance latitudinal migrations between summer and winter grounds, but because of their elusive nature, few aspects of their biology are well understood. The need for migratory stopover sites to rest and refuel, such as used by birds, has been repeatedly suggested, but not previously tested empirically in bats. 2. We studied migrating silver-haired bats (Lasionycteris noctivagans) at Long Point, ON, Canada. We used digital radio-transmitters to track 30 bats using an array of five towers that effectively covered the entire region (c. 20 × 40 km). We measured stopover duration and departure direction, and documented movement patterns, foraging activity and roost sites. We measured body composition on arrival using quantitative magnetic resonance and simulated long-distance migration using observed body composition to predict migration range and rate. 3. Migration occurred in two waves (late August and mid-September). Most bats stayed 1-2 days, although two remained >2 weeks. One third of the bats foraged while at the site, many foraging opportunistically on nights when rain precluded continued migration. Bats roosted in a variety of tree species and manmade structures in natural and developed areas. Half of the bats departed across Lake Erie (minimum crossing distance c. 38 km) while half departed along the shoreline. 4. Simulations predicted a migration rate of c. 250-275 km per day and suggest that all but one of the bats in our study carried sufficient fuel stores to reach the putative wintering area (estimated distance 1500 km) without further refuelling. 5. Our results suggest that migrating bats stopover for sanctuary or short-term rest as opposed to extended rest and refuelling as in many songbirds. Daily torpor could reduce energy costs when not in flight, minimizing the need for extended stopovers and allowing bats to potentially complete their migration at a fraction of the time and energy cost of similar sized birds.
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Affiliation(s)
- Liam P McGuire
- Department of Biology, Advanced Facility for Avian Research, University of Western Ontario, 1151 Richmond St N, London, ON N6A 5B7, Canada.
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Calvert AM, Mackenzie SA, Flemming JM, Taylor PD, Walde SJ. Variation in songbird migratory behavior offers clues about adaptability to environmental change. Oecologia 2011; 168:849-61. [PMID: 21927912 DOI: 10.1007/s00442-011-2119-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 08/29/2011] [Indexed: 11/30/2022]
Abstract
For seasonally migrating birds, aspects of migratory behavior, such as the use of temperate versus tropical wintering areas, may influence their ability to respond to environmental change. Here, we infer potential flexibility in songbird migration from variation in two alternative stopover behaviors. Hierarchical Bayesian mark-recapture modeling was used to quantify stopover decisions over 19 years for four temperate and four tropical migratory species at a stopover site in southern Canada. Short-distance temperate migrants exhibited higher variability in behavior and greater responses to local weather than longer-distance tropical migrants, as measured by transience (the proportion of birds stopping <24 h, i.e. seeking brief sanctuary or subsequently relocating) and departure (re-initiation of migration by birds that stopped over for >24 h). In contrast to many previous works on climate-migration associations, annual variation in stopover behavior did not show strong links to broad-scale climatic fluctuations for either temperate or tropical migrants, nor was there any indication of directional changes in stopover behavior over the past two decades. In addition to suggesting that migratory songbirds-particularly tropical-wintering species-may face increasing threats with future climatic variability, our study highlights the potential importance of flexibility in en-route behavior for resilience to environmental change.
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Affiliation(s)
- Anna M Calvert
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
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11
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Mackenzie SA, Pring DR, Bassett MJ, Chase CD. Mitochondrial DNA rearrangement associated with fertility restoration and cytoplasmic reversion to fertility in cytoplasmic male sterile Phaseolus vulgaris L. Proc Natl Acad Sci U S A 2010; 85:2714-7. [PMID: 16593926 PMCID: PMC280069 DOI: 10.1073/pnas.85.8.2714] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Restoration of pollen fertility to cytoplasmic male sterile (CMS) Phaseolus vulgaris by a nuclear restorer gene provides a system for studying nuclear-cytoplasmic interactions. Introduction of a nuclear restorer gene to this CMS line of P. vulgaris (CMS-Sprite) results in a mitochondrial genome rearrangement similar to that observed upon spontaneous cytoplasmic reversion to fertility. Three spontaneous heritable cytoplasmic revertants were derived from CMS-Sprite. Five fully fertile restored lines were also produced by using restorer line R-351 (BC(3)F(3) populations). Comparison of the mitochondrial DNA restriction patterns of CMS-Sprite, the three fertile revertants, and the five restored lines revealed loss of a 6.0-kilobase (kb) Pst I fragment in all restored and revertant lines. Southern hybridizations with a 1.3-kb BamHI clone, internal to the 6.0-kb Pst I fragment, as a probe revealed two configurations of 6.0-kb homologous sequences in the sterile cytoplasm; one of the configurations was lost upon reversion or restoration. Mitochondrial DNA rearrangement has thus been observed upon restoration by a nuclear restorer gene in this CMS system.
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Affiliation(s)
- S A Mackenzie
- Vegetable Crops Department, University of Florida, Gainesville, FL 32611
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Feng X, Kaur AP, Mackenzie SA, Dweikat IM. Substoichiometric shifting in the fertility reversion of cytoplasmic male sterile pearl millet. Theor Appl Genet 2009; 118:1361-70. [PMID: 19234685 DOI: 10.1007/s00122-009-0986-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 01/30/2009] [Indexed: 05/17/2023]
Abstract
Cytoplasmic male sterility (CMS) represents an important agricultural trait in pearl millet [Pennisetum glaucum (L.) R. Br.] with a value to the seed industry in facilitating economical hybrid seed production. Among the CMS systems available in millet, the A1 source is the most commonly used for hybrid production, but it can undergo low frequency reversion to fertility. Plant mitochondrial genomes are highly recombinogenic, becoming unstable and prone to ectopic recombination under conditions of tissue culture, somatic hybridization, or interspecific crossing. Similarly, CMS systems prone to spontaneous fertility reversion experience sporadic mitochondrial genome instability. We compared mitochondrial genome configurations between the male-sterile A1 line and fertile revertants of pearl millet to develop a model for millet mitochondrial genome reorganization upon reversion. Relative copy number of a subgenomic molecule containing the CoxI-1-2 junction region, a component of the recombination process for reversion, is amplified tenfold following reversion, relative to the CMS A1 line. We propose that increased copy number of this molecule in a small number of cells or at low frequency triggers a recombination cascade, likely during reproductive development. The proposed recombination process initiates with ectopic recombination through a 7-bp repeat to produce a novel CoxI-3-2 junction molecule and an unstable recombination intermediate. Subsequent intra-molecular recombination stabilizes the intermediate to form a new copy of CoxI accompanied by a deletion. This study furthers the argument that substoichiometric shifting within the plant mitochondrial genome plays an important role in the evolution of the mitochondrial genome and plant reproductive dynamics.
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Affiliation(s)
- X Feng
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, 68583-0915, USA
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Andrews CB, Mackenzie SA, Gregory TR. Genome size and wing parameters in passerine birds. Proc Biol Sci 2009; 276:55-61. [PMID: 18765340 PMCID: PMC2614259 DOI: 10.1098/rspb.2008.1012] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 08/05/2008] [Accepted: 08/06/2008] [Indexed: 11/12/2022] Open
Abstract
Despite their status as the most speciose group of terrestrial vertebrates, birds exhibit the smallest and least variable genome sizes among tetrapods. It has been suggested that this is because powered flight imposes metabolic constraints on cell size, and thus on genome size. This notion has been supported by analyses of genome size and cell size versus resting metabolic rate and other parameters across birds, but most previous studies suffer from one or more limitations that have left the question open. The present study provides new insights into this issue through an examination of newly measured genome sizes, nucleus and cell sizes, body masses and wing parameters for 74 species of birds in the order Passeriformes. A positive relationship was found between genome size and nucleus/cell size, as well as between genome size and wing loading index, which is interpreted as an indicator of adaptations for efficient flight. This represents the single largest dataset presented for birds to date, and is the first to analyse a distinctly flight-related parameter along with genome size using phylogenetic comparative analyses. The results lend additional support to the hypothesis that the small genomes of birds are indeed related in some manner to flight, though the mechanistic and historical bases for this association remain an interesting area of investigation.
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Affiliation(s)
- Chandler B Andrews
- Department of Integrative Biology, University of GuelphGuelph, Ontario, Canada N1G 2W1
| | - Stuart A Mackenzie
- Long Point Bird Observatory, Bird Studies CanadaPort Rowan, Ontario, Canada N0E 1M0
| | - T. Ryan Gregory
- Department of Integrative Biology, University of GuelphGuelph, Ontario, Canada N1G 2W1
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Astua-Monge G, Lyznik A, Jones V, Mackenzie SA, Vallejos CE. Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases. Theor Appl Genet 2002; 104:48-53. [PMID: 12579427 PMCID: PMC7079927 DOI: 10.1007/s001220200005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An insertion-sequence of prokaryotic origin was detected in a genomic clone obtained from a Phaseolus vulgaris bacterial artificial chromosome (BAC) library. This BAC clone, characterized as part of a contig constructed near a virus resistance gene, exhibited restriction fragment length polymorphism with an overlapping clone of the contig. Restriction analysis of DNA obtained from individual colonies of the stock culture indicated the presence of a mixed population of wild-type and insertional mutants. Sequence analysis of both members of the population revealed the presence of IS 10R, an insertion-sequence from Escherichia coli. A BLAST search for IS 10-like sequences detected unexpected homologies with a large number of eukaryotic sequences from Homo sapiens, Arabidopsis thaliana, Drosophila melanogasterand Caenorhabditis elegans. Southern analysis of a random sample of BAC clones failed to detect IS 10 in the BAC DNA. However, prolonged sub-culturing of a set of 15 clones resulted in transposition into the BAC DNA. Eventually, all cultures acquired a 2.3-kb fragment that hybridized strongly with IS 10. Sequence analysis revealed the presence of a preferred site for transposition in the BAC vector. These results indicate that a large number, if not all, of the BAC libraries from different organisms are contaminated with IS 10R. The source of this element has been identified as the DH10B strain of E. coli used as the host for BAC libraries.
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Affiliation(s)
- G Astua-Monge
- Department of Horticultural Sciences, and Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611-0690, USA
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Sarria R, Lyznik A, Vallejos CE, Mackenzie SA. A cytoplasmic male sterility-associated mitochondrial peptide in common bean is post-translationally regulated. Plant Cell 1998; 10:1217-28. [PMID: 9668139 PMCID: PMC144055 DOI: 10.1105/tpc.10.7.1217] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cytoplasmic male sterility in the common bean plant is associated with a dominant mitochondrial mutation designated pvs-or f 239 (for Phaseolus vulgaris sterility sequence open reading frame 239). The sequence is transcribed in both vegetative and reproductive tissues, but the translation product, ORF239, is present only in reproductive tissues. We present evidence to support a model of post-translational regulation of ORF239 expression based on the following observations. In organello translation experiments using purified mitochondria from young seedlings demonstrated accumulation of ORF239 only when a protease inhibitor was included. Proteolytic activity against ORF239 was observed in mitochondrial extracts fractionating with the mitochondrial inner membrane. The DNA sequence encoding a serine-type protease, similar to the lon protease gene of Escherichia coli, was cloned from the Arabidopsis genome. The expression product of this sequence demonstrated proteolytic activity against ORF239 in vitro, with features resembling the activity detected in mitochondrial inner membrane preparations. Antibodies generated against the overexpressed Lon homolog reduced proteolytic activity against ORF239 when added to mitochondrial extracts. Our data suggest that ORF239 was undetected in vegetative tissue due to rapid turnover by at least one mitochondrial protease that acts against ORF239 post-translationally.
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Affiliation(s)
- R Sarria
- Department of Agronomy, Lilly Hall, Purdue University, West Lafayette, Indiana 47907, USA
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16
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Janska H, Sarria R, Woloszynska M, Arrieta-Montiel M, Mackenzie SA. Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility. Plant Cell 1998; 10:1163-80. [PMID: 9668135 PMCID: PMC144058 DOI: 10.1105/tpc.10.7.1163] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The plant mitochondrial genome is characterized by a complex, multipartite structure. In cytoplasmic male-sterile (CMS) common bean, the sterility-inducing mitochondrial configuration maps as three autonomous DNA molecules, one containing the sterility-associated sequence pvs-or f 239. We constructed a physical map of the mitochondrial genome from the direct progenitors to the CMS cytoplasm and have shown that it maps as a single, circular master configuration. With long-exposure autoradiography of DNA gel blots and polymerase chain reaction analysis, we demonstrate that the three-molecule CMS-associated configuration was present at unusually low copy number within the progenitor genome and that the progenitor form was present substoichiometrically within the genome of the CMS line. Furthermore, upon spontaneous reversion to fertility, the progenitor genomic configuration as well as the molecule containing the pvs-or f 239 sterility-associated sequence were both maintained at substoichiometric levels within the revertant genome. In vitro mitochondrial incubation results demonstrated that the genomic shift of the pvs-or f 239-containing molecule to substoichiometric levels upon spontaneous reversion was a reversible phenomenon. Moreover, we demonstrate that substoichiometric forms, apparently silent with regard to gene expression, are transcriptionally and translationally active once amplified. Thus, copy number suppression may serve as an effective means of regulating gene expression in plant mitochondria.
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Affiliation(s)
- H Janska
- Institute of Biochemistry and Molecular Biology, University of Wroclaw, Tamka, 2, 50-137 Wroclaw, Poland
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17
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He S, Abad AR, Gelvin SB, Mackenzie SA. A cytoplasmic male sterility-associated mitochondrial protein causes pollen disruption in transgenic tobacco. Proc Natl Acad Sci U S A 1996; 93:11763-8. [PMID: 8876211 PMCID: PMC38132 DOI: 10.1073/pnas.93.21.11763] [Citation(s) in RCA: 52] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In higher plants, dominant mitochondrial mutations are associated with pollen sterility. This phenomenon is known as cytoplasmic male sterility (CMS). It is thought that the disruption in pollen development is a consequence of mitochondrial dysfunction. To provide definitive evidence that expression of an abnormal mitochondrial gene can interrupt pollen development, a CMS-associated mitochondrial DNA sequence from common bean, orf239, was introduced into the tobacco nuclear genome. Several transformants containing the orf239 gene constructs, with or without a mitochondrial targeting sequence, exhibited a semi sterile or male-sterile phenotype. Expression of the gene fusions in transformed anthers was confirmed using RNA gel blotting, ELISA, and light and electron microscopic immunocytochemistry. Immunocytological analysis showed that the ORF239 protein could associate with the cell wall of aberrant developing microspores. This pattern of extracellular localization was earlier observed in the CMS common bean line containing orf239 in the mitochondrial genome. Results presented here demonstrate that ORF239 causes pollen disruption in transgenic tobacco plants and may do so without targeting of the protein to the mitochondrion.
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Affiliation(s)
- S He
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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18
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Abstract
Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.
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Affiliation(s)
- C A Moeykens
- Department of Agronomy, Iowa State University, Ames 50011, USA
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He S, Yu ZH, Vallejos CE, Mackenzie SA. Pollen fertility restoration by nuclear gene Fr in CMS common bean: an Fr linkage map and the mode of Fr action. Theor Appl Genet 1995; 90:1056-1062. [PMID: 24173062 DOI: 10.1007/bf00222921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/1994] [Accepted: 12/29/1994] [Indexed: 06/02/2023]
Abstract
The Fr gene in common bean, Phaseolus vulgaris L., is a unique gene for the study of plant nuclear-mitochondrial interactions because it appears to directly influence plant mitochondrial genome structure, resulting in the restoration of pollen fertility in cytoplasmic male sterile plants. This gene action is distinct from other pollen fertility restoration systems characterized to date. As a first step towards the map-based cloning of this unusual nuclear gene, we identified RAPD markers linked to Fr using bulked segregant analysis of near-isogenic lines. Using DNA gel blot hybridization, we localized the identified RAPD markers to a linkage group on the common bean RFLP map and constructed a linkage map of the Fr region using both RAPD markers and RFLP markers. Analysis of the mode of Fr action with the aid of identified Fr-linked DNA markers indicated that Fr functions in a semidominant fashion, showing dosage effect in controlling the dynamics of a heteroplasmic mitochondrial population. We also present our observations on the developmental distinctions, crucial in the accurate mapping of the Fr gene, between spontaneous cytoplasmic reversion and Fr-driven fertility restoration, two phenomena that are phenotypically indistinguishable.
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Affiliation(s)
- S He
- Department of Agronomy, Purdue University, 47907, West Lafayette, IN, USA
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Abad AR, Mehrtens BJ, Mackenzie SA. Specific expression in reproductive tissues and fate of a mitochondrial sterility-associated protein in cytoplasmic male-sterile bean. Plant Cell 1995; 7:271-85. [PMID: 7734962 PMCID: PMC160781 DOI: 10.1105/tpc.7.3.271] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In common bean, cytoplasmic male sterility has been associated with a unique sequence found in the mitochondrial genome, designated pvs (for Phaseolus vulgaris sterility sequence). Within the pvs sequence, two open reading frames are encoded, ORF98 and ORF239. We have raised rabbit polyclonal antibodies against Pvs-ORF239 to evaluate the role of this putative male sterility-associated protein. Histological investigation of pollen development revealed that in the male-sterile bean line, callose deposition was abnormal and microspores remained as tetrads as previously reported. Pvs-ORF239 was found to be localized within the reproductive tissues of the male-sterile bean line, in contrast to all other cytoplasmic male sterility systems studied to date. This protein was associated with mitochondria, the callose layer, and developing primary cell walls during microsporogenesis. Expression of pvs-orf239 was not detected in fertile plants containing restorer gene Fr2. These observations, together with previous reports, suggest that nuclear restorer gene Fr2 interferes with expression of the pvs region post-transcriptionally.
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Affiliation(s)
- A R Abad
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907-1150
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Janska H, Mackenzie SA. Unusual mitochondrial genome organization in cytoplasmic male sterile common bean and the nature of cytoplasmic reversion to fertility. Genetics 1993; 135:869-79. [PMID: 8293985 PMCID: PMC1205726 DOI: 10.1093/genetics/135.3.869] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Spontaneous reversion to pollen fertility and fertility restoration by the nuclear gene Fr in cytoplasmic male sterile common bean (Phaseolus vulgaris L.) are associated with the loss of a large portion of the mitochondrial genome. To understand better the molecular events responsible for this DNA loss, we have constructed a physical map of the mitochondrial genome of a stable fertile revertant line, WPR-3, and the cytoplasmic male sterile line (CMS-Sprite) from which it was derived. This involved a cosmid clone walking strategy with comparative DNA gel blot hybridizations. Mapping data suggested that the simplest model for the structure of the CMS-Sprite genome consists of three autonomous chromosomes differing only in short, unique regions. The unique region contained on one of these chromosomes is the male sterility-associated 3-kb sequence designated pvs. Based on genomic environments surrounding repeated sequences, we predict that chromosomes can undergo intra- and intermolecular recombination. The mitochondrial genome of the revertant line appeared to contain only two of the three chromosomes; the region containing the pvs sequence was absent. Therefore, the process of spontaneous cytoplasmic reversion to fertility likely involves the disappearance of an entire mitochondrial chromosome. This model is supported by the fact that we detected no evidence of recombination, excision or deletion events within the revertant genome that could account for the loss of a large segment of mitochondrial DNA.
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Affiliation(s)
- H Janska
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
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Abstract
Previous investigations into the genetic mechanism of fertility restoration in cytoplasmic male sterile Phaseolus vulgaris suggested that this is a particularly interesting system for the study of nuclear-mitochondrial interactions. This study was conducted to investigate the nature of nuclear-mitochondrial compatibility in fertile accession line G08063, the reported progenitor to the cytoplasmic male sterile line. Results from genetic analysis indicated that fertile line G08063 carried a sterility-inducing cytoplasm with a fertility restoring nuclear genotype. Mitochondrial DNA analysis indicated that the mechanism of fertility restoration by line G08063 was different from that conditioned by Fr, a previously described restorer gene. A mitochondrial DNA sequence associated with sterility and lost upon fertility restoration by nuclear gene Fr was present in the mitochondrial genome of fertile line G08063; this sequence was not carried within the mitochondrial genome of any other P. vulgaris accession line tested.
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Affiliation(s)
- S A Mackenzie
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
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Mackenzie SA, Pring DR, Bassett MJ. Large double-stranded RNA molecules in Phaseolus vulgaris L. are not associated with cytoplasmic male sterility. Theor Appl Genet 1988; 76:59-63. [PMID: 24231983 DOI: 10.1007/bf00288832] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/1987] [Accepted: 11/30/1987] [Indexed: 06/02/2023]
Abstract
Two large double-stranded RNA molecules, 15 and 16 kilobases, were detected in cytoplasmic male sterile (CMS) Phaseolus vulgaris by agarose gel electrophoresis. A number of smaller RNA molecules were observed in 'Sprite', a maintainer line, and recurrent backcrossing of CMS P. vulgarisx'Sprite' resulted in a combined electrophoretic pattern of the two large and numerous small RNA molecules. The large RNA molecules were seed and pollen-transmissible, but were not transmitted by grafting. The RNAs were present in revertant and restored lines derived from CMS-Sprite and therefore were not associated with the cytoplasmic male sterile trait.
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Affiliation(s)
- S A Mackenzie
- Department of Vegetable Crops, University of Florida, 32611, Gainesville, FL, USA
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Mackenzie SA, Bassett MJ. Genetics of fertility restoration in cytoplasmic male sterile Phaseolus vulgaris L. : 1. Cytoplasmic alteration by a nuclear restorer gene. Theor Appl Genet 1987; 74:642-645. [PMID: 24240221 DOI: 10.1007/bf00288864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/1987] [Accepted: 04/02/1987] [Indexed: 06/02/2023]
Abstract
Restoration of fertility in cytoplasmic male sterile Phaseolus vulgaris by line R-351 was controlled by a single gene. The restorer gene (Fr) displayed incomplete dominance leading to partial restoration of fertility in F1 generations; full restoration was not achieved until the F2 generation. Once full restoration of fertility was produced in the F2 generation, no segregation for sterility was observed in subsequent generations derived from heterozygotes Frfr, either by testcrossing (restored × maintainer) or in F3 progenies. Implications of the irreversible nature of this restoration are discussed.
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Affiliation(s)
- S A Mackenzie
- Vegetable Crops Department, University of Florida, 32611, Gainesville, FL, USA
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Cerny T, Owens SE, Mackenzie SA, Nuttall PM, Gosh AK, Smith DB, Thatcher N. Immunoscintigraphy with 99mTc labelled F(ab')2 fragments of an anti melanoma monoclonal antibody (225.28S) in patients with metastatic malignant melanoma. Eur J Nucl Med 1987; 13:130-3. [PMID: 3622556 DOI: 10.1007/bf00289024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Immunoscintigraphy was performed in 25 patients with malignant melanoma using a 99mTc labelled monoclonal antibody (225.28S). In four cases, imaging was repeated following treatment with recombinant gamma interferon. In 11 cases, tissue samples of metastatic lesions were investigated for the expression of melanoma associated antigens by immunohistochemical techniques. Overall, 59% of known lesions were detected by imaging. The highest rates of detection were in bone, liver and lymph nodes and the lowest in lung, stomach and bowel. Six lesions were detected which had not shown up on routine clinical and radiological examination. There was no evidence of enhanced or induced HMW-MAA expression following interferon treatment. This technique has been found to be useful in staging patients and has been free from side effects.
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Mackenzie SA, Oltenacu EA, Leighton E. Heritability estimate for temperament scores in German shepherd dogs and its genetic correlation with hip dysplasia. Behav Genet 1985; 15:475-82. [PMID: 4074273 DOI: 10.1007/bf01066240] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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