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Baytar AA, Yanar EG, Frary A, Doğanlar S. Association mapping and candidate gene identification for yield traits in European hazelnut ( Corylus avellana L.). PLANT DIRECT 2024; 8:e625. [PMID: 39170862 PMCID: PMC11336203 DOI: 10.1002/pld3.625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/23/2024]
Abstract
European hazelnut (Corylus avellana L.) is an important nut crop due to its nutritional benefits, culinary uses, and economic value. Türkiye is the leading producer of hazelnut, followed by Italy and the United States. Quantitative trait locus studies offer promising opportunities for breeders and geneticists to identify genomic regions controlling desirable traits in hazelnut. A genome-wide association analysis was conducted with 5,567 single nucleotide polymorphisms on a Turkish core set of 86 hazelnut accessions, revealing 189 quantitative trait nucleotides (QTNs) associated with 22 of 31 traits (p < 2.9E-07). These QTNs were associated with plant and leaf, phenological, reproductive, nut, and kernel traits. Based on the close physical distance of QTNs associated with the same trait, we identified 23 quantitative trait loci. Furthermore, we identified 23 loci of multiple QTs comprising chromosome locations associated with more than one trait at the same position or in close proximity. A total of 159 candidate genes were identified for 189 QTNs, with 122 of them containing significant conserved protein domains. Some candidate matches to known proteins/domains were highly significant, suggesting that they have similar functions as their matches. This comprehensive study provides valuable insights for the development of breeding strategies and the improvement of hazelnut and enhances the understanding of the genetic architecture of complex traits by proposing candidate genes and potential functions.
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Affiliation(s)
- Asena Akköse Baytar
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
| | - Ertuğrul Gazi Yanar
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
| | - Anne Frary
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
| | - Sami Doğanlar
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
- Plant Science and Technology Application and Research CenterIzmir Institute of TechnologyIzmirTürkiye
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2
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Matich P, Plumlee JD, Bubley W, Curtis TH, Drymon JM, Mullins LL, Shipley ON, TinHan TC, Fisher MR. Long-term effects of climate change on juvenile bull shark migratory patterns. J Anim Ecol 2024. [PMID: 39016072 DOI: 10.1111/1365-2656.14140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/08/2024] [Indexed: 07/18/2024]
Abstract
Seasonal variability in environmental conditions is a strong determinant of animal migrations, but warming temperatures associated with climate change are anticipated to alter this phenomenon with unknown consequences. We used a 40-year fishery-independent survey to assess how a changing climate has altered the migration timing, duration and first-year survival of juvenile bull sharks (Carcharhinus leucas). From 1982 to 2021, estuaries in the western Gulf of Mexico (Texas) experienced a mean increase of 1.55°C in autumn water temperatures, and delays in autumn cold fronts by ca. 0.5 days per year. Bull shark migrations in more northern estuaries concomitantly changed, with departures 25-36 days later in 2021 than in 1982. Later, migrations resulted in reduced overwintering durations by up to 81 days, and the relative abundance of post-overwintering age 0-1 sharks increased by >50% during the 40-year study period. Yet, reductions in prey availability were the most influential factor delaying migrations. Juvenile sharks remained in natal estuaries longer when prey were less abundant. Long-term declines in prey reportedly occurred due to reduced spawning success associated with climate change based on published reports. Consequently, warming waters likely enabled and indirectly caused the observed changes in shark migratory behaviour. As water temperatures continue to rise, bull sharks in the north-western Gulf of Mexico could forgo their winter migrations in the next 50-100 years based on current trends and physiological limits, thereby altering their ecological roles in estuarine ecosystems and recruitment into the adult population. It is unclear if estuarine food webs will be able to support changing residency patterns as climate change affects the spawning success of forage species. We expect these trends are not unique to the western Gulf of Mexico or bull sharks, and migratory patterns of predators in subtropical latitudes are similarly changing at a global scale.
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Affiliation(s)
- Philip Matich
- Saving the Blue, Cooper City, Florida, USA
- Marine Biology Department, Texas A&M University Galveston, Galveston, Texas, USA
| | - Jeffrey D Plumlee
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Walter Bubley
- Marine Resources Division, South Carolina Department of Natural Resources, Charleston, South Carolina, USA
| | - Tobey H Curtis
- Atlantic Highly Migratory Species Management Division, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Gloucester, Massachusetts, USA
| | - J Marcus Drymon
- Coastal Research and Extension Center, Mississippi State University, Biloxi, Mississippi, USA
- Mississippi-Alabama Sea Grant Consortium, Ocean Springs, Mississippi, USA
| | - Lindsay L Mullins
- Coastal Research and Extension Center, Mississippi State University, Biloxi, Mississippi, USA
- Northern Gulf Institute, Starkville, Mississippi, USA
| | - Oliver N Shipley
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Thomas C TinHan
- Pacific Islands Ocean Observing System, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Mark R Fisher
- Coastal Fisheries Division, Texas Parks and Wildlife Department, Rockport Marine Science Laboratory, Rockport, Texas, USA
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3
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GRAS-Di SNP-based molecular characterization and fingerprinting of a Turkish Corylus avellana core set provide insights into the cultivation and breeding of hazelnut in Turkey. Mol Genet Genomics 2023; 298:413-426. [PMID: 36595074 DOI: 10.1007/s00438-022-01990-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Hazelnut (Corylus avellana L.) is an economically and socially important product for Turkey, the country that leads global production of this crop. The preservation of Turkish hazelnut genetic diversity and informed breeding of new cultivars are crucial for maintaining quality and crop yield stability. In this study, genotyping by random amplicon sequencing (GRAS-Di) was used to identify single-nucleotide polymorphisms (SNPs) in a panel of 96 individuals representing the Turkish national hazelnut collection. The resulting 7609 high-quality SNPs were physically mapped to the Tombul cultivar reference genome and used for population structure and diversity analyses. These analyses revealed that cultivars are not less diverse than wild accessions and that 44% of the panel had admixed ancestry. The results also indicated that recently released Turkish cultivars are highly similar to each other, suggesting that diversity analysis is an important tool that should be employed to prevent future genetic bottlenecks in this crop. A minimal marker algorithm was used to select a set of seven SNP markers that were capable of differentiating the panel accessions. These fingerprinting markers should be useful for the propagation of true-to-type elite cultivars that can be used to renew Turkey's aging hazelnut orchards.
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Matich P, Bigelow CL, Chambers B, Dodds JJ, Hebert JA, Lemieux A, Pittman CM, Trapp J, Bianco B, Cadena CP, Castillo EI, Castillo GI, Dawdy A, Dominguez AI, Dominique N, French DR, Glenn CF, Jackson ECH, Johnson B, Kohl G, Manka C, Martin JK, Pappas M, Reedholm AJ, Snead KM, Tyree MK, Fisher M. Delineation of blacktip shark (Carcharhinus limbatus) nursery habitats in the north-western Gulf of Mexico. JOURNAL OF FISH BIOLOGY 2022; 101:236-248. [PMID: 35591772 DOI: 10.1111/jfb.15103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Coevolution with predators leads to the use of low-risk habitats by many prey species, which promotes survival during early developmental phases. These nurseries are valued by conservation and management agencies because of their contributions to adult populations. However, the physical and geographic characteristics, like shallow depths and isolation from other marine habitats, that restrict access to predators and thereby reduce risk to juvenile animals can also limit scientific research. Consequently, many nursery habitats are still unidentified and understudied. Here we used gillnet monitoring from 1982 to 2018 to delineate blacktip shark (Carcharhinus limbatus) nurseries in the north-western Gulf of Mexico and elucidated their physical, environmental and biological characteristics. Nursery habitats within estuaries (<2% of spatial area) were proximate to the Gulf of Mexico and exhibited significantly lower variability in salinity than non-nurseries. However, relative abundances of predators and prey were not significant delineators of nursery habitats. As such, food and risk may not influence juvenile blacktip habitat use as expected. Alternatively, reduced osmoregulatory stress attributed to predictable environments likely provides advantageous conditions for blacktips to develop foraging and antipredator tactics, which is vital prior to the winter migration of juvenile sharks into the Gulf of Mexico.
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Affiliation(s)
| | - Camryn L Bigelow
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Barrett Chambers
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Jillian J Dodds
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Jessica A Hebert
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Alexis Lemieux
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Christy M Pittman
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Julianna Trapp
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Brooke Bianco
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Carolina P Cadena
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Emily I Castillo
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Gabriela I Castillo
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Alexandra Dawdy
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Alina I Dominguez
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Nicholas Dominique
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Donavon R French
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Callie F Glenn
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Elena C H Jackson
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Breidon Johnson
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Gunnar Kohl
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Cameron Manka
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Jared K Martin
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Matthew Pappas
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Audrey J Reedholm
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Kailey M Snead
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Matthew K Tyree
- Marine Biology Department, Texas A & M University at Galveston, Galveston, Texas, USA
| | - Mark Fisher
- Texas Parks and Wildlife Department, Coastal Fisheries Division, Rockport Marine Science Laboratory, Rockport, Texas, USA
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Matich P, Plumlee JD, Fisher M. Grow fast, die young: Does compensatory growth reduce survival of juvenile blacktip sharks ( Carcharhinus limbatus) in the western Gulf of Mexico? Ecol Evol 2021; 11:16280-16295. [PMID: 34824827 PMCID: PMC8601900 DOI: 10.1002/ece3.8311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/01/2022] Open
Abstract
Effective conservation and management necessitate an understanding of the ecological mechanisms that shape species life histories in order to predict how variability in natural and anthropogenic impacts will alter growth rates, recruitment, and survival. Among these mechanisms, the interaction between parturition timing and prey availability frequently influences offspring success, particularly when postnatal care is absent. Here, we assess how parturition timing and nursery conditions, including prey abundance and environmental conditions, influence the growth and potential survival of blacktip sharks (Carcharhinus limbatus) in western Gulf of Mexico (GOM) estuaries over their first year. Catch data from long-term gillnet monitoring allowed for clear delineation of cohorts based on size frequency distribution plots, and showed that late parturition cohorts born in estuaries with fewer prey resources exhibited more rapid growth than early parturition cohorts that experienced more abundant prey. Compensatory behaviors that promoted accelerated growth led to reduced second year residency, likely due to reduced survival resultant from greater risk taking and potentially due to reduced site fidelity attributed to larger body size. Water temperatures influenced blacktip growth rates through physiological increases in metabolism and potential premigratory foraging cues associated with cooling temperatures. Gradual warming of the GOM (0.03°C year-1) was also correlated with earlier parturition across the study period (1982-2017), similar to other migratory species. Considering current trends in climate and associated phenological shifts in many animals, testing hypotheses assessing compensatory growth-risk trade-offs is important moving forward to predict changes in life histories and associated recruitment in concert with current and future conservation actions, like wildlife management.
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Affiliation(s)
- Philip Matich
- Marine Biology DepartmentTexas A & M University at GalvestonGalvestonTexasUSA
| | - Jeffrey D. Plumlee
- Institute of Marine SciencesUniversity of North Carolina at Chapel HillMorehead CityNorth CarolinaUSA
| | - Mark Fisher
- Rockport Marine Science LaboratoryCoastal Fisheries DivisionTexas Parks and Wildlife DepartmentRockportTexasUSA
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Rooker JR, Wells RJD, Addis P, Arrizabalaga H, Baptista M, Bearzi G, Dance MA, Fraile I, Lacoue-Labarthe T, Lee JM, Megalofonou P, Rosa R, Sobrino I, Sykes AV, Villanueva R. Natural geochemical markers reveal environmental history and population connectivity of common cuttlefish in the Atlantic Ocean and Mediterranean Sea. J R Soc Interface 2020. [PMCID: PMC7423417 DOI: 10.1098/rsif.2020.0309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Natural markers (δ13C and δ18O stable isotopes) in the cuttlebones of the European common cuttlefish (Sepia officinalis) were determined for individuals collected across a substantial portion of their range in the Northeast Atlantic Ocean (NEAO) and Mediterranean Sea. Cuttlebone δ13C and δ18O were quantified for core and edge material to characterize geochemical signatures associated with early (juvenile) and recent (sub-adult/adult) life-history periods, respectively. Regional shifts in cuttlebone δ13C and δ18O values were detected across the 12 sites investigated. Individuals collected from sites in the NEAO displayed more enriched δ13C and δ18O values relative to sites in the Mediterranean Sea, with the latter also showing salient differences in both markers among western, central and eastern collection areas. Classification success based on cuttlebone δ13C and δ18O values to four geographical regions (NEAO, western, central and eastern Mediterranean Sea) was relatively high, suggesting that environmental conditions in each region were distinct and produced area-specific geochemical signatures on the cuttlebones of S. officinalis. A modified δ13C and δ18O baseline was developed from sites proximal to the Strait of Gibraltar in both the NEAO and Mediterranean Sea to assess potential mixing through this corridor. Nearly, all (95%) of δ13C and δ18O signatures of S. officinalis collected in the area of the NEAO closest to the Strait of Gibraltar (Gulf of Cadiz) matched the signatures of specimens collected in the western Mediterranean, signifying potential movement and mixing of individuals through this passageway. This study extends the current application of these geochemical markers for assessing the natal origin and population connectivity of this species and potentially other taxa that inhabit this geographical area.
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Affiliation(s)
- Jay R. Rooker
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA
| | - R. J. David Wells
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA
| | - Piero Addis
- Department of Environmental and Life Science, University of Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy
| | - Haritz Arrizabalaga
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea z/g, 20110 Pasaia – Gipuzkoa, Spain
| | - Miguel Baptista
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Giovanni Bearzi
- Dolphin Biology and Conservation, Cordenons, Pordenone, Italy
| | - Michael A. Dance
- Department of Oceanography and Coastal Sciences, Louisiana State University, 2255 Energy, Coast and Environment Building, Baton Rouge, LA 70803, USA
| | - Igaratza Fraile
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea z/g, 20110 Pasaia – Gipuzkoa, Spain
| | - Thomas Lacoue-Labarthe
- Littoral Environnement et Sociétés (LIENSs) - UMR 7266 Bâtiment ILE, 2, rue Olympe de Gouges, 17000 La Rochelle, France
| | - Jessica M. Lee
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA
| | - Persefoni Megalofonou
- Department of Biology, National and Kapodistrian University of Athens,15784 Athens, Greece
| | - Rui Rosa
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Ignacio Sobrino
- Instituto Español de Oceanografía, Puerto Pesquero s/n, 11006, Cádiz, Spain
| | - António V. Sykes
- Center of Marine Sciences, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Roger Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Maritim 37-49, 08003 Barcelona, Spain
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TinHan TC, O'Leary SJ, Portnoy DS, Rooker JR, Gelpi CG, Wells RJD. Natural tags identify nursery origin of a coastal elasmobranch
Carcharhinus leucas. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas C. TinHan
- Department of Marine Biology Texas A&M University at Galveston Galveston TX USA
| | - Shannon J. O'Leary
- Department of Life Sciences Texas A&M University‐Corpus Christi Corpus Christi TX USA
| | - David S. Portnoy
- Department of Life Sciences Texas A&M University‐Corpus Christi Corpus Christi TX USA
| | - Jay R. Rooker
- Department of Marine Biology Texas A&M University at Galveston Galveston TX USA
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
| | - Carey G. Gelpi
- Coastal Fisheries Division Texas Parks and Wildlife Department Port Arthur TX USA
| | - R. J. David Wells
- Department of Marine Biology Texas A&M University at Galveston Galveston TX USA
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
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